=>> Building biology/ucsc-userapps build started at Fri May 2 10:05:19 BST 2025 port directory: /usr/ports/biology/ucsc-userapps package name: ucsc-userapps-474 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2533 Dec 29 14:16 /usr/ports/biology/ucsc-userapps/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work/.cache HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ucsc-userapps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ucsc-userapps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- BINDIR=/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr/local OPENSSLDIR=/usr/local/openssl OPENSSLINC=/usr/local/include OPENSSLLIB=/usr/local/lib OPENSSLRPATH=/usr/local/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work/.cache HOME=/wrkdirs/usr/ports/biology/ucsc-userapps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ucsc-userapps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ucsc-userapps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG -isystem /usr/local/include" LDFLAGS=" -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/ucsc-userapps" EXAMPLESDIR="share/examples/ucsc-userapps" DATADIR="share/ucsc-userapps" WWWDIR="www/ucsc-userapps" ETCDIR="etc/ucsc-userapps" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ucsc-userapps DOCSDIR=/usr/local/share/doc/ucsc-userapps EXAMPLESDIR=/usr/local/share/examples/ucsc-userapps WWWDIR=/usr/local/www/ucsc-userapps ETCDIR=/usr/local/etc/ucsc-userapps --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ucsc-userapps-474 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> ucsc-userapps-474 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ucsc-userapps-474 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ucsc-userapps-474 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ucsc-userapps-474 for building => SHA256 Checksum OK for userApps.v474.src.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ucsc-userapps-474 for building ===> Extracting for ucsc-userapps-474 => SHA256 Checksum OK for userApps.v474.src.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for ucsc-userapps-474 ===> Applying FreeBSD patches for ucsc-userapps-474 from /usr/ports/biology/ucsc-userapps/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ucsc-userapps-474 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... done ===> ucsc-userapps-474 depends on executable: bash - found ===> Returning to build of ucsc-userapps-474 ===> ucsc-userapps-474 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> ucsc-userapps-474 depends on package: gmake>=4.4.1 - found ===> Returning to build of ucsc-userapps-474 ===> ucsc-userapps-474 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.12.pkg [pkg-builder.dan.net.uk] Installing python311-3.11.12... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] Extracting python311-3.11.12: .......... done ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> ucsc-userapps-474 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of ucsc-userapps-474 ===> ucsc-userapps-474 depends on file: /usr/local/lib/libcrypto.so.12 - found ===> ucsc-userapps-474 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_3.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_3: .......... done ===> ucsc-userapps-474 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of ucsc-userapps-474 ===> ucsc-userapps-474 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> ucsc-userapps-474 depends on file: /usr/local/bin/ccache - found ===> Returning to build of ucsc-userapps-474 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ucsc-userapps-474 depends on shared library: libmysqlclient.so - not found ===> Installing existing package /packages/All/mysql80-client-8.0.42.pkg [pkg-builder.dan.net.uk] Installing mysql80-client-8.0.42... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing cyrus-sasl-2.1.28_5... *** Added group `cyrus' (id 60) *** Added user `cyrus' (id 60) [pkg-builder.dan.net.uk] `-- Extracting cyrus-sasl-2.1.28_5: .......... done [pkg-builder.dan.net.uk] `-- Installing groff-1.23.0_4... [pkg-builder.dan.net.uk] | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing psutils-1.17_6... [pkg-builder.dan.net.uk] | | `-- Installing libpaper-1.1.28_1... [pkg-builder.dan.net.uk] | | `-- Extracting libpaper-1.1.28_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting psutils-1.17_6: .......... done [pkg-builder.dan.net.uk] | `-- Installing uchardet-0.0.8_1... [pkg-builder.dan.net.uk] | `-- Extracting uchardet-0.0.8_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting groff-1.23.0_4: .......... done [pkg-builder.dan.net.uk] `-- Installing hidapi-0.14.0... [pkg-builder.dan.net.uk] `-- Extracting hidapi-0.14.0: .......... done [pkg-builder.dan.net.uk] `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libedit-3.1.20250104,1... [pkg-builder.dan.net.uk] `-- Extracting libedit-3.1.20250104,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libevent-2.1.12... [pkg-builder.dan.net.uk] `-- Extracting libevent-2.1.12: .......... done [pkg-builder.dan.net.uk] `-- Installing libfido2-1.15.0... [pkg-builder.dan.net.uk] | `-- Installing libcbor-0.12.0... [pkg-builder.dan.net.uk] | | `-- Installing libcjson-1.7.18_2... [pkg-builder.dan.net.uk] | | `-- Extracting libcjson-1.7.18_2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libcbor-0.12.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting libfido2-1.15.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libunwind-20240221_2... [pkg-builder.dan.net.uk] `-- Extracting libunwind-20240221_2: .......... done [pkg-builder.dan.net.uk] `-- Installing openldap26-client-2.6.9_1... [pkg-builder.dan.net.uk] `-- Extracting openldap26-client-2.6.9_1: .......... done [pkg-builder.dan.net.uk] Extracting mysql80-client-8.0.42: .......... done ===== Message from cyrus-sasl-2.1.28_5: -- You can use sasldb2 for authentication, to add users use: saslpasswd2 -c username If you want to enable SMTP AUTH with the system Sendmail, read Sendmail.README NOTE: This port has been compiled with a default pwcheck_method of auxprop. If you want to authenticate your user by /etc/passwd, PAM or LDAP, install ports/security/cyrus-sasl2-saslauthd and set sasl_pwcheck_method to saslauthd after installing the Cyrus-IMAPd 2.X port. You should also check the /usr/local/lib/sasl2/*.conf files for the correct pwcheck_method. If you want to use GSSAPI mechanism, install ports/security/cyrus-sasl2-gssapi. If you want to use SRP mechanism, install ports/security/cyrus-sasl2-srp. If you want to use LDAP auxprop plugin, install ports/security/cyrus-sasl2-ldapdb. ===== Message from groff-1.23.0_4: -- In order to be able to use the html driver, you need to install the following packages: - ghostscript - netpbm -- ===> NOTICE: The groff port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from openldap26-client-2.6.9_1: -- The OpenLDAP client package has been successfully installed. Edit /usr/local/etc/openldap/ldap.conf to change the system-wide client defaults. Try `man ldap.conf' and visit the OpenLDAP FAQ-O-Matic at http://www.OpenLDAP.org/faq/index.cgi?file=3 for more information. ===== Message from mysql80-client-8.0.42: -- This is the mysql CLIENT without the server. for complete server and client, please install databases/mysql80-server ===> ucsc-userapps-474 depends on shared library: libmysqlclient.so - found (/usr/local/lib/mysql/libmysqlclient.so) ===> Returning to build of ucsc-userapps-474 ===> ucsc-userapps-474 depends on shared library: libunwind.so - found (/usr/local/lib/libunwind.so) ===> ucsc-userapps-474 depends on shared library: libfreetype.so - not found ===> Installing existing package /packages/All/freetype2-2.13.3.pkg [pkg-builder.dan.net.uk] Installing freetype2-2.13.3... [pkg-builder.dan.net.uk] Extracting freetype2-2.13.3: .......... done ===== Message from freetype2-2.13.3: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===> ucsc-userapps-474 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> Returning to build of ucsc-userapps-474 ===> ucsc-userapps-474 depends on shared library: libpng.so - not found ===> Installing existing package /packages/All/png-1.6.47.pkg [pkg-builder.dan.net.uk] Installing png-1.6.47... [pkg-builder.dan.net.uk] Extracting png-1.6.47: .......... done ===> ucsc-userapps-474 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> Returning to build of ucsc-userapps-474 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for ucsc-userapps-474 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for ucsc-userapps-474 cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o aliType.o -c aliType.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoAssembly.o -c annoAssembly.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoFilter.o -c annoFilter.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoFormatter.o -c annoFormatter.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoFormatTab.o -c annoFormatTab.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoGrator.o -c annoGrator.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoGrateWig.o -c annoGrateWig.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoGratorQuery.o -c annoGratorQuery.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoOption.o -c annoOption.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoRow.o -c annoRow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoStreamer.o -c annoStreamer.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoStreamBigBed.o -c annoStreamBigBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoStreamBigWig.o -c annoStreamBigWig.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoStreamTab.o -c annoStreamTab.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoStreamLongTabix.o -c annoStreamLongTabix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o annoStreamVcf.o -c annoStreamVcf.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o apacheLog.o -c apacheLog.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o asParse.o -c asParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o aveStats.o -c aveStats.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o axt.o -c axt.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o axtAffine.o -c axtAffine.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bamFile.o -c bamFile.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o base64.o -c base64.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o basicBed.o -c basicBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bbiAlias.o -c bbiAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bbiRead.o -c bbiRead.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bbiWrite.o -c bbiWrite.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bedTabix.o -c bedTabix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bigBed.o -c bigBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bigBedCmdSupport.o -c bigBedCmdSupport.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o binRange.o -c binRange.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bits.o -c bits.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o blastOut.o -c blastOut.c blastOut.c:555:9: warning: variable 'ii' set but not used [-Wunused-but-set-variable] 555 | int ii = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o blastParse.o -c blastParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o boxClump.o -c boxClump.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o boxLump.o -c boxLump.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bPlusTree.o -c bPlusTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cacheTwoBit.o -c cacheTwoBit.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bwgCreate.o -c bwgCreate.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bwgQuery.o -c bwgQuery.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bwgValsOnChrom.o -c bwgValsOnChrom.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cda.o -c cda.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o chain.o -c chain.c chain.c:401:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] 401 | int usedCount = 0, count = 0; | ^ chain.c:401:20: warning: variable 'count' set but not used [-Wunused-but-set-variable] 401 | int usedCount = 0, count = 0; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o chainBlock.o -c chainBlock.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o chainConnect.o -c chainConnect.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o chainToAxt.o -c chainToAxt.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o chainToPsl.o -c chainToPsl.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cheapcgi.o -c cheapcgi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cirTree.o -c cirTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o codebias.o -c codebias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o colHash.o -c colHash.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o common.o -c common.c common.c:354:13: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 354 | freeFunc(&el); | ^ common.c:403:13: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 403 | free(el); | ^ common.c:1090:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1090 | freeFunc(el->val); | ^ 3 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o correlate.o -c correlate.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o crTree.o -c crTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o csv.o -c csv.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dgRange.o -c dgRange.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o diGraph.o -c diGraph.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dlist.o -c dlist.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dnaLoad.o -c dnaLoad.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dnaMarkov.o -c dnaMarkov.c dnaMarkov.c:111:5: warning: variable 'total' set but not used [-Wunused-but-set-variable] 111 | int total = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dnaMotif.o -c dnaMotif.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dnaseq.o -c dnaseq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dnautil.o -c dnautil.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dtdParse.o -c dtdParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dyOut.o -c dyOut.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o dystring.o -c dystring.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o elmTree.o -c elmTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o emblParse.o -c emblParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o errCatch.o -c errCatch.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o errAbort.o -c errAbort.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fa.o -c fa.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ffAli.o -c ffAli.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ffScore.o -c ffScore.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fieldedTable.o -c fieldedTable.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o filePath.o -c filePath.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fixColor.o -c fixColor.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o flydna.o -c flydna.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fof.o -c fof.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier10.o -c font/mgCourier10.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier12.o -c font/mgCourier12.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier14.o -c font/mgCourier14.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier18.o -c font/mgCourier18.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier24.o -c font/mgCourier24.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier34.o -c font/mgCourier34.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgCourier8.o -c font/mgCourier8.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica10.o -c font/mgHelvetica10.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica12.o -c font/mgHelvetica12.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica14.o -c font/mgHelvetica14.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica18.o -c font/mgHelvetica18.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica24.o -c font/mgHelvetica24.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica34.o -c font/mgHelvetica34.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelvetica8.o -c font/mgHelvetica8.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold10.o -c font/mgHelveticaBold10.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold12.o -c font/mgHelveticaBold12.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold14.o -c font/mgHelveticaBold14.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold18.o -c font/mgHelveticaBold18.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold24.o -c font/mgHelveticaBold24.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold34.o -c font/mgHelveticaBold34.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgHelveticaBold8.o -c font/mgHelveticaBold8.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgSixhi6.o -c font/mgSixhi6.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgSail8.o -c font/mgSail8.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes10.o -c font/mgTimes10.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes12.o -c font/mgTimes12.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes14.o -c font/mgTimes14.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes18.o -c font/mgTimes18.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes24.o -c font/mgTimes24.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes34.o -c font/mgTimes34.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgTimes8.o -c font/mgTimes8.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o font/mgMenlo12.o -c font/mgMenlo12.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fq.o -c fq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o freeType.o -c freeType.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fuzzyShow.o -c fuzzyShow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gapCalc.o -c gapCalc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gdf.o -c gdf.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gemfont.o -c gemfont.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o genomeRangeTree.o -c genomeRangeTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfNet.o -c gfNet.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gff.o -c gff.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gff3.o -c gff3.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfxPoly.o -c gfxPoly.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gifLabel.o -c gifLabel.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hacTree.o -c hacTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hash.o -c hash.c hash.c:719:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 719 | freeFunc(&hel->val); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hex.o -c hex.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o histogram.o -c histogram.c histogram.c:165:10: warning: variable 'missed' set but not used [-Wunused-but-set-variable] 165 | unsigned missed = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hmmPfamParse.o -c hmmPfamParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hmmstats.o -c hmmstats.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o htmlColor.o -c htmlColor.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o htmlPage.o -c htmlPage.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o htmshell.o -c htmshell.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hmac.o -c hmac.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o https.o -c https.c https.c:117:5: warning: 'ERR_load_SSL_strings' is deprecated [-Wdeprecated-declarations] 117 | ERR_load_SSL_strings(); | ^ /usr/local/include/openssl/sslerr_legacy.h:29:1: note: 'ERR_load_SSL_strings' has been explicitly marked deprecated here 29 | OSSL_DEPRECATEDIN_3_0 int ERR_load_SSL_strings(void); | ^ /usr/local/include/openssl/macros.h:182:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0' 182 | # define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0) | ^ /usr/local/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED' 62 | # define OSSL_DEPRECATED(since) __attribute__((deprecated)) | ^ https.c:44:22: warning: unused function 'openssl_id_callback' [-Wunused-function] 44 | static unsigned long openssl_id_callback(void) | ^~~~~~~~~~~~~~~~~~~ https.c:49:13: warning: unused function 'openssl_locking_callback' [-Wunused-function] 49 | static void openssl_locking_callback(int mode, int n, const char * file, int line) | ^~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o intExp.o -c intExp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o intValTree.o -c intValTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o internet.o -c internet.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o itsa.o -c itsa.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o iupac.o -c iupac.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o jointalign.o -c jointalign.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o jpegSize.o -c jpegSize.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o jsonParse.o -c jsonParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o jsonQuery.o -c jsonQuery.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o jsonWrite.o -c jsonWrite.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o keys.o -c keys.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o knetUdc.o -c knetUdc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o kxTok.o -c kxTok.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o linefile.o -c linefile.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o lineFileOnBigBed.o -c lineFileOnBigBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o localmem.o -c localmem.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o log.o -c log.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o longTabix.o -c longTabix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o longToList.o -c longToList.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o maf.o -c maf.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mafFromAxt.o -c mafFromAxt.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mafScore.o -c mafScore.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mailViaPipe.o -c mailViaPipe.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o md5.o -c md5.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o matrixMarket.o -c matrixMarket.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o memalloc.o -c memalloc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o memgfx.o -c memgfx.c memgfx.c:866:17: warning: passing arguments to 'ftInitialize' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 866 | ftInitialize(fontFile); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o meta.o -c meta.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o metaWig.o -c metaWig.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mgCircle.o -c mgCircle.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mgPolygon.o -c mgPolygon.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mime.o -c mime.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o mmHash.o -c mmHash.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o net.o -c net.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o nib.o -c nib.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o nibTwo.o -c nibTwo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o nt4.o -c nt4.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o numObscure.o -c numObscure.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o obscure.o -c obscure.c obscure.c:1055:5: warning: call to undeclared function 'thr_self'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 1055 | thr_self(&tid); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o oldGff.o -c oldGff.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o oligoTm.o -c oligoTm.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o options.o -c options.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o osunix.o -c osunix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pairHmm.o -c pairHmm.c pairHmm.c:267:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 267 | { | ^ pairHmm.c:264:5: note: previous statement is here 264 | for (pair = pairList; pair->next != NULL; pair = pair->next) | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pairDistance.o -c pairDistance.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o paraFetch.o -c paraFetch.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o peakCluster.o -c peakCluster.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o phyloTree.o -c phyloTree.c phyloTree.c:286:6: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 286 | fprintf(f,":%0.04g", tree->ident->length); | ^ phyloTree.c:283:2: note: previous statement is here 283 | if (tree->ident->name) | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pipeline.o -c pipeline.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o portimpl.o -c portimpl.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pngwrite.o -c pngwrite.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o psGfx.o -c psGfx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o psPoly.o -c psPoly.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pscmGfx.o -c pscmGfx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o psl.o -c psl.c psl.c:1423:9: warning: variable 'qE' set but not used [-Wunused-but-set-variable] 1423 | int qE = qS + sz; | ^ psl.c:1509:9: warning: variable 'tE' set but not used [-Wunused-but-set-variable] 1509 | int tE = tS + sz; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pslGenoShow.o -c pslGenoShow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pslShow.o -c pslShow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pslTbl.o -c pslTbl.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pslTransMap.o -c pslTransMap.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pthreadDoList.o -c pthreadDoList.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o pthreadWrap.o -c pthreadWrap.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o qa.o -c qa.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o quickHeap.o -c quickHeap.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o quotedP.o -c quotedP.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ra.o -c ra.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rainbow.o -c rainbow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o raToStruct.o -c raToStruct.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rbTree.o -c rbTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rangeTree.o -c rangeTree.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o regexHelper.o -c regexHelper.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o repMask.o -c repMask.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rle.o -c rle.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rnautil.o -c rnautil.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rqlEval.o -c rqlEval.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rqlParse.o -c rqlParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rqlToSql.o -c rqlToSql.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o rudp.o -c rudp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o scoreWindow.o -c scoreWindow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o seg.o -c seg.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o seqOut.o -c seqOut.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o seqStats.o -c seqStats.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o servBrcMcw.o -c servBrcMcw.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o servCrunx.o -c servCrunx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o servcis.o -c servcis.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o servcl.o -c servcl.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o servmsII.o -c servmsII.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o servpws.o -c servpws.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o shaRes.o -c shaRes.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o slog.o -c slog.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o snof.o -c snof.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o snofmake.o -c snofmake.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o snofsig.o -c snofsig.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o spaceSaver.o -c spaceSaver.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o spacedColumn.o -c spacedColumn.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o spacedSeed.o -c spacedSeed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sparseMatrix.o -c sparseMatrix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o splatAli.o -c splatAli.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sqlList.o -c sqlList.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sqlNum.o -c sqlNum.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sqlReserved.o -c sqlReserved.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o strex.o -c strex.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o subText.o -c subText.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sufa.o -c sufa.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sufx.o -c sufx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o synQueue.o -c synQueue.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tabRow.o -c tabRow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tagSchema.o -c tagSchema.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tagStorm.o -c tagStorm.c tagStorm.c:170:5: warning: variable 'stanzaCount' set but not used [-Wunused-but-set-variable] 170 | int stanzaCount = 0; | ^ tagStorm.c:171:5: warning: variable 'tagCount' set but not used [-Wunused-but-set-variable] 171 | int tagCount = 0; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tagToJson.o -c tagToJson.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tagToSql.o -c tagToSql.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o textOut.o -c textOut.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tokenizer.o -c tokenizer.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o trix.o -c trix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o twoBit.o -c twoBit.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o udc.o -c udc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o uuid.o -c uuid.c uuid.c:16:1: warning: call to undeclared function 'uuid_generate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 16 | uuid_generate(uuid); | ^ uuid.c:17:1: warning: call to undeclared function 'uuid_unparse_lower'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 17 | uuid_unparse_lower(uuid, buf); | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vcf.o -c vcf.c vcf.c:414:17: warning: 'sizeof (((void *)0))' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 414 | int wordCount = chopTabs(line+1, NULL); | ^~~~~~~~~~~~~~~~~~~~~~ ../inc/common.h:1020:65: note: expanded from macro 'chopTabs' 1020 | #define chopTabs(string, words) chopByChar(string, '\t', words, ArraySize(words)) | ^~~~~~~~~~~~~~~~ ../inc/common.h:173:32: note: expanded from macro 'ArraySize' 173 | #define ArraySize(a) (sizeof(a)/sizeof((a)[0])) | ~~~~~~~~~^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vcfBits.o -c vcfBits.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vGfx.o -c vGfx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vPng.o -c vPng.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o verbose.o -c verbose.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vMatrix.o -c vMatrix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o wildcmp.o -c wildcmp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o windowsToAscii.o -c windowsToAscii.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o wormdna.o -c wormdna.c wormdna.c:614:5: warning: variable 'lineCount' set but not used [-Wunused-but-set-variable] 614 | int lineCount = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xAli.o -c xAli.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xa.o -c xa.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xap.o -c xap.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xenshow.o -c xenshow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xmlEscape.o -c xmlEscape.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xp.o -c xp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o zlibFace.o -c zlibFace.c mkdir -p amd64 ar rcus amd64/jkweb.a aliType.o annoAssembly.o annoFilter.o annoFormatter.o annoFormatTab.o annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o annoStreamBigBed.o annoStreamBigWig.o annoStreamTab.o annoStreamLongTabix.o annoStreamVcf.o apacheLog.o asParse.o aveStats.o axt.o axtAffine.o bamFile.o base64.o basicBed.o bbiAlias.o bbiRead.o bbiWrite.o bedTabix.o bigBed.o bigBedCmdSupport.o binRange.o bits.o blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o cacheTwoBit.o bwgCreate.o bwgQuery.o bwgValsOnChrom.o cacheTwoBit.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o cheapcgi.o cirTree.o codebias.o colHash.o common.o correlate.o crTree.o csv.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o dnautil.o dtdParse.o dyOut.o dystring.o elmTree.o emblParse.o errCatch.o errAbort.o fa.o ffAli.o ffScore.o fieldedTable.o filePath.o fixColor.o flydna.o fof.o font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o font/mgMenlo12.o fq.o freeType.o fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o hacTree.o hash.o hex.o histogram.o hmmPfamParse.o hmmstats.o htmlColor.o htmlPage.o htmshell.o hmac.o https.o intExp.o intValTree.o internet.o itsa.o iupac.o jointalign.o jpegSize.o jsonParse.o jsonQuery.o jsonWrite.o keys.o knetUdc.o kxTok.o linefile.o lineFileOnBigBed.o localmem.o log.o longTabix.o longToList.o maf.o mafFromAxt.o mafScore.o mailViaPipe.o md5.o matrixMarket.o memalloc.o memgfx.o meta.o metaWig.o mgCircle.o mgPolygon.o mime.o mmHash.o net.o nib.o nibTwo.o nt4.o numObscure.o obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o pairDistance.o paraFetch.o peakCluster.o phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadDoList.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rainbow.o raToStruct.o rbTree.o rangeTree.o regexHelper.o repMask.o rle.o rnautil.o rqlEval.o rqlParse.o rqlToSql.o rudp.o scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o sparseMatrix.o splatAli.o sqlList.o sqlNum.o sqlReserved.o strex.o subText.o sufa.o sufx.o synQueue.o tabRow.o tagSchema.o tagStorm.o tagToJson.o tagToSql.o textOut.o tokenizer.o trix.o twoBit.o udc.o uuid.o vcf.o vcfBits.o vGfx.o vPng.o verbose.o vMatrix.o wildcmp.o windowsToAscii.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o kfunc.o -c kfunc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o knetfile.o -c knetfile.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o kstring.o -c kstring.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bgzf.o -c bgzf.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o faidx.o -c faidx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hfile.o -c hfile.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hfile_net.o -c hfile_net.c echo '#define HTS_VERSION "1.3"' > version.h cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o hts.o -c hts.c hts.c:48:5: warning: unused function 'ks_getc' [-Wunused-function] 48 | KSTREAM_INIT2(, BGZF*, bgzf_read, 65536) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2' 152 | __KS_INLINED(__read) | ^~~~~~~~~~~~~~~~~~~~ ./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED' 68 | static inline int ks_getc(kstream_t *ks) \ | ^~~~~~~ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o md5.o -c md5.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o regidx.o -c regidx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o sam.o -c sam.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o synced_bcf_reader.o -c synced_bcf_reader.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vcf_sweep.o -c vcf_sweep.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o tbx.o -c tbx.c tbx.c:75:27: warning: variable 'ncols' set but not used [-Wunused-but-set-variable] 75 | int i, b = 0, id = 1, ncols = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vcf.o -c vcf.c vcf.c:590:14: warning: variable 'needs_sync' set but not used [-Wunused-but-set-variable] 590 | int len, needs_sync = 0; | ^ vcf.c:2352:50: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 2352 | int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o vcfutils.o -c vcfutils.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_codecs.o -c cram/cram_codecs.c cram/cram_codecs.c:1195:19: warning: variable 'ntot' set but not used [-Wunused-but-set-variable] 1195 | int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_decode.o -c cram/cram_decode.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_encode.o -c cram/cram_encode.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_external.o -c cram/cram_external.c cram/cram_external.c:128:21: warning: address of array 'ch->codecs' will always evaluate to 'true' [-Wpointer-bool-conversion] 128 | if (!ch || !ch->codecs || !ch->codecs[ds]) | ~~~~~^~~~~~ cram/cram_external.c:167:21: warning: address of array 'ch->codecs' will always evaluate to 'true' [-Wpointer-bool-conversion] 167 | if (!ch || !ch->codecs) | ~~~~~^~~~~~ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_index.o -c cram/cram_index.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_io.o -c cram/cram_io.c cram/cram_io.c:3091:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3091 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:388: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~^~~~~ cram/cram_io.c:3091:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3091 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~~^~~~~ cram/cram_io.c:3091:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3091 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~~^~~~~ cram/cram_io.c:3091:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3091 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~^~~~~~~~~~~~~~~~~ cram/cram_io.c:3149:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3149 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:388: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~^~~~~ cram/cram_io.c:3149:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3149 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~~^~~~~ cram/cram_io.c:3149:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3149 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~~^~~~~ cram/cram_io.c:3149:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3149 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../htslib/cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' 97 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~^~~~~~~~~~~~~~~~~ 8 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_samtools.o -c cram/cram_samtools.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/cram_stats.o -c cram/cram_stats.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/files.o -c cram/files.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/mFILE.o -c cram/mFILE.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/open_trace_file.o -c cram/open_trace_file.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/pooled_alloc.o -c cram/pooled_alloc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/rANS_static.o -c cram/rANS_static.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/sam_header.o -c cram/sam_header.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/string_alloc.o -c cram/string_alloc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/thread_pool.o -c cram/thread_pool.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/vlen.o -c cram/vlen.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o cram/zfio.o -c cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bandExt.o -c bandExt.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o crudeali.o -c crudeali.c crudeali.c:754:17: warning: variable 'pEnd' set but not used [-Wunused-but-set-variable] 754 | int pStart = 0, pEnd = probeSize; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ffAliHelp.o -c ffAliHelp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ffSeedExtend.o -c ffSeedExtend.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fuzzyFind.o -c fuzzyFind.c fuzzyFind.c:583:5: warning: variable 'trimCount' set but not used [-Wunused-but-set-variable] 583 | int trimCount = 0; | ^ fuzzyFind.c:1013:5: warning: variable 'lumpCount' set but not used [-Wunused-but-set-variable] 1013 | int lumpCount = 1; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o genoFind.o -c genoFind.c genoFind.c:343:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] 343 | size_t count = 0; | ^ genoFind.c:373:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] 373 | size_t count = 0; | ^ genoFind.c:851:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] 851 | int usedCount = 0, overusedCount = 0; | ^ genoFind.c:851:20: warning: variable 'overusedCount' set but not used [-Wunused-but-set-variable] 851 | int usedCount = 0, overusedCount = 0; | ^ genoFind.c:998:5: warning: variable 'overCount' set but not used [-Wunused-but-set-variable] 998 | int overCount = 0; | ^ genoFind.c:1016:5: warning: variable 'overCount' set but not used [-Wunused-but-set-variable] 1016 | int overCount = 0; | ^ genoFind.c:1883:5: warning: variable 'totalHits' set but not used [-Wunused-but-set-variable] 1883 | int totalHits = 0, usedHits = 0, clumpCount = 0; | ^ genoFind.c:1883:20: warning: variable 'usedHits' set but not used [-Wunused-but-set-variable] 1883 | int totalHits = 0, usedHits = 0, clumpCount = 0; | ^ genoFind.c:1883:34: warning: variable 'clumpCount' set but not used [-Wunused-but-set-variable] 1883 | int totalHits = 0, usedHits = 0, clumpCount = 0; | ^ genoFind.c:2189:14: warning: variable 'endList' set but not used [-Wunused-but-set-variable] 2189 | endListPart *endList; | ^ genoFind.c:2251:14: warning: variable 'endList' set but not used [-Wunused-but-set-variable] 2251 | endListPart *endList; | ^ genoFind.c:2325:8: warning: variable 'endList' is uninitialized when used here [-Wuninitialized] 2325 | endList += 3; | ^~~~~~~ genoFind.c:2251:21: note: initialize the variable 'endList' to silence this warning 2251 | endListPart *endList; | ^ | = NULL 12 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfBlatLib.o -c gfBlatLib.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfClientLib.o -c gfClientLib.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfInternal.o -c gfInternal.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfOut.o -c gfOut.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfPcrLib.o -c gfPcrLib.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfWebLib.o -c gfWebLib.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ooc.o -c ooc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o patSpace.o -c patSpace.c patSpace.c:152:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] 152 | int usedCount = 0, overusedCount = 0; | ^ patSpace.c:152:20: warning: variable 'overusedCount' set but not used [-Wunused-but-set-variable] 152 | int usedCount = 0, overusedCount = 0; | ^ patSpace.c:261:5: warning: variable 'total' set but not used [-Wunused-but-set-variable] 261 | int total = 0; | ^ 3 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o splix.o -c splix.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o supStitch.o -c supStitch.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o trans3.o -c trans3.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xenbig.o -c xenbig.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xensmall.o -c xensmall.c ar rcus ../lib/amd64/jkOwnLib.a bandExt.o crudeali.o ffAliHelp.o ffSeedExtend.o fuzzyFind.o genoFind.o gfBlatLib.o gfClientLib.o gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o patSpace.o splix.o supStitch.o trans3.o xenbig.o xensmall.o cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o bandExtHuge.o -c bandExt.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o crudealiHuge.o -c crudeali.c crudeali.c:754:17: warning: variable 'pEnd' set but not used [-Wunused-but-set-variable] 754 | int pStart = 0, pEnd = probeSize; | ^ 1 warning generated. cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ffAliHelpHuge.o -c ffAliHelp.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o ffSeedExtendHuge.o -c ffSeedExtend.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o fuzzyFindHuge.o -c fuzzyFind.c fuzzyFind.c:583:5: warning: variable 'trimCount' set but not used [-Wunused-but-set-variable] 583 | int trimCount = 0; | ^ fuzzyFind.c:1013:5: warning: variable 'lumpCount' set but not used [-Wunused-but-set-variable] 1013 | int lumpCount = 1; | ^ 2 warnings generated. cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o genoFindHuge.o -c genoFind.c genoFind.c:343:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] 343 | size_t count = 0; | ^ genoFind.c:373:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] 373 | size_t count = 0; | ^ genoFind.c:851:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] 851 | int usedCount = 0, overusedCount = 0; | ^ genoFind.c:851:20: warning: variable 'overusedCount' set but not used [-Wunused-but-set-variable] 851 | int usedCount = 0, overusedCount = 0; | ^ genoFind.c:998:5: warning: variable 'overCount' set but not used [-Wunused-but-set-variable] 998 | int overCount = 0; | ^ genoFind.c:1016:5: warning: variable 'overCount' set but not used [-Wunused-but-set-variable] 1016 | int overCount = 0; | ^ genoFind.c:1883:5: warning: variable 'totalHits' set but not used [-Wunused-but-set-variable] 1883 | int totalHits = 0, usedHits = 0, clumpCount = 0; | ^ genoFind.c:1883:20: warning: variable 'usedHits' set but not used [-Wunused-but-set-variable] 1883 | int totalHits = 0, usedHits = 0, clumpCount = 0; | ^ genoFind.c:1883:34: warning: variable 'clumpCount' set but not used [-Wunused-but-set-variable] 1883 | int totalHits = 0, usedHits = 0, clumpCount = 0; | ^ genoFind.c:2189:14: warning: variable 'endList' set but not used [-Wunused-but-set-variable] 2189 | endListPart *endList; | ^ genoFind.c:2251:14: warning: variable 'endList' set but not used [-Wunused-but-set-variable] 2251 | endListPart *endList; | ^ genoFind.c:2325:8: warning: variable 'endList' is uninitialized when used here [-Wuninitialized] 2325 | endList += 3; | ^~~~~~~ genoFind.c:2251:21: note: initialize the variable 'endList' to silence this warning 2251 | endListPart *endList; | ^ | = NULL 12 warnings generated. cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfBlatLibHuge.o -c gfBlatLib.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfClientLibHuge.o -c gfClientLib.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfInternalHuge.o -c gfInternal.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfOutHuge.o -c gfOut.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfPcrLibHuge.o -c gfPcrLib.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o gfWebLibHuge.o -c gfWebLib.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o oocHuge.o -c ooc.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o patSpaceHuge.o -c patSpace.c patSpace.c:152:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] 152 | int usedCount = 0, overusedCount = 0; | ^ patSpace.c:152:20: warning: variable 'overusedCount' set but not used [-Wunused-but-set-variable] 152 | int usedCount = 0, overusedCount = 0; | ^ patSpace.c:261:5: warning: variable 'total' set but not used [-Wunused-but-set-variable] 261 | int total = 0; | ^ 3 warnings generated. cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o splixHuge.o -c splix.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o supStitchHuge.o -c supStitch.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o trans3Huge.o -c trans3.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xenbigHuge.o -c xenbig.c cc -DGFSERVER_HUGE -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/local/include/libpng16 -o xensmallHuge.o -c xensmall.c ar rcus ../lib/amd64/jkOwnLibHuge.a bandExtHuge.o crudealiHuge.o ffAliHelpHuge.o ffSeedExtendHuge.o fuzzyFindHuge.o genoFindHuge.o gfBlatLibHuge.o gfClientLibHuge.o gfInternalHuge.o gfOutHuge.o gfPcrLibHuge.o gfWebLibHuge.o oocHuge.o patSpaceHuge.o splixHuge.o supStitchHuge.o trans3Huge.o xenbigHuge.o xensmallHuge.o cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o adjacency.o -c adjacency.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affyPairs.o -c affyPairs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o agpFrag.o -c agpFrag.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o agpGap.o -c agpGap.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o alignSeqSizes.o -c alignSeqSizes.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o altGraphX.o -c altGraphX.c altGraphX.c:1649:5: warning: variable 'count' set but not used [-Wunused-but-set-variable] 1649 | int count =0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o asmAlias.o -c asmAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o asmEquivalent.o -c asmEquivalent.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o asmSummary.o -c asmSummary.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o assemblyList.o -c assemblyList.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o autoUpgrade.o -c autoUpgrade.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o axtInfo.o -c axtInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartBed.o -c barChartBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartCategory.o -c barChartCategory.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartUi.o -c barChartUi.c In file included from barChartUi.c:14: ../inc/hCommon.h:111:9: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype] 111 | boolean validateGisaidUser(); | ^ ../inc/web.h:343:9: note: conflicting prototype is here 343 | boolean validateGisaidUser(struct cart *cart); | ^ In file included from barChartUi.c:18: ../inc/barChartUi.h:97:8: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 97 | double barChartUiMaxMedianScore(); | ^ barChartUi.c:145:8: note: conflicting prototype is here 145 | double barChartUiMaxMedianScore(struct trackDb *tdb) | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed.o -c bed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed12Source.o -c bed12Source.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bedDetail.o -c bedDetail.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigBedFind.o -c bigBedFind.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigBedLabel.o -c bigBedLabel.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigChain.o -c bigChain.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigDbSnp.o -c bigDbSnp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigGenePred.o -c bigGenePred.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigLink.o -c bigLink.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigPsl.o -c bigPsl.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o blastTab.o -c blastTab.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o borf.o -c borf.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o botDelay.o -c botDelay.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cart.o -c cart.c In file included from cart.c:5: ../inc/hCommon.h:111:9: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 111 | boolean validateGisaidUser(); | ^ ../inc/web.h:343:9: note: conflicting prototype is here 343 | boolean validateGisaidUser(struct cart *cart); | ^ cart.c:2378:53: warning: passing arguments to 'loginValidateCookies' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2378 | struct slName *newCookies = loginValidateCookies(cart), *sl; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cartDb.o -c cartDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsEvidence.o -c cdsEvidence.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsOrtho.o -c cdsOrtho.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsPick.o -c cdsPick.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgapSage/cgapSage.o -c cgapSage/cgapSage.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgapSage/cgapSageLib.o -c cgapSage/cgapSageLib.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgiApoptosis.o -c cgiApoptosis.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainCart.o -c chainCart.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainDb.o -c chainDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainLink.o -c chainLink.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainNet.o -c chainNet.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainNetDbLoad.o -c chainNetDbLoad.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromAlias.o -c chromAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromBins.o -c chromBins.c chromBins.c:29:31: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 29 | (*chromBins->freeFunc)(&be->val); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromGraph.o -c chromGraph.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromGraphFactory.o -c chromGraphFactory.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromInfo.o -c chromInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromInserts.o -c chromInserts.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromKeeper.o -c chromKeeper.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o clonePos.o -c clonePos.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cpgIsland.o -c cpgIsland.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ctgPos.o -c ctgPos.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customAdjacency.o -c customAdjacency.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customComposite.o -c customComposite.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customFactory.o -c customFactory.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customPp.o -c customPp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customTrack.o -c customTrack.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cv.o -c cv.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cytoBand.o -c cytoBand.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dbDb.o -c dbDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o decoration.o -c decoration.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o decoratorUi.o -c decoratorUi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o defaultDb.o -c defaultDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dnaMotifSql.o -c dnaMotifSql.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dupTrack.o -c dupTrack.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeErge.o -c encode/encodeErge.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeErgeHssCellLines.o -c encode/encodeErgeHssCellLines.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeExp.o -c encode/encodeExp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeHapMapAlleleFreq.o -c encode/encodeHapMapAlleleFreq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeIndels.o -c encode/encodeIndels.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodePeak.o -c encode/encodePeak.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeRegionInfoCustom.o -c encode/encodeRegionInfoCustom.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeRna.o -c encode/encodeRna.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeStanfordPromoters.o -c encode/encodeStanfordPromoters.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeStanfordPromotersAverage.o -c encode/encodeStanfordPromotersAverage.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/peptideMapping.o -c encode/peptideMapping.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeAnnotationRemark.o -c encode/wgEncodeGencodeAnnotationRemark.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeAttrs.o -c encode/wgEncodeGencodeAttrs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeEntrezGene.o -c encode/wgEncodeGencodeEntrezGene.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeExonSupport.o -c encode/wgEncodeGencodeExonSupport.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeGeneSource.o -c encode/wgEncodeGencodeGeneSource.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeGeneSymbol.o -c encode/wgEncodeGencodeGeneSymbol.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodePdb.o -c encode/wgEncodeGencodePdb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodePubMed.o -c encode/wgEncodeGencodePubMed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeRefSeq.o -c encode/wgEncodeGencodeRefSeq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTag.o -c encode/wgEncodeGencodeTag.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTranscriptSource.o -c encode/wgEncodeGencodeTranscriptSource.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTranscriptSupport.o -c encode/wgEncodeGencodeTranscriptSupport.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTranscriptionSupportLevel.o -c encode/wgEncodeGencodeTranscriptionSupportLevel.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeUniProt.o -c encode/wgEncodeGencodeUniProt.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode3/encode3Valid.o -c encode3/encode3Valid.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o estOrientInfo.o -c estOrientInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o expData.o -c expData.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o exportedDataHubs.o -c exportedDataHubs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o expRecord.o -c expRecord.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o facetField.o -c facetField.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o facetedTable.o -c facetedTable.c In file included from facetedTable.c:9: ../inc/hCommon.h:111:9: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype] 111 | boolean validateGisaidUser(); | ^ ../inc/web.h:343:9: note: conflicting prototype is here 343 | boolean validateGisaidUser(struct cart *cart); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o featureBits.o -c featureBits.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o findKGAlias.o -c findKGAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o fakeCurl.o -c fakeCurl.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o findKGProtAlias.o -c findKGProtAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbSeq.o -c gbSeq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbExtFile.o -c gbExtFile.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gcPercent.o -c gcPercent.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genark.o -c genark.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genbank.o -c genbank.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genbankBlackList.o -c genbankBlackList.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gencodeTracksCommon.o -c gencodeTracksCommon.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gencodeAttrs.o -c gencodeAttrs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gencodeToRefSeq.o -c gencodeToRefSeq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneGraph.o -c geneGraph.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genePred.o -c genePred.c genePred.c:670:5: warning: variable 'numCdsExons' set but not used [-Wunused-but-set-variable] 670 | int numCdsExons = 0; | ^ genePred.c:671:5: warning: variable 'numFrameExons' set but not used [-Wunused-but-set-variable] 671 | int numFrameExons = 0; | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genePredReader.o -c genePredReader.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geoMirror.o -c geoMirror.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggCluster.o -c ggCluster.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggDump.o -c ggDump.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggGraph.o -c ggGraph.c ggGraph.c:132:5: warning: variable 'totalWithDupes' set but not used [-Wunused-but-set-variable] 132 | int totalWithDupes = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggMrnaAli.o -c ggMrnaAli.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggTypes.o -c ggTypes.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o glDbRep.o -c glDbRep.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o googleAnalytics.o -c googleAnalytics.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gpFx.o -c gpFx.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o grp.o -c grp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexAse.o -c gtexAse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexDonor.o -c gtexDonor.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexGeneBed.o -c gtexGeneBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexInfo.o -c gtexInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexSample.o -c gtexSample.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexSampleData.o -c gtexSampleData.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexTissue.o -c gtexTissue.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexTissueMedian.o -c gtexTissueMedian.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexUi.o -c gtexUi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hCommon.o -c hCommon.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hPrint.o -c hPrint.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hVarSubst.o -c hVarSubst.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapAllelesOrtho.o -c hapmapAllelesOrtho.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapPhaseIIISummary.o -c hapmapPhaseIIISummary.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapSnps.o -c hapmapSnps.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hdb.o -c hdb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgColors.o -c hgColors.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgConfig.o -c hgConfig.c In file included from hgConfig.c:8: ../inc/hgConfig.h:41:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 41 | struct slName *cfgNamesWithPrefix(); | ^ hgConfig.c:325:16: note: conflicting prototype is here 325 | struct slName *cfgNamesWithPrefix(char* prefix) | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgFind.o -c hgFind.c In file included from hgFind.c:8: ../inc/hCommon.h:111:9: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 111 | boolean validateGisaidUser(); | ^ ../inc/web.h:343:9: note: conflicting prototype is here 343 | boolean validateGisaidUser(struct cart *cart); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgFindSpec.o -c hgFindSpec.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgFindSpecCustom.o -c hgFindSpecCustom.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgHgvs.o -c hgHgvs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgHgvsParse.o -c hgHgvsParse.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgMaf.o -c hgMaf.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgRelate.o -c hgRelate.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hic.o -c hic.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hicUi.o -c hicUi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hubConnect.o -c hubConnect.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hubPublic.o -c hubPublic.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hubSearchText.o -c hubSearchText.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hui.o -c hui.c In file included from hui.c:16: ../inc/hCommon.h:111:9: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 111 | boolean validateGisaidUser(); | ^ ../inc/web.h:343:9: note: conflicting prototype is here 343 | boolean validateGisaidUser(struct cart *cart); | ^ hui.c:2435:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 2435 | { | ^ hui.c:2431:1: note: previous statement is here 2431 | if (selectedName == NULL) | ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o imageClone.o -c imageClone.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o indelShift.o -c indelShift.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o interact.o -c interact.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o interactUi.o -c interactUi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o itemAttr.o -c itemAttr.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jksql.o -c jksql.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o joiner.o -c joiner.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jsHelper.o -c jsHelper.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o kgAlias.o -c kgAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o kgProtAlias.o -c kgProtAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o kgXref.o -c kgXref.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o knownInfo.o -c knownInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o knownMore.o -c knownMore.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o lav.o -c lav.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o lfs.o -c lfs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o liftOver.o -c liftOver.c liftOver.c:1313:21: warning: 'sizeof (((void *)0))' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 1313 | wordCount = chopLine(line, NULL); | ^~~~~~~~~~~~~~~~~~~~ ../../inc/common.h:1002:56: note: expanded from macro 'chopLine' 1002 | #define chopLine(line, words) chopByWhite(line, words, ArraySize(words)) | ^~~~~~~~~~~~~~~~ ../../inc/common.h:173:32: note: expanded from macro 'ArraySize' 173 | #define ArraySize(a) (sizeof(a)/sizeof((a)[0])) | ~~~~~~~~~^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o liftOverChain.o -c liftOverChain.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o liftUp.o -c liftUp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o longRange.o -c longRange.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o lrg.o -c lrg.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o lsSnpPdb.o -c lsSnpPdb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o mafFrames.o -c mafFrames.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o mafGene.o -c mafGene.c mafGene.c:708:9: warning: variable 'thisSize' set but not used [-Wunused-but-set-variable] 708 | int thisSize = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o mafSummary.o -c mafSummary.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o makeItemsItem.o -c makeItemsItem.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o mdb.o -c mdb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o microarray.o -c microarray.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o minChromSize.o -c minChromSize.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o namedSessionDb.o -c namedSessionDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o netAlign.o -c netAlign.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o netCart.o -c netCart.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o pepPred.o -c pepPred.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o pgPhenoAssoc.o -c pgPhenoAssoc.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o pgSnp.o -c pgSnp.c pgSnp.c:471:18: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value] 471 | int diff = abs((item->chromEnd - item->chromStart) - strlen(allele[i])); | ^ pgSnp.c:471:18: note: remove the call to 'abs' since unsigned values cannot be negative 471 | int diff = abs((item->chromEnd - item->chromStart) - strlen(allele[i])); | ^~~ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o pslReader.o -c pslReader.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o qaSeq.o -c qaSeq.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o quickLift.o -c quickLift.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o quickLiftChain.o -c quickLiftChain.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rankProp.o -c rankProp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o refLink.o -c refLink.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o refSeqStatus.o -c refSeqStatus.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rikenCluster.o -c rikenCluster.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rmskAlign.o -c rmskAlign.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rmskJoined.o -c rmskJoined.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rmskOut.o -c rmskOut.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rmskOut2.o -c rmskOut2.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o rnaGene.o -c rnaGene.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sage.o -c sage.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sageCounts.o -c sageCounts.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o samAlignment.o -c samAlignment.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sample.o -c sample.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sanger22extra.o -c sanger22extra.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o scoredRef.o -c scoredRef.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sessionData.o -c sessionData.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o seqWindow.o -c seqWindow.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o snakeUi.o -c snakeUi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o snp.o -c snp.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o snpExceptions.o -c snpExceptions.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o soTerm.o -c soTerm.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o spDb.o -c spDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sqlProg.o -c sqlProg.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o sqlSanity.o -c sqlSanity.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o stanMad.o -c stanMad.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o stsAlias.o -c stsAlias.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o stsInfo2.o -c stsInfo2.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o stsMap.o -c stsMap.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o stsMarker.o -c stsMarker.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o tableStatus.o -c tableStatus.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o tablesTables.o -c tablesTables.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o tagRepo.o -c tagRepo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o tfbsCons.o -c tfbsCons.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o tigrCmrGene.o -c tigrCmrGene.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o traceInfo.o -c traceInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o trackDb.o -c trackDb.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o trackDbCache.o -c trackDbCache.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o trackDbCustom.o -c trackDbCustom.c trackDbCustom.c:1059:5: warning: variable 'countOfSortedContainers' set but not used [-Wunused-but-set-variable] 1059 | int countOfSortedContainers = 0; | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o trackHub.o -c trackHub.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o trackVersion.o -c trackVersion.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o trashDir.o -c trashDir.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txAliDiff.o -c txAliDiff.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txCluster.o -c txCluster.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txCommon.o -c txCommon.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txEdgeBed.o -c txEdgeBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txGraph.o -c txGraph.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txInfo.o -c txInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o txRnaAccs.o -c txRnaAccs.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o variantProjector.o -c variantProjector.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o vcfUi.o -c vcfUi.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o vegaInfo.o -c vegaInfo.c sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o web.o -c web.c In file included from web.c:6: ../inc/hCommon.h:111:9: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 111 | boolean validateGisaidUser(); | ^ ../inc/web.h:343:9: note: conflicting prototype is here 343 | boolean validateGisaidUser(struct cart *cart); | ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o wigAsciiToBinary.o -c wigAsciiToBinary.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o wigDataStream.o -c wigDataStream.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o wiggle.o -c wiggle.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o wiggleCart.o -c wiggleCart.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o wiggleUtils.o -c wiggleUtils.c wiggleUtils.c:167:5: warning: variable 'spanCount' set but not used [-Wunused-but-set-variable] 167 | int spanCount = 0; | ^ wiggleUtils.c:264:5: warning: variable 'spanCount' set but not used [-Wunused-but-set-variable] 264 | int spanCount = 0; | ^ wiggleUtils.c:457:5: warning: variable 'noData' set but not used [-Wunused-but-set-variable] 457 | int noData = 0; | ^ wiggleUtils.c:777:5: warning: variable 'rowCount' set but not used [-Wunused-but-set-variable] 777 | int rowCount = 0; | ^ wiggleUtils.c:786:5: warning: variable 'spanCount' set but not used [-Wunused-but-set-variable] 786 | int spanCount = 0; | ^ 5 warnings generated. cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o wikiLink.o -c wikiLink.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigRmskAlignBed.o -c bigRmskAlignBed.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigRmskBed.o -c bigRmskBed.c cd straw && /usr/local/bin/gmake straw gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/hg/lib/straw' c++ straw.cpp -I../../../inc -g -c -lz -std=c++11 -o straw.o c++: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] straw.cpp:1587:32: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1587 | chromosome chromosomes[chromosomeMap.size()]; | ^~~~~~~~~~~~~~~~~~~~ straw.cpp:1587:32: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function 1 warning generated. c++ cStraw.cpp -I../../../inc -g -c -lz -std=c++11 -o cStraw.o c++: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] ld -r -o ../straw.o straw.o cStraw.o gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/hg/lib/straw' mkdir -p ../../lib/amd64 ar rcus ../../lib/amd64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o assemblyList.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o sessionData.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o straw.o cd addCols && echo addCols && /usr/local/bin/gmake addCols gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/addCols' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o addCols.o -c addCols.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/addCols addCols.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/addCols gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/addCols' cd ave && echo ave && /usr/local/bin/gmake ave gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/ave' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o ave.o -c ave.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/ave ave.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/ave gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/ave' cd aveCols && echo aveCols && /usr/local/bin/gmake aveCols gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/aveCols' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o aveCols.o -c aveCols.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/aveCols aveCols.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/aveCols gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/aveCols' cd bamToPsl && echo bamToPsl && /usr/local/bin/gmake bamToPsl gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bamToPsl' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bamToPsl.o -c bamToPsl.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bamToPsl bamToPsl.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bamToPsl gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bamToPsl' cd bedClip && echo bedClip && /usr/local/bin/gmake bedClip gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedClip' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedClip.o -c bedClip.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedClip bedClip.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedClip gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedClip' cd bedGraphToBigWig && echo bedGraphToBigWig && /usr/local/bin/gmake bedGraphToBigWig gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedGraphToBigWig' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedGraphToBigWig.o -c bedGraphToBigWig.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedGraphToBigWig bedGraphToBigWig.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedGraphToBigWig gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedGraphToBigWig' cd bedJoinTabOffset && echo bedJoinTabOffset && /usr/local/bin/gmake bedJoinTabOffset gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedJoinTabOffset' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedJoinTabOffset.o -c bedJoinTabOffset.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedJoinTabOffset bedJoinTabOffset.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedJoinTabOffset gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedJoinTabOffset' cd bedToBigBed && echo bedToBigBed && /usr/local/bin/gmake bedToBigBed gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedToBigBed' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedToBigBed.o -c bedToBigBed.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedToBigBed bedToBigBed.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedToBigBed gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedToBigBed' cd bigBedInfo && echo bigBedInfo && /usr/local/bin/gmake bigBedInfo gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedInfo' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigBedInfo.o -c bigBedInfo.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedInfo bigBedInfo.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedInfo gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedInfo' cd bigBedNamedItems && echo bigBedNamedItems && /usr/local/bin/gmake bigBedNamedItems gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedNamedItems' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigBedNamedItems.o -c bigBedNamedItems.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedNamedItems bigBedNamedItems.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedNamedItems gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedNamedItems' cd bigBedSummary && echo bigBedSummary && /usr/local/bin/gmake bigBedSummary gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedSummary' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigBedSummary.o -c bigBedSummary.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedSummary bigBedSummary.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedSummary gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedSummary' cd bigBedToBed && echo bigBedToBed && /usr/local/bin/gmake bigBedToBed gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedToBed' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigBedToBed.o -c bigBedToBed.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedToBed bigBedToBed.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigBedToBed gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigBedToBed' cd bedCommonRegions && echo bedCommonRegions && /usr/local/bin/gmake bedCommonRegions gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedCommonRegions' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedCommonRegions.o -c bedCommonRegions.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedCommonRegions bedCommonRegions.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedCommonRegions gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedCommonRegions' cd bedGeneParts && echo bedGeneParts && /usr/local/bin/gmake bedGeneParts gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedGeneParts' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedGeneParts.o -c bedGeneParts.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedGeneParts bedGeneParts.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedGeneParts gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedGeneParts' cd bedGraphPack && echo bedGraphPack && /usr/local/bin/gmake bedGraphPack gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedGraphPack' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedGraphPack.o -c bedGraphPack.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedGraphPack bedGraphPack.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedGraphPack gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedGraphPack' cd bedPileUps && echo bedPileUps && /usr/local/bin/gmake bedPileUps gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedPileUps' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedPileUps.o -c bedPileUps.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedPileUps bedPileUps.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedPileUps gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedPileUps' cd bedRemoveOverlap && echo bedRemoveOverlap && /usr/local/bin/gmake bedRemoveOverlap gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedRemoveOverlap' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedRemoveOverlap.o -c bedRemoveOverlap.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedRemoveOverlap bedRemoveOverlap.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedRemoveOverlap gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedRemoveOverlap' cd bedRestrictToPositions && echo bedRestrictToPositions && /usr/local/bin/gmake bedRestrictToPositions gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedRestrictToPositions' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bedRestrictToPositions.o -c bedRestrictToPositions.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedRestrictToPositions bedRestrictToPositions.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bedRestrictToPositions gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bedRestrictToPositions' cd bigWigAverageOverBed && echo bigWigAverageOverBed && /usr/local/bin/gmake bigWigAverageOverBed gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigAverageOverBed' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigAverageOverBed.o -c bigWigAverageOverBed.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigAverageOverBed bigWigAverageOverBed.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigAverageOverBed gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigAverageOverBed' cd bigWigCat && echo bigWigCat && /usr/local/bin/gmake bigWigCat gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigCat' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigCat.o -c bigWigCat.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigCat bigWigCat.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigCat gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigCat' cd bigWigCorrelate && echo bigWigCorrelate && /usr/local/bin/gmake bigWigCorrelate gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigCorrelate' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigCorrelate.o -c bigWigCorrelate.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigCorrelate bigWigCorrelate.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigCorrelate gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigCorrelate' cd bigWigCluster && echo bigWigCluster && /usr/local/bin/gmake bigWigCluster gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigCluster' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigCluster.o -c bigWigCluster.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigCluster bigWigCluster.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigCluster gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigCluster' cd bigWigInfo && echo bigWigInfo && /usr/local/bin/gmake bigWigInfo gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigInfo' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigInfo.o -c bigWigInfo.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigInfo bigWigInfo.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigInfo gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigInfo' cd bigWigMerge && echo bigWigMerge && /usr/local/bin/gmake bigWigMerge gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigMerge' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigMerge.o -c bigWigMerge.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigMerge bigWigMerge.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigMerge gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigMerge' cd bigWigSummary && echo bigWigSummary && /usr/local/bin/gmake bigWigSummary gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigSummary' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigSummary.o -c bigWigSummary.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigSummary bigWigSummary.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigSummary gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigSummary' cd bigWigToBedGraph && echo bigWigToBedGraph && /usr/local/bin/gmake bigWigToBedGraph gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigToBedGraph' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigToBedGraph.o -c bigWigToBedGraph.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigToBedGraph bigWigToBedGraph.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigToBedGraph gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigToBedGraph' cd bigWigToWig && echo bigWigToWig && /usr/local/bin/gmake bigWigToWig gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigToWig' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o bigWigToWig.o -c bigWigToWig.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigToWig bigWigToWig.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/bigWigToWig gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/bigWigToWig' cd calc && echo calc && /usr/local/bin/gmake calc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/calc' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o calc.o -c calc.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/calc calc.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/calc gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/calc' cd catDir && echo catDir && /usr/local/bin/gmake catDir gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/catDir' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o catDir.o -c catDir.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/catDir catDir.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/catDir gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/catDir' cd catUncomment && echo catUncomment && /usr/local/bin/gmake catUncomment gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/catUncomment' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o catUncomment.o -c catUncomment.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/catUncomment catUncomment.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/catUncomment gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/catUncomment' cd chopFaLines && echo chopFaLines && /usr/local/bin/gmake chopFaLines gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/chopFaLines' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o chopFaLines.o -c chopFaLines.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/chopFaLines chopFaLines.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/chopFaLines gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/chopFaLines' cd colTransform && echo colTransform && /usr/local/bin/gmake colTransform gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/colTransform' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o colTransform.o -c colTransform.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/colTransform colTransform.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/colTransform gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/colTransform' cd countChars && echo countChars && /usr/local/bin/gmake countChars gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/countChars' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o countChars.o -c countChars.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/countChars countChars.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/countChars gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/countChars' cd endsInLf && echo endsInLf && /usr/local/bin/gmake endsInLf gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/endsInLf' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o endsInLf.o -c endsInLf.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/endsInLf endsInLf.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/endsInLf gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/endsInLf' cd clusterMatrixToBarChartBed && echo clusterMatrixToBarChartBed && /usr/local/bin/gmake clusterMatrixToBarChartBed gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/clusterMatrixToBarChartBed' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o clusterMatrixToBarChartBed.o -c clusterMatrixToBarChartBed.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/clusterMatrixToBarChartBed clusterMatrixToBarChartBed.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/clusterMatrixToBarChartBed gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/clusterMatrixToBarChartBed' cd cpgIslandExt && echo cpgIslandExt && /usr/local/bin/gmake cpgIslandExt gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/cpgIslandExt' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o cpg_lh.o -c cpg_lh.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o readseq.o -c readseq.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/cpg_lh cpg_lh.o readseq.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/cpg_lh gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/cpgIslandExt' cd faAlign && echo faAlign && /usr/local/bin/gmake faAlign gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faAlign' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faAlign.o -c faAlign.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faAlign faAlign.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faAlign gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faAlign' cd fastqToFa && echo fastqToFa && /usr/local/bin/gmake fastqToFa gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/fastqToFa' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o fastqToFa.o -c fastqToFa.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/fastqToFa fastqToFa.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/fastqToFa gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/fastqToFa' cd fastqStatsAndSubsample && echo fastqStatsAndSubsample && /usr/local/bin/gmake fastqStatsAndSubsample gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/fastqStatsAndSubsample' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o fastqStatsAndSubsample.o -c fastqStatsAndSubsample.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/fastqStatsAndSubsample fastqStatsAndSubsample.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/fastqStatsAndSubsample gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/fastqStatsAndSubsample' cd faCmp && echo faCmp && /usr/local/bin/gmake faCmp gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faCmp' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faCmp.o -c faCmp.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faCmp faCmp.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faCmp gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faCmp' cd faCount && echo faCount && /usr/local/bin/gmake faCount gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faCount' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faCount.o -c faCount.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faCount faCount.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faCount gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faCount' cd faFilterN && echo faFilterN && /usr/local/bin/gmake faFilterN gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFilterN' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faFilterN.o -c faFilterN.c faFilterN.c:130:5: warning: variable 'seqCount' set but not used [-Wunused-but-set-variable] 130 | int seqCount = 0, passCount = 0; | ^ faFilterN.c:130:19: warning: variable 'passCount' set but not used [-Wunused-but-set-variable] 130 | int seqCount = 0, passCount = 0; | ^ 2 warnings generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFilterN faFilterN.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFilterN gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFilterN' cd faFilter && echo faFilter && /usr/local/bin/gmake faFilter gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFilter' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faFilter.o -c faFilter.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFilter faFilter.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFilter gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFilter' cd faFrag && echo faFrag && /usr/local/bin/gmake faFrag gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFrag' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faFrag.o -c faFrag.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFrag faFrag.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFrag gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFrag' cd faNoise && echo faNoise && /usr/local/bin/gmake faNoise gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faNoise' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faNoise.o -c faNoise.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faNoise faNoise.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faNoise gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faNoise' cd faOneRecord && echo faOneRecord && /usr/local/bin/gmake faOneRecord gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faOneRecord' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faOneRecord.o -c faOneRecord.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faOneRecord faOneRecord.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faOneRecord gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faOneRecord' cd faPolyASizes && echo faPolyASizes && /usr/local/bin/gmake faPolyASizes gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faPolyASizes' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faPolyASizes.o -c faPolyASizes.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faPolyASizes faPolyASizes.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faPolyASizes gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faPolyASizes' cd faRandomize && echo faRandomize && /usr/local/bin/gmake faRandomize gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faRandomize' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faRandomize.o -c faRandomize.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faRandomize faRandomize.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faRandomize gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faRandomize' cd faRc && echo faRc && /usr/local/bin/gmake faRc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faRc' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faRc.o -c faRc.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faRc faRc.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faRc gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faRc' cd faSize && echo faSize && /usr/local/bin/gmake faSize gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSize' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faSize.o -c faSize.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSize faSize.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSize gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSize' cd faSomeRecords && echo faSomeRecords && /usr/local/bin/gmake faSomeRecords gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSomeRecords' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faSomeRecords.o -c faSomeRecords.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSomeRecords faSomeRecords.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSomeRecords gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSomeRecords' cd faSplit && echo faSplit && /usr/local/bin/gmake faSplit gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSplit' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faSplit.o -c faSplit.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSplit faSplit.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSplit gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSplit' cd faToFastq && echo faToFastq && /usr/local/bin/gmake faToFastq gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToFastq' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faToFastq.o -c faToFastq.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToFastq faToFastq.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToFastq gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToFastq' cd faToTab && echo faToTab && /usr/local/bin/gmake faToTab gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToTab' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faToTab.o -c faToTab.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToTab faToTab.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToTab gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToTab' cd faToTwoBit && echo faToTwoBit && /usr/local/bin/gmake faToTwoBit gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToTwoBit' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faToTwoBit.o -c faToTwoBit.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToTwoBit faToTwoBit.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToTwoBit gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToTwoBit' cd faTrans && echo faTrans && /usr/local/bin/gmake faTrans gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faTrans' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faTrans.o -c faTrans.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faTrans faTrans.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faTrans gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faTrans' cd findMotif && echo findMotif && /usr/local/bin/gmake findMotif gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/findMotif' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o findMotif.o -c findMotif.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/findMotif findMotif.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/findMotif gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/findMotif' cd headRest && echo headRest && /usr/local/bin/gmake headRest gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/headRest' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o headRest.o -c headRest.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/headRest headRest.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/headRest gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/headRest' cd htmlCheck && echo htmlCheck && /usr/local/bin/gmake htmlCheck gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/htmlCheck' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o htmlCheck.o -c htmlCheck.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/htmlCheck htmlCheck.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/htmlCheck gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/htmlCheck' cd matrixClusterColumns && echo matrixClusterColumns && /usr/local/bin/gmake matrixClusterColumns gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixClusterColumns' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o matrixClusterColumns.o -c matrixClusterColumns.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixClusterColumns matrixClusterColumns.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixClusterColumns gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixClusterColumns' cd matrixMarketToTsv && echo matrixMarketToTsv && /usr/local/bin/gmake matrixMarketToTsv gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixMarketToTsv' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o matrixMarketToTsv.o -c matrixMarketToTsv.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixMarketToTsv matrixMarketToTsv.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixMarketToTsv gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixMarketToTsv' cd matrixNormalize && echo matrixNormalize && /usr/local/bin/gmake matrixNormalize gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixNormalize' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o matrixNormalize.o -c matrixNormalize.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixNormalize matrixNormalize.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixNormalize gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixNormalize' cd matrixToBarChartBed && echo matrixToBarChartBed && /usr/local/bin/gmake matrixToBarChartBed gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixToBarChartBed' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o matrixToBarChartBed.o -c matrixToBarChartBed.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixToBarChartBed matrixToBarChartBed.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/matrixToBarChartBed gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/matrixToBarChartBed' cd newProg && echo newProg && /usr/local/bin/gmake newProg gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/newProg' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o newProg.o -c newProg.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/newProg newProg.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/newProg gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/newProg' cd newPythonProg && echo newPythonProg && /usr/local/bin/gmake newPythonProg gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/newPythonProg' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o newPythonProg.o -c newPythonProg.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/newPythonProg newPythonProg.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/newPythonProg gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/newPythonProg' cd nibFrag && echo nibFrag && /usr/local/bin/gmake nibFrag gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/nibFrag' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o nibFrag.o -c nibFrag.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/nibFrag nibFrag.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/nibFrag gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/nibFrag' cd nibSize && echo nibSize && /usr/local/bin/gmake nibSize gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/nibSize' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o nibSize.o -c nibSize.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/nibSize nibSize.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/nibSize gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/nibSize' cd paraFetch && echo paraFetch && /usr/local/bin/gmake paraFetch gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/paraFetch' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o paraFetch.o -c paraFetch.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/paraFetch paraFetch.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/paraFetch gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/paraFetch' cd paraSync && echo paraSync && /usr/local/bin/gmake paraSync gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/paraSync' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o paraSync.o -c paraSync.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/paraSync paraSync.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/paraSync gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/paraSync' cd pslMap && echo pslMap && /usr/local/bin/gmake pslMap gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslMap' echo '/* GENERATED CODE, DO NOT EDIT */' > usage.msg.tmp sed -Ee 's/^.*$/"&\\n"/' usage.txt >> usage.msg.tmp mv -f usage.msg.tmp usage.msg cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslMap.o -c pslMap.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslMap pslMap.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslMap gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslMap' cd pslMapPostChain && echo pslMapPostChain && /usr/local/bin/gmake pslMapPostChain gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslMapPostChain' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslMapPostChain.o -c pslMapPostChain.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslMapPostChain pslMapPostChain.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslMapPostChain gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslMapPostChain' cd pslPosTarget && echo pslPosTarget && /usr/local/bin/gmake pslPosTarget gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslPosTarget' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslPosTarget.o -c pslPosTarget.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslPosTarget pslPosTarget.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslPosTarget gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslPosTarget' cd pslProtToRnaCoords && echo pslProtToRnaCoords && /usr/local/bin/gmake pslProtToRnaCoords gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslProtToRnaCoords' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslProtToRnaCoords.o -c pslProtToRnaCoords.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslProtToRnaCoords pslProtToRnaCoords.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslProtToRnaCoords gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslProtToRnaCoords' cd pslRc && echo pslRc && /usr/local/bin/gmake pslRc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslRc' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslRc.o -c pslRc.c pslRc.c:50:25: warning: too many arguments in call to 'usage' 50 | usage("wrong # args"); | ~~~~~ ^ pslRc.c:50:10: warning: passing arguments to 'usage' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 50 | usage("wrong # args"); | ^ 2 warnings generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslRc pslRc.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslRc gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslRc' cd pslRemoveFrameShifts && echo pslRemoveFrameShifts && /usr/local/bin/gmake pslRemoveFrameShifts gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslRemoveFrameShifts' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslRemoveFrameShifts.o -c pslRemoveFrameShifts.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslRemoveFrameShifts pslRemoveFrameShifts.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslRemoveFrameShifts gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslRemoveFrameShifts' cd pslScore && echo pslScore && /usr/local/bin/gmake pslScore gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslScore' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslScore.o -c pslScore.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslScore pslScore.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslScore gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslScore' cd pslSpliceJunctions && echo pslSpliceJunctions && /usr/local/bin/gmake pslSpliceJunctions gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslSpliceJunctions' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslSpliceJunctions.o -c pslSpliceJunctions.c pslSpliceJunctions.c:64:23: warning: sizeof on array function parameter will return size of 'char *' instead of 'char[3]' [-Wsizeof-array-argument] 64 | safecpy(junc5p, sizeof(junc5p), juncA->dna); | ^ pslSpliceJunctions.c:47:56: note: declared here 47 | struct twoBitFile *genomeFh, char junc5p[3], char junc3p[3]) | ^ pslSpliceJunctions.c:65:23: warning: sizeof on array function parameter will return size of 'char *' instead of 'char[3]' [-Wsizeof-array-argument] 65 | safecpy(junc3p, sizeof(junc3p), juncB->dna); | ^ pslSpliceJunctions.c:47:72: note: declared here 47 | struct twoBitFile *genomeFh, char junc5p[3], char junc3p[3]) | ^ 2 warnings generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslSpliceJunctions pslSpliceJunctions.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslSpliceJunctions gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslSpliceJunctions' cd pslSwap && echo pslSwap && /usr/local/bin/gmake pslSwap gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslSwap' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslSwap.o -c pslSwap.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslSwap pslSwap.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslSwap gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslSwap' cd pslToPslx && echo pslToPslx && /usr/local/bin/gmake pslToPslx gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslToPslx' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslToPslx.o -c pslToPslx.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslToPslx pslToPslx.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslToPslx gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslToPslx' cd randomLines && echo randomLines && /usr/local/bin/gmake randomLines gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/randomLines' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o randomLines.o -c randomLines.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/randomLines randomLines.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/randomLines gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/randomLines' cd raToTab && echo raToTab && /usr/local/bin/gmake raToTab gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToTab' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o raToTab.o -c raToTab.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/raToTab raToTab.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/raToTab gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToTab' cd raToLines && echo raToLines && /usr/local/bin/gmake raToLines gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToLines' cd raToLines && /usr/local/bin/gmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToLines/raToLines' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/local/include/libpng16 -o raToLines.o -c raToLines.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/raToLines raToLines.o ../../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/raToLines gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToLines/raToLines' cd linesToRa && /usr/local/bin/gmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToLines/linesToRa' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/local/include/libpng16 -o linesToRa.o -c linesToRa.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/linesToRa linesToRa.o ../../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/linesToRa gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToLines/linesToRa' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/raToLines' cd rmFaDups && echo rmFaDups && /usr/local/bin/gmake rmFaDups gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/rmFaDups' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o rmFaDups.o -c rmFaDups.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/rmFaDups rmFaDups.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/rmFaDups gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/rmFaDups' cd rowsToCols && echo rowsToCols && /usr/local/bin/gmake rowsToCols gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/rowsToCols' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o rowsToCols.o -c rowsToCols.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/rowsToCols rowsToCols.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/rowsToCols gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/rowsToCols' cd sizeof && echo sizeof && /usr/local/bin/gmake sizeof gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/sizeof' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o sizeof.o -c sizeof.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/sizeof sizeof.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/sizeof gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/sizeof' cd spacedToTab && echo spacedToTab && /usr/local/bin/gmake spacedToTab gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/spacedToTab' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o spacedToTab.o -c spacedToTab.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/spacedToTab spacedToTab.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/spacedToTab gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/spacedToTab' cd splitFile && echo splitFile && /usr/local/bin/gmake splitFile gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/splitFile' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o splitFile.o -c splitFile.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/splitFile splitFile.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/splitFile gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/splitFile' cd splitFileByColumn && echo splitFileByColumn && /usr/local/bin/gmake splitFileByColumn gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/splitFileByColumn' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o splitFileByColumn.o -c splitFileByColumn.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/splitFileByColumn splitFileByColumn.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/splitFileByColumn gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/splitFileByColumn' cd strexCalc && echo strexCalc && /usr/local/bin/gmake strexCalc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/strexCalc' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o strexCalc.o -c strexCalc.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/strexCalc strexCalc.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/strexCalc gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/strexCalc' cd stringify && echo stringify && /usr/local/bin/gmake stringify gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/stringify' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o stringify.o -c stringify.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/stringify stringify.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/stringify gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/stringify' cd subChar && echo subChar && /usr/local/bin/gmake subChar gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/subChar' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o subChar.o -c subChar.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/subChar subChar.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/subChar gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/subChar' cd subColumn && echo subColumn && /usr/local/bin/gmake subColumn gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/subColumn' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o subColumn.o -c subColumn.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/subColumn subColumn.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/subColumn gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/subColumn' cd tailLines && echo tailLines && /usr/local/bin/gmake tailLines gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tailLines' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o tailLines.o -c tailLines.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tailLines tailLines.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tailLines gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tailLines' cd textHistogram && echo textHistogram && /usr/local/bin/gmake textHistogram gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/textHistogram' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o textHistogram.o -c textHistogram.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/textHistogram textHistogram.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/textHistogram gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/textHistogram' cd tickToDate && echo tickToDate && /usr/local/bin/gmake tickToDate gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tickToDate' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o tickToDate.o -c tickToDate.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tickToDate tickToDate.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tickToDate gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tickToDate' cd timing && echo timing && /usr/local/bin/gmake timing gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing' cd gmtime && /usr/local/bin/gmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing/gmtime' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/local/include/libpng16 -o gmtime.o -c gmtime.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/gmtime gmtime.o ../../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/gmtime gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing/gmtime' cd mktime && /usr/local/bin/gmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing/mktime' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/local/include/libpng16 -o mktime.o -c mktime.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/mktime mktime.o ../../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/mktime gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing/mktime' cd localtime && /usr/local/bin/gmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing/localtime' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/local/include/libpng16 -o localtime.o -c localtime.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/localtime localtime.o ../../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/localtime gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing/localtime' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/timing' cd toLower && echo toLower && /usr/local/bin/gmake toLower gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/toLower' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o toLower.o -c toLower.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/toLower toLower.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/toLower gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/toLower' cd toUpper && echo toUpper && /usr/local/bin/gmake toUpper gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/toUpper' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o toUpper.o -c toUpper.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/toUpper toUpper.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/toUpper gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/toUpper' cd trackDbIndexBb && echo trackDbIndexBb && /usr/local/bin/gmake trackDbIndexBb gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/trackDbIndexBb' rm -f /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/trackDbIndexBb cp -p trackDbIndexBb /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/trackDbIndexBb gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/trackDbIndexBb' cd twoBitDup && echo twoBitDup && /usr/local/bin/gmake twoBitDup gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/twoBitDup' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o twoBitDup.o -c twoBitDup.c twoBitDup.c:80:2: warning: 'MD5' is deprecated [-Wdeprecated-declarations] 80 | MD5((unsigned char *)seq->dna, strlen(seq->dna), md5Result); | ^ /usr/local/include/openssl/md5.h:52:1: note: 'MD5' has been explicitly marked deprecated here 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, | ^ /usr/local/include/openssl/macros.h:182:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0' 182 | # define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0) | ^ /usr/local/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED' 62 | # define OSSL_DEPRECATED(since) __attribute__((deprecated)) | ^ 1 warning generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/twoBitDup twoBitDup.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/twoBitDup gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/twoBitDup' cd twoBitInfo && echo twoBitInfo && /usr/local/bin/gmake twoBitInfo gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/twoBitInfo' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o twoBitInfo.o -c twoBitInfo.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/twoBitInfo twoBitInfo.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/twoBitInfo gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/twoBitInfo' cd twoBitToFa && echo twoBitToFa && /usr/local/bin/gmake twoBitToFa gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/twoBitToFa' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o twoBitToFa.o -c twoBitToFa.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/twoBitToFa twoBitToFa.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/twoBitToFa gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/twoBitToFa' cd wigCorrelate && echo wigCorrelate && /usr/local/bin/gmake wigCorrelate gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/wigCorrelate' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o wigCorrelate.o -c wigCorrelate.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/wigCorrelate wigCorrelate.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/wigCorrelate gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/wigCorrelate' cd wigToBigWig && echo wigToBigWig && /usr/local/bin/gmake wigToBigWig gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/wigToBigWig' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o wigToBigWig.o -c wigToBigWig.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/wigToBigWig wigToBigWig.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/wigToBigWig gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/wigToBigWig' cd wordLine && echo wordLine && /usr/local/bin/gmake wordLine gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/wordLine' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o wordLine.o -c wordLine.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/wordLine wordLine.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/wordLine gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/wordLine' cd aNotB && echo aNotB && /usr/local/bin/gmake aNotB gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/aNotB' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o aNotB.o -c aNotB.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/aNotB aNotB.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/aNotB gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/aNotB' cd ccCp && echo ccCp && /usr/local/bin/gmake ccCp gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/ccCp' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o ccCp.o -c ccCp.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/ccCp ccCp.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/ccCp gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/ccCp' cd convolve && echo convolve && /usr/local/bin/gmake convolve gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/convolve' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o convolve.o -c convolve.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/convolve convolve.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/convolve gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/convolve' cd detab && echo detab && /usr/local/bin/gmake detab gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/detab' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o detab.o -c detab.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/detab detab.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/detab gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/detab' cd dnsInfo && echo dnsInfo && /usr/local/bin/gmake dnsInfo gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/dnsInfo' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o dnsInfo.o -c dnsInfo.c cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/dnsInfo dnsInfo.o ../../lib/amd64/jkweb.a -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/dnsInfo gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/dnsInfo' cd faFlyBaseToUcsc && echo faFlyBaseToUcsc && /usr/local/bin/gmake faFlyBaseToUcsc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFlyBaseToUcsc' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faFlyBaseToUcsc.o -c faFlyBaseToUcsc.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFlyBaseToUcsc faFlyBaseToUcsc.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faFlyBaseToUcsc gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faFlyBaseToUcsc' cd faGapLocs && echo faGapLocs && /usr/local/bin/gmake faGapLocs gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faGapLocs' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faGapLocs.o -c faGapLocs.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faGapLocs faGapLocs.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faGapLocs gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faGapLocs' cd faGapSizes && echo faGapSizes && /usr/local/bin/gmake faGapSizes gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faGapSizes' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faGapSizes.o -c faGapSizes.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faGapSizes faGapSizes.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faGapSizes gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faGapSizes' cd faNcbiToUcsc && echo faNcbiToUcsc && /usr/local/bin/gmake faNcbiToUcsc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faNcbiToUcsc' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faNcbiToUcsc.o -c faNcbiToUcsc.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faNcbiToUcsc faNcbiToUcsc.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faNcbiToUcsc gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faNcbiToUcsc' cd faRenameRecords && echo faRenameRecords && /usr/local/bin/gmake faRenameRecords gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faRenameRecords' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faRenameRecords.o -c faRenameRecords.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faRenameRecords faRenameRecords.o ../../lib/amd64/jkweb.a -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faRenameRecords gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faRenameRecords' cd faSimplify && echo faSimplify && /usr/local/bin/gmake faSimplify gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSimplify' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faSimplify.o -c faSimplify.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSimplify faSimplify.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faSimplify gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faSimplify' cd faToNib && echo faToNib && /usr/local/bin/gmake faToNib gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToNib' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faToNib.o -c faToNib.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToNib faToNib.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faToNib gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faToNib' cd faTrimPolyA && echo faTrimPolyA && /usr/local/bin/gmake faTrimPolyA gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faTrimPolyA' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faTrimPolyA.o -c faTrimPolyA.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faTrimPolyA faTrimPolyA.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faTrimPolyA gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faTrimPolyA' cd faTrimRead && echo faTrimRead && /usr/local/bin/gmake faTrimRead gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faTrimRead' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o faTrimRead.o -c faTrimRead.c faTrimRead.c:228:5: warning: variable 'seqCount' set but not used [-Wunused-but-set-variable] 228 | int seqCount = 0; | ^ 1 warning generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faTrimRead faTrimRead.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/faTrimRead gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/faTrimRead' cd fixCr && echo fixCr && /usr/local/bin/gmake fixCr gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/fixCr' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o fixCr.o -c fixCr.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/fixCr fixCr.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/fixCr gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/fixCr' cd gapSplit && echo gapSplit && /usr/local/bin/gmake gapSplit gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/gapSplit' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o gapSplit.o -c gapSplit.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/gapSplit gapSplit.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/gapSplit gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/gapSplit' cd gitTools && echo gitTools && /usr/local/bin/gmake gitTools gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/gitTools' chmod a+rx gitFiles rm -f /wrkdirs/usr/ports/biology/ucsc-userapps/work/bin/scripts/gitFiles cp -pf gitFiles /wrkdirs/usr/ports/biology/ucsc-userapps/work/bin/scripts/gitFiles chmod a+rx gilt rm -f /wrkdirs/usr/ports/biology/ucsc-userapps/work/bin/scripts/gilt cp -pf gilt /wrkdirs/usr/ports/biology/ucsc-userapps/work/bin/scripts/gilt chmod a+rx gitu rm -f /wrkdirs/usr/ports/biology/ucsc-userapps/work/bin/scripts/gitu cp -pf gitu /wrkdirs/usr/ports/biology/ucsc-userapps/work/bin/scripts/gitu gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/gitTools' cd gffPeek && echo gffPeek && /usr/local/bin/gmake gffPeek gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/gffPeek' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o gffPeek.o -c gffPeek.c gffPeek.c:92:5: warning: variable 'commentCount' set but not used [-Wunused-but-set-variable] 92 | int commentCount = 0; | ^ gffPeek.c:93:5: warning: variable 'badCount' set but not used [-Wunused-but-set-variable] 93 | int badCount = 0; | ^ 2 warnings generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/gffPeek gffPeek.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/gffPeek gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/gffPeek' cd git-reports && echo git-reports && /usr/local/bin/gmake git-reports gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/git-reports' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o git-reports.o -c git-reports.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/git-reports git-reports.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/git-reports gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/git-reports' cd htmlPics && echo htmlPics && /usr/local/bin/gmake htmlPics gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/htmlPics' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o htmlPics.o -c htmlPics.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/htmlPics htmlPics.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/htmlPics gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/htmlPics' cd jkUniq && echo jkUniq && /usr/local/bin/gmake jkUniq gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/jkUniq' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o jkUniq.o -c jkUniq.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/jkUniq jkUniq.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/jkUniq gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/jkUniq' cd lineCount && echo lineCount && /usr/local/bin/gmake lineCount gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/lineCount' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o lineCount.o -c lineCount.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/lineCount lineCount.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/lineCount gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/lineCount' cd nt4Frag && echo nt4Frag && /usr/local/bin/gmake nt4Frag gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/nt4Frag' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o nt4Frag.o -c nt4Frag.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/nt4Frag nt4Frag.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/nt4Frag gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/nt4Frag' cd pslToXa && echo pslToXa && /usr/local/bin/gmake pslToXa gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslToXa' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o pslToXa.o -c pslToXa.c pslToXa.c:123:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 123 | { | ^ pslToXa.c:119:1: note: previous statement is here 119 | if (!seqFile->isNib) | ^ 1 warning generated. cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslToXa pslToXa.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/pslToXa gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/pslToXa' cd scrambleFa && echo scrambleFa && /usr/local/bin/gmake scrambleFa gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/scrambleFa' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o scrambleFa.o -c scrambleFa.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/scrambleFa scrambleFa.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/scrambleFa gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/scrambleFa' cd subs && echo subs && /usr/local/bin/gmake subs gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/subs' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o subs.o -c subs.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/subs subs.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/subs gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/subs' cd tabToMmHash && echo tabToMmHash && /usr/local/bin/gmake tabToMmHash gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tabToMmHash' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o tabToMmHash.o -c tabToMmHash.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tabToMmHash tabToMmHash.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tabToMmHash gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tabToMmHash' cd tableSum && echo tableSum && /usr/local/bin/gmake tableSum gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tableSum' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o tableSum.o -c tableSum.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tableSum tableSum.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/tableSum gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/tableSum' cd textHist2 && echo textHist2 && /usr/local/bin/gmake textHist2 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/textHist2' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o textHist2.o -c textHist2.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/textHist2 textHist2.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/textHist2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/textHist2' cd udcCleanup && echo udcCleanup && /usr/local/bin/gmake udcCleanup gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/udcCleanup' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o udcCleanup.o -c udcCleanup.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/udcCleanup udcCleanup.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/udcCleanup gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/udcCleanup' cd undupFa && echo undupFa && /usr/local/bin/gmake undupFa gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/undupFa' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o undupFa.o -c undupFa.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/undupFa undupFa.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/undupFa gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/undupFa' cd upper && echo upper && /usr/local/bin/gmake upper gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/upper' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o upper.o -c upper.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/upper upper.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/upper gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/upper' cd vcfFilter && echo vcfFilter && /usr/local/bin/gmake vcfFilter gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/vcfFilter' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o vcfFilter.o -c vcfFilter.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/vcfFilter vcfFilter.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/vcfFilter gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/vcfFilter' cd venn && echo venn && /usr/local/bin/gmake venn gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/venn' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o venn.o -c venn.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/venn venn.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/venn gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/venn' cd verticalSplitSqlTable && echo verticalSplitSqlTable && /usr/local/bin/gmake verticalSplitSqlTable gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/verticalSplitSqlTable' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o verticalSplitSqlTable.o -c verticalSplitSqlTable.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/verticalSplitSqlTable verticalSplitSqlTable.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/verticalSplitSqlTable gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/verticalSplitSqlTable' cd weedLines && echo weedLines && /usr/local/bin/gmake weedLines gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/weedLines' cc -O -g -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/local/include/libpng16 -o weedLines.o -c weedLines.c cc -O -g -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/weedLines weedLines.o ../../lib/amd64/jkweb.a -L/usr/local/lib/mysql -lmysqlclient -lpthread -lssl -lcrypto -lm -lrt -lexecinfo -L/usr/local/lib -lunwind -lstdc++ -lrt -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib -lpthread -lssl -lcrypto -ldl -ldl ../../htslib/libhts.a -L/usr/local/lib -lpng16 -lm -lz -lm true /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin/weedLines gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/kent/src/utils/weedLines' cp -p bedJoinTabOffset.py/bedJoinTabOffset.py /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p expMatrixToBarchartBed/expMatrixToBarchartBed /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p barChartMaxLimit/barChartMaxLimit /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p ucscApiClient/ucscApiClient /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p tdbRename/tdbRename /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p tdbSort/tdbSort /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p webSync/webSync /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p chromToUcsc/chromToUcsc /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p bigHeat/bigHeat /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cp -p bigGuessDb/bigGuessDb /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/bin cc -DUCSC_PREFIX="\"/usr/local/userapps\"" /usr/ports/biology/ucsc-userapps/files/kent.c -o /wrkdirs/usr/ports/biology/ucsc-userapps/work/kent =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ucsc-userapps-474 depends on executable: bash - found ===> ucsc-userapps-474 depends on file: /usr/local/bin/python3.11 - found ===> ucsc-userapps-474 depends on file: /usr/local/lib/libcrypto.so.12 - found ===> ucsc-userapps-474 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for ucsc-userapps-474 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/binaries/* /wrkdirs/usr/ports/biology/ucsc-userapps/work/stage/usr/local/userapps/bin install -m 555 /wrkdirs/usr/ports/biology/ucsc-userapps/work/userApps/scripts/* /wrkdirs/usr/ports/biology/ucsc-userapps/work/stage/usr/local/userapps/bin install -m 555 /wrkdirs/usr/ports/biology/ucsc-userapps/work/ucsc-shell /wrkdirs/usr/ports/biology/ucsc-userapps/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/ucsc-userapps/work/kent /wrkdirs/usr/ports/biology/ucsc-userapps/work/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-02T09:05:19+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for ucsc-userapps-474 ===> Building ucsc-userapps-474 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for ucsc-userapps-474 build of biology/ucsc-userapps | ucsc-userapps-474 ended at Fri May 2 10:10:47 BST 2025 build time: 00:05:29