=>> Building biology/ucsc-userapps build started at Sun Apr 7 09:26:49 BST 2024 port directory: /usr/ports/biology/ucsc-userapps package name: ucsc-userapps-414_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2646 Dec 30 12:03 /usr/ports/biology/ucsc-userapps/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 9ee2e860d4 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-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/13-amd64-default-dan/18/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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=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/python3.9" 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=/ccache/libexec/ccache:/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" CCACHE_DIR="/root/.ccache" --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=/ccache/libexec/ccache:/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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -Wl,-rpath,/usr/local/lib -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " CCACHE_DIR="/root/.ccache" 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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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 mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/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 --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-414_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> ucsc-userapps-414_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ucsc-userapps-414_1 =========================================================================== =================================================== ===== 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-414_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ucsc-userapps-414_1 for building => SHA256 Checksum OK for userApps.v414.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-414_1 for building ===> Extracting for ucsc-userapps-414_1 => SHA256 Checksum OK for userApps.v414.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-414_1 ===> Applying FreeBSD patches for ucsc-userapps-414_1 from /usr/ports/biology/ucsc-userapps/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ucsc-userapps-414_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.26_1.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.26_1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting bash-5.2.26_1: .......... done ===> ucsc-userapps-414_1 depends on executable: bash - found ===> Returning to build of ucsc-userapps-414_1 ===> ucsc-userapps-414_1 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-414_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of ucsc-userapps-414_1 ===> ucsc-userapps-414_1 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18_1.pkg [pkg-builder.dan.net.uk] Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting python39-3.9.18_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> ucsc-userapps-414_1 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of ucsc-userapps-414_1 ===> ucsc-userapps-414_1 depends on file: /usr/local/lib/libcrypto.so.12 - found ===> ucsc-userapps-414_1 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_1.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_1: .......... done ===> ucsc-userapps-414_1 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of ucsc-userapps-414_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ucsc-userapps-414_1 depends on shared library: libiconv.so - not found ===> Installing existing package /packages/All/libiconv-1.17_1.pkg [pkg-builder.dan.net.uk] Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] Extracting libiconv-1.17_1: .......... done ===> ucsc-userapps-414_1 depends on shared library: libiconv.so - found (/usr/local/lib/libiconv.so) ===> Returning to build of ucsc-userapps-414_1 ===> ucsc-userapps-414_1 depends on shared library: libpng.so - not found ===> Installing existing package /packages/All/png-1.6.43.pkg [pkg-builder.dan.net.uk] Installing png-1.6.43... [pkg-builder.dan.net.uk] Extracting png-1.6.43: .......... done ===> ucsc-userapps-414_1 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> Returning to build of ucsc-userapps-414_1 ===> ucsc-userapps-414_1 depends on shared library: libmysqlclient.so.21 - not found ===> Installing existing package /packages/All/mysql80-client-8.0.35.pkg [pkg-builder.dan.net.uk] Installing mysql80-client-8.0.35... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [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 libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing cyrus-sasl-2.1.28_4... *** Added group `cyrus' (id 60) *** Added user `cyrus' (id 60) [pkg-builder.dan.net.uk] `-- Extracting cyrus-sasl-2.1.28_4: .......... done [pkg-builder.dan.net.uk] `-- Installing groff-1.23.0_3... [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_3: .......... 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-74.2,1... [pkg-builder.dan.net.uk] `-- Extracting icu-74.2,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libedit-3.1.20230828_1,1... [pkg-builder.dan.net.uk] `-- Extracting libedit-3.1.20230828_1,1: .......... 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 libfido2-1.14.0... [pkg-builder.dan.net.uk] | `-- Installing libcbor-0.11.0... [pkg-builder.dan.net.uk] | | `-- Installing libcjson-1.7.17... [pkg-builder.dan.net.uk] | | `-- Extracting libcjson-1.7.17: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libcbor-0.11.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting libfido2-1.14.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libunwind-20240221... [pkg-builder.dan.net.uk] `-- Extracting libunwind-20240221: .......... done [pkg-builder.dan.net.uk] `-- Installing openldap26-client-2.6.7... [pkg-builder.dan.net.uk] `-- Extracting openldap26-client-2.6.7: .......... done [pkg-builder.dan.net.uk] Extracting mysql80-client-8.0.35: .......... done ===== Message from cyrus-sasl-2.1.28_4: -- 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_3: -- In order to be able to use the html driver, you need to install the following packages: - ghostscript - netpbm ===== Message from openldap26-client-2.6.7: -- 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-8.0.35: -- This is the mysql CLIENT without the server. for complete server and client, please install databases/mysql80-server ===> ucsc-userapps-414_1 depends on shared library: libmysqlclient.so.21 - found (/usr/local/lib/mysql/libmysqlclient.so.21) ===> Returning to build of ucsc-userapps-414_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for ucsc-userapps-414_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for ucsc-userapps-414_1 cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o aliType.o -c aliType.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoAssembly.o -c annoAssembly.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoFilter.o -c annoFilter.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoFormatter.o -c annoFormatter.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoFormatTab.o -c annoFormatTab.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoGrator.o -c annoGrator.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoGrateWig.o -c annoGrateWig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoGratorQuery.o -c annoGratorQuery.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoOption.o -c annoOption.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoRow.o -c annoRow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoStreamer.o -c annoStreamer.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoStreamBigBed.o -c annoStreamBigBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoStreamBigWig.o -c annoStreamBigWig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoStreamTab.o -c annoStreamTab.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoStreamLongTabix.o -c annoStreamLongTabix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o annoStreamVcf.o -c annoStreamVcf.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o apacheLog.o -c apacheLog.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o asParse.o -c asParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o aveStats.o -c aveStats.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o axt.o -c axt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o axtAffine.o -c axtAffine.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bamFile.o -c bamFile.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o base64.o -c base64.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o basicBed.o -c basicBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bbiRead.o -c bbiRead.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bbiWrite.o -c bbiWrite.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bedTabix.o -c bedTabix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bigBed.o -c bigBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o binRange.o -c binRange.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bits.o -c bits.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o blastOut.o -c blastOut.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o blastParse.o -c blastParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o boxClump.o -c boxClump.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o boxLump.o -c boxLump.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bPlusTree.o -c bPlusTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bwgCreate.o -c bwgCreate.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bwgQuery.o -c bwgQuery.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bwgValsOnChrom.o -c bwgValsOnChrom.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o cda.o -c cda.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o chain.o -c chain.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o chainBlock.o -c chainBlock.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o chainConnect.o -c chainConnect.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o chainToAxt.o -c chainToAxt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o chainToPsl.o -c chainToPsl.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o cheapcgi.o -c cheapcgi.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o cirTree.o -c cirTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o codebias.o -c codebias.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o colHash.o -c colHash.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o common.o -c common.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o correlate.o -c correlate.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o crTree.o -c crTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o csv.o -c csv.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dgRange.o -c dgRange.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o diGraph.o -c diGraph.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dlist.o -c dlist.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dnaLoad.o -c dnaLoad.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -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] int total = 0; ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dnaMotif.o -c dnaMotif.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dnaseq.o -c dnaseq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dnautil.o -c dnautil.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dtdParse.o -c dtdParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dyOut.o -c dyOut.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o dystring.o -c dystring.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o elmTree.o -c elmTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o emblParse.o -c emblParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o errCatch.o -c errCatch.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o errAbort.o -c errAbort.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fa.o -c fa.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o ffAli.o -c ffAli.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o ffScore.o -c ffScore.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fieldedTable.o -c fieldedTable.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o filePath.o -c filePath.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fixColor.o -c fixColor.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o flydna.o -c flydna.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fof.o -c fof.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier10.o -c font/mgCourier10.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier12.o -c font/mgCourier12.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier14.o -c font/mgCourier14.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier18.o -c font/mgCourier18.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier24.o -c font/mgCourier24.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier34.o -c font/mgCourier34.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgCourier8.o -c font/mgCourier8.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica10.o -c font/mgHelvetica10.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica12.o -c font/mgHelvetica12.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica14.o -c font/mgHelvetica14.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica18.o -c font/mgHelvetica18.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica24.o -c font/mgHelvetica24.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica34.o -c font/mgHelvetica34.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelvetica8.o -c font/mgHelvetica8.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold10.o -c font/mgHelveticaBold10.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold12.o -c font/mgHelveticaBold12.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold14.o -c font/mgHelveticaBold14.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold18.o -c font/mgHelveticaBold18.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold24.o -c font/mgHelveticaBold24.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold34.o -c font/mgHelveticaBold34.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgHelveticaBold8.o -c font/mgHelveticaBold8.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgSixhi6.o -c font/mgSixhi6.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgSail8.o -c font/mgSail8.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes10.o -c font/mgTimes10.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes12.o -c font/mgTimes12.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes14.o -c font/mgTimes14.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes18.o -c font/mgTimes18.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes24.o -c font/mgTimes24.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes34.o -c font/mgTimes34.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgTimes8.o -c font/mgTimes8.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o font/mgMenlo12.o -c font/mgMenlo12.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fq.o -c fq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o freeType.o -c freeType.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fuzzyShow.o -c fuzzyShow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gapCalc.o -c gapCalc.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gdf.o -c gdf.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gemfont.o -c gemfont.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o genomeRangeTree.o -c genomeRangeTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfNet.o -c gfNet.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gff.o -c gff.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gff3.o -c gff3.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfxPoly.o -c gfxPoly.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gifLabel.o -c gifLabel.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o hacTree.o -c hacTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o hash.o -c hash.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o hex.o -c hex.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o histogram.o -c histogram.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o hmmPfamParse.o -c hmmPfamParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o hmmstats.o -c hmmstats.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o htmlColor.o -c htmlColor.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o htmlPage.o -c htmlPage.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o htmshell.o -c htmshell.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o hmac.o -c hmac.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o https.o -c https.c https.c:77:5: warning: 'ERR_load_SSL_strings' is deprecated [-Wdeprecated-declarations] ERR_load_SSL_strings(); ^ /usr/local/include/openssl/sslerr_legacy.h:29:1: note: 'ERR_load_SSL_strings' has been explicitly marked deprecated here 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' # define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0) ^ /usr/local/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED' # define OSSL_DEPRECATED(since) __attribute__((deprecated)) ^ https.c:22:22: warning: unused function 'openssl_id_callback' [-Wunused-function] static unsigned long openssl_id_callback(void) ^ https.c:27:13: warning: unused function 'openssl_locking_callback' [-Wunused-function] static void openssl_locking_callback(int mode, int n, const char * file, int line) ^ 3 warnings generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o intExp.o -c intExp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o intValTree.o -c intValTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o internet.o -c internet.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o itsa.o -c itsa.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o iupac.o -c iupac.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o jointalign.o -c jointalign.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o jpegSize.o -c jpegSize.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o jsonParse.o -c jsonParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o jsonQuery.o -c jsonQuery.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o jsonWrite.o -c jsonWrite.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o keys.o -c keys.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o knetUdc.o -c knetUdc.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o kxTok.o -c kxTok.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o linefile.o -c linefile.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o lineFileOnBigBed.o -c lineFileOnBigBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o localmem.o -c localmem.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o log.o -c log.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o longTabix.o -c longTabix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o longToList.o -c longToList.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o maf.o -c maf.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o mafFromAxt.o -c mafFromAxt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o mafScore.o -c mafScore.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o mailViaPipe.o -c mailViaPipe.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o md5.o -c md5.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o matrixMarket.o -c matrixMarket.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o memalloc.o -c memalloc.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o memgfx.o -c memgfx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o meta.o -c meta.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o metaWig.o -c metaWig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o mgCircle.o -c mgCircle.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o mgPolygon.o -c mgPolygon.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o mime.o -c mime.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o net.o -c net.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o nib.o -c nib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o nibTwo.o -c nibTwo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o nt4.o -c nt4.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o numObscure.o -c numObscure.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o obscure.o -c obscure.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o oldGff.o -c oldGff.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o oligoTm.o -c oligoTm.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o options.o -c options.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o osunix.o -c osunix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -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] { ^ pairHmm.c:264:5: note: previous statement is here for (pair = pairList; pair->next != NULL; pair = pair->next) ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pairDistance.o -c pairDistance.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o paraFetch.o -c paraFetch.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o peakCluster.o -c peakCluster.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -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] fprintf(f,":%0.04g", tree->ident->length); ^ phyloTree.c:283:2: note: previous statement is here if (tree->ident->name) ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pipeline.o -c pipeline.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o portimpl.o -c portimpl.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pngwrite.o -c pngwrite.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o psGfx.o -c psGfx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o psPoly.o -c psPoly.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pscmGfx.o -c pscmGfx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o psl.o -c psl.c psl.c:1413:9: warning: variable 'qE' set but not used [-Wunused-but-set-variable] int qE = qS + sz; ^ psl.c:1499:9: warning: variable 'tE' set but not used [-Wunused-but-set-variable] int tE = tS + sz; ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pslGenoShow.o -c pslGenoShow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pslShow.o -c pslShow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pslTbl.o -c pslTbl.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pslTransMap.o -c pslTransMap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pthreadDoList.o -c pthreadDoList.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o pthreadWrap.o -c pthreadWrap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o qa.o -c qa.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o quickHeap.o -c quickHeap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o quotedP.o -c quotedP.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o ra.o -c ra.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rainbow.o -c rainbow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o raToStruct.o -c raToStruct.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rbTree.o -c rbTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rangeTree.o -c rangeTree.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o regexHelper.o -c regexHelper.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o repMask.o -c repMask.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rle.o -c rle.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rnautil.o -c rnautil.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rqlEval.o -c rqlEval.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rqlParse.o -c rqlParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rqlToSql.o -c rqlToSql.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o rudp.o -c rudp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o scoreWindow.o -c scoreWindow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o seg.o -c seg.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o seqOut.o -c seqOut.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o seqStats.o -c seqStats.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o servBrcMcw.o -c servBrcMcw.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o servCrunx.o -c servCrunx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o servcis.o -c servcis.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o servcl.o -c servcl.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o servmsII.o -c servmsII.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o servpws.o -c servpws.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o shaRes.o -c shaRes.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o slog.o -c slog.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o snof.o -c snof.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o snofmake.o -c snofmake.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o snofsig.o -c snofsig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o spaceSaver.o -c spaceSaver.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o spacedColumn.o -c spacedColumn.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o spacedSeed.o -c spacedSeed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o sparseMatrix.o -c sparseMatrix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o splatAli.o -c splatAli.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o sqlList.o -c sqlList.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o sqlNum.o -c sqlNum.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o sqlReserved.o -c sqlReserved.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o strex.o -c strex.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o subText.o -c subText.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o sufa.o -c sufa.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o sufx.o -c sufx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o synQueue.o -c synQueue.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o tabRow.o -c tabRow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o tagSchema.o -c tagSchema.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o tagStorm.o -c tagStorm.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o tagToJson.o -c tagToJson.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o tagToSql.o -c tagToSql.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o textOut.o -c textOut.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o tokenizer.o -c tokenizer.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o trix.o -c trix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o twoBit.o -c twoBit.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o udc.o -c udc.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o uuid.o -c uuid.c uuid.c:16:1: warning: implicit declaration of function 'uuid_generate' is invalid in C99 [-Wimplicit-function-declaration] uuid_generate(uuid); ^ uuid.c:17:1: warning: implicit declaration of function 'uuid_unparse_lower' is invalid in C99 [-Wimplicit-function-declaration] uuid_unparse_lower(uuid, buf); ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o vcf.o -c vcf.c vcf.c:413:17: warning: 'sizeof (((void *)0))' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] int wordCount = chopLine(line+1, NULL); ^~~~~~~~~~~~~~~~~~~~~~ ../inc/common.h:984:56: note: expanded from macro 'chopLine' #define chopLine(line, words) chopByWhite(line, words, ArraySize(words)) ^~~~~~~~~~~~~~~~ ../inc/common.h:173:32: note: expanded from macro 'ArraySize' #define ArraySize(a) (sizeof(a)/sizeof((a)[0])) ~~~~~~~~~^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o vcfBits.o -c vcfBits.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o vGfx.o -c vGfx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o vPng.o -c vPng.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o verbose.o -c verbose.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o vMatrix.o -c vMatrix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o wildcmp.o -c wildcmp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o windowsToAscii.o -c windowsToAscii.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o wormdna.o -c wormdna.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xAli.o -c xAli.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xa.o -c xa.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xap.o -c xap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xenshow.o -c xenshow.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xmlEscape.o -c xmlEscape.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xp.o -c xp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o zlibFace.o -c zlibFace.c mkdir 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 bbiRead.o bbiWrite.o bedTabix.o bigBed.o binRange.o bits.o blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o bwgCreate.o bwgQuery.o bwgValsOnChrom.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 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 -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/include -I/usr/local/include/libpng16 -o kfunc.o -c kfunc.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o knetfile.o -c knetfile.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o kstring.o -c kstring.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o bgzf.o -c bgzf.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o faidx.o -c faidx.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o hfile.o -c hfile.c cc -O -g -O2 -pipe -fcommon -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/include -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 -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/include -I/usr/local/include/libpng16 -o hts.o -c hts.c hts.c:48:5: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT2(, BGZF*, bgzf_read, 65536) ^ ../htslib/htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2' __KS_INLINED(__read) ^ ../htslib/htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o md5.o -c md5.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o regidx.o -c regidx.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o sam.o -c sam.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o synced_bcf_reader.o -c synced_bcf_reader.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o vcf_sweep.o -c vcf_sweep.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o tbx.o -c tbx.c cc -O -g -O2 -pipe -fcommon -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/include -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] int len, needs_sync = 0; ^ vcf.c:2352:50: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0; ^ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o vcfutils.o -c vcfutils.c cc -O -g -O2 -pipe -fcommon -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/include -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] int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k; ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/cram_decode.o -c cram/cram_decode.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/cram_encode.o -c cram/cram_encode.c cc -O -g -O2 -pipe -fcommon -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/include -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] 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] if (!ch || !ch->codecs) ~~~~~^~~~~~ 2 warnings generated. cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/cram_index.o -c cram/cram_index.c cc -O -g -O2 -pipe -fcommon -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/include -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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:388: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:388: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' #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] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' #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 -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/include -I/usr/local/include/libpng16 -o cram/cram_samtools.o -c cram/cram_samtools.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/cram_stats.o -c cram/cram_stats.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/files.o -c cram/files.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/mFILE.o -c cram/mFILE.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/open_trace_file.o -c cram/open_trace_file.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/pooled_alloc.o -c cram/pooled_alloc.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/rANS_static.o -c cram/rANS_static.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/sam_header.o -c cram/sam_header.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/string_alloc.o -c cram/string_alloc.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/thread_pool.o -c cram/thread_pool.c cc -O -g -O2 -pipe -fcommon -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/include -I/usr/local/include/libpng16 -o cram/vlen.o -c cram/vlen.c cc -O -g -O2 -pipe -fcommon -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/include -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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o bandExt.o -c bandExt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -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] int pStart = 0, pEnd = probeSize; ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o ffAliHelp.o -c ffAliHelp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o ffSeedExtend.o -c ffSeedExtend.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o fuzzyFind.o -c fuzzyFind.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o genoFind.o -c genoFind.c genoFind.c:254:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] size_t count = 0; ^ genoFind.c:284:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] size_t count = 0; ^ genoFind.c:753:20: warning: variable 'overusedCount' set but not used [-Wunused-but-set-variable] int usedCount = 0, overusedCount = 0; ^ genoFind.c:753:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] int usedCount = 0, overusedCount = 0; ^ genoFind.c:1791:20: warning: variable 'usedHits' set but not used [-Wunused-but-set-variable] int totalHits = 0, usedHits = 0, clumpCount = 0; ^ 5 warnings generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfBlatLib.o -c gfBlatLib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfClientLib.o -c gfClientLib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfInternal.o -c gfInternal.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfOut.o -c gfOut.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfPcrLib.o -c gfPcrLib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o gfWebLib.o -c gfWebLib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o ooc.o -c ooc.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -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] int usedCount = 0, overusedCount = 0; ^ patSpace.c:152:20: warning: variable 'overusedCount' set but not used [-Wunused-but-set-variable] int usedCount = 0, overusedCount = 0; ^ patSpace.c:261:5: warning: variable 'total' set but not used [-Wunused-but-set-variable] int total = 0; ^ 3 warnings generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o splix.o -c splix.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o supStitch.o -c supStitch.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o trans3.o -c trans3.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/local/include/libpng16 -o xenbig.o -c xenbig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -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 -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o acemblyClass.o -c acemblyClass.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o adjacency.o -c adjacency.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affyAllExonProbe.o -c affyAllExonProbe.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affyAtlas.o -c affyAtlas.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affy10KDetails.o -c affy10KDetails.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affy120KDetails.o -c affy120KDetails.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affyOffset.o -c affyOffset.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o affyPairs.o -c affyPairs.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o agp.o -c agp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o agpFrag.o -c agpFrag.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o agpGap.o -c agpGap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o alignSeqSizes.o -c alignSeqSizes.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o altGraph.o -c altGraph.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o altGraphX.o -c altGraphX.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ancientRref.o -c ancientRref.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoFormatVep.o -c annoFormatVep.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoGratorGpVar.o -c annoGratorGpVar.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoGrateWigDb.o -c annoGrateWigDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoStreamDb.o -c annoStreamDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoStreamDbFactorSource.o -c annoStreamDbFactorSource.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoStreamDbPslPlus.o -c annoStreamDbPslPlus.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o annoStreamWig.o -c annoStreamWig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o api.o -c api.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o atomDb.o -c atomDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o autoUpgrade.o -c autoUpgrade.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o axtInfo.o -c axtInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o axtLib.o -c axtLib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bactigPos.o -c bactigPos.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgBam.o -c hgBam.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartBed.o -c barChartBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartCategory.o -c barChartCategory.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartUi.o -c barChartUi.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartData.o -c barChartData.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o barChartSample.o -c barChartSample.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o baseMaskCommon.o -c baseMaskCommon.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bdgpExprLink.o -c bdgpExprLink.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bdgpGeneInfo.o -c bdgpGeneInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed.o -c bed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed5FloatScore.o -c bed5FloatScore.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed5Pval.o -c bed5Pval.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed6FloatScore.o -c bed6FloatScore.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed8Attrs.o -c bed8Attrs.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed12Source.o -c bed12Source.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bed12wSeq.o -c bed12wSeq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bedCart.o -c bedCart.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bgiGeneInfo.o -c bgiGeneInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bgiGeneSnp.o -c bgiGeneSnp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bgiSnp.o -c bgiSnp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigBedFind.o -c bigBedFind.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigBedLabel.o -c bigBedLabel.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigDbSnp.o -c bigDbSnp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigGenePred.o -c bigGenePred.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigPsl.o -c bigPsl.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bigTransMap.o -c bigTransMap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bioImage.o -c bioImage.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o blastTab.o -c blastTab.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o blastzNet.o -c blastzNet.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o blatServers.o -c blatServers.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o borf.o -c borf.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o borkPseudoHom.o -c borkPseudoHom.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o botDelay.o -c botDelay.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cart.o -c cart.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cartDb.o -c cartDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cartJson.o -c cartJson.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cartTrackDb.o -c cartTrackDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsEvidence.o -c cdsEvidence.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsOrtho.o -c cdsOrtho.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsPick.o -c cdsPick.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cdsSpec.o -c cdsSpec.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ccdsInfo.o -c ccdsInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ccdsNotes.o -c ccdsNotes.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ccdsGeneMap.o -c ccdsGeneMap.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o celeraCoverage.o -c celeraCoverage.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o celeraDupPositive.o -c celeraDupPositive.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgapSage/cgapSage.o -c cgapSage/cgapSage.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgapSage/cgapSageLib.o -c cgapSage/cgapSageLib.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgh.o -c cgh.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainCart.o -c chainCart.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainDb.o -c chainDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainLink.o -c chainLink.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainNet.o -c chainNet.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chainNetDbLoad.o -c chainNetDbLoad.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chicken13kInfo.o -c chicken13kInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromBins.o -c chromBins.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromAlias.o -c chromAlias.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chr18deletions.o -c chr18deletions.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromGraph.o -c chromGraph.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromGraphFactory.o -c chromGraphFactory.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromInfo.o -c chromInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromInserts.o -c chromInserts.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o chromKeeper.o -c chromKeeper.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o clinvarSub.o -c clinvarSub.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o clonePos.o -c clonePos.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o codeBlast.o -c codeBlast.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o codeBlastScore.o -c codeBlastScore.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cogs.o -c cogs.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cogsxra.o -c cogsxra.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o columnInfo.o -c columnInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o contigAcc.o -c contigAcc.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o coordConv.o -c coordConv.c coordConv.c:322:14: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] int origD1 = abs(ccr->upStart - ccr->midStart); ^ coordConv.c:322:14: note: remove the call to 'abs' since unsigned values cannot be negative int origD1 = abs(ccr->upStart - ccr->midStart); ^~~ coordConv.c:323:14: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] int origD2 = abs(ccr->midStart - ccr->downStart); ^ coordConv.c:323:14: note: remove the call to 'abs' since unsigned values cannot be negative int origD2 = abs(ccr->midStart - ccr->downStart); ^~~ coordConv.c:331:13: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] aveD1 = fabs( ((pc->d1 - origD1) + (pc->d2 - origD2))/2 ); ^ coordConv.c:331:13: note: use function 'abs' instead aveD1 = fabs( ((pc->d1 - origD1) + (pc->d2 - origD2))/2 ); ^~~~ abs coordConv.c:332:15: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] bestD1 = fabs( ((bestPc->d1 - origD1) + (bestPc->d2 - origD2))/2 ); ^ coordConv.c:332:15: note: use function 'abs' instead bestD1 = fabs( ((bestPc->d1 - origD1) + (bestPc->d2 - origD2))/2 ); ^~~~ abs coordConv.c:368:14: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] int origD1 = abs(ccr->upStart - ccr->midStart); ^ coordConv.c:368:14: note: remove the call to 'abs' since unsigned values cannot be negative int origD1 = abs(ccr->upStart - ccr->midStart); ^~~ coordConv.c:369:14: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value] int origD2 = abs(ccr->midStart - ccr->downStart); ^ coordConv.c:369:14: note: remove the call to 'abs' since unsigned values cannot be negative int origD2 = abs(ccr->midStart - ccr->downStart); ^~~ 6 warnings generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpIafrate.o -c cnpIafrate.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpIafrate2.o -c cnpIafrate2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpLocke.o -c cnpLocke.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpRedon.o -c cnpRedon.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpSebat.o -c cnpSebat.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpSebat2.o -c cnpSebat2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpSharp2.o -c cnpSharp2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpSharpCutoff.o -c cnpSharpCutoff.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpSharpSample.o -c cnpSharpSample.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cnpSharp.o -c cnpSharp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cpgIsland.o -c cpgIsland.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cpgIslandExt.o -c cpgIslandExt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ctgPos.o -c ctgPos.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ctgPos2.o -c ctgPos2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customComposite.o -c customComposite.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o bedDetail.o -c bedDetail.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cgiApoptosis.o -c cgiApoptosis.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customAdjacency.o -c customAdjacency.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customFactory.o -c customFactory.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customPp.o -c customPp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o customTrack.o -c customTrack.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cutter.o -c cutter.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cv.o -c cv.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o cytoBand.o -c cytoBand.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dbDb.o -c dbDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dbRIP.o -c dbRIP.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dbSnpDetails.o -c dbSnpDetails.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dbSnpRs.o -c dbSnpRs.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o defaultDb.o -c defaultDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o delConrad2.o -c delConrad2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o delHinds2.o -c delHinds2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dgv.o -c dgv.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dgvPlus.o -c dgvPlus.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dless.o -c dless.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dnaMotifSql.o -c dnaMotifSql.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dnaMarkovSql.o -c dnaMarkovSql.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dnaProbe.o -c dnaProbe.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dv.o -c dv.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dvBed.o -c dvBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o dvXref2.o -c dvXref2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o easyGene.o -c easyGene.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ec.o -c ec.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ecCode.o -c ecCode.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ecAttribute.o -c ecAttribute.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ecAttributeCode.o -c ecAttributeCode.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeErge.o -c encode/encodeErge.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeErgeHssCellLines.o -c encode/encodeErgeHssCellLines.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeHapMapAlleleFreq.o -c encode/encodeHapMapAlleleFreq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeIndels.o -c encode/encodeIndels.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodePeak.o -c encode/encodePeak.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeRegionInfo.o -c encode/encodeRegionInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeRegionInfoCustom.o -c encode/encodeRegionInfoCustom.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeRna.o -c encode/encodeRna.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeStanfordPromoters.o -c encode/encodeStanfordPromoters.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeStanfordPromotersAverage.o -c encode/encodeStanfordPromotersAverage.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/pairedTagAlign.o -c encode/pairedTagAlign.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/peptideMapping.o -c encode/peptideMapping.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/tagAlign.o -c encode/tagAlign.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeAttrs.o -c encode/wgEncodeGencodeAttrs.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeExonSupport.o -c encode/wgEncodeGencodeExonSupport.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeEntrezGene.o -c encode/wgEncodeGencodeEntrezGene.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTag.o -c encode/wgEncodeGencodeTag.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeGeneSymbol.o -c encode/wgEncodeGencodeGeneSymbol.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodePdb.o -c encode/wgEncodeGencodePdb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodePubMed.o -c encode/wgEncodeGencodePubMed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeRefSeq.o -c encode/wgEncodeGencodeRefSeq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeGeneSource.o -c encode/wgEncodeGencodeGeneSource.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTranscriptSource.o -c encode/wgEncodeGencodeTranscriptSource.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTranscriptSupport.o -c encode/wgEncodeGencodeTranscriptSupport.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeTranscriptionSupportLevel.o -c encode/wgEncodeGencodeTranscriptionSupportLevel.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeUniProt.o -c encode/wgEncodeGencodeUniProt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodePolyAFeature.o -c encode/wgEncodeGencodePolyAFeature.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeGencodeAnnotationRemark.o -c encode/wgEncodeGencodeAnnotationRemark.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/wgEncodeCell.o -c encode/wgEncodeCell.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode/encodeExp.o -c encode/encodeExp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode3/encode2Manifest.o -c encode3/encode2Manifest.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o encode3/encode3Valid.o -c encode3/encode3Valid.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ensFace.o -c ensFace.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ensInfo.o -c ensInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ensPhusionBlast.o -c ensPhusionBlast.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ensXRefZfish.o -c ensXRefZfish.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o est3.o -c est3.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o estOrientInfo.o -c estOrientInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o estPair.o -c estPair.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o exoFish.o -c exoFish.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o expData.o -c expData.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o expRecord.o -c expRecord.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o exprBed.o -c exprBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o facetedTable.o -c facetedTable.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o facetField.o -c facetField.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o factorSource.o -c factorSource.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o fbTables.o -c fbTables.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o featureBits.o -c featureBits.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o fileUi.o -c fileUi.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o findKGAlias.o -c findKGAlias.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o findKGProtAlias.o -c findKGProtAlias.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o fishClones.o -c fishClones.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o flyBase2004Xref.o -c flyBase2004Xref.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o flyBaseSwissProt.o -c flyBaseSwissProt.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o flyreg.o -c flyreg.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o flyreg2.o -c flyreg2.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbExtFile.o -c gbExtFile.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbWarn.o -c gbWarn.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbMiscDiff.o -c gbMiscDiff.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbProtAnn.o -c gbProtAnn.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gcPercent.o -c gcPercent.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gbSeq.o -c gbSeq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genbank.o -c genbank.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genbankBlackList.o -c genbankBlackList.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gencodeGeneClass.o -c gencodeGeneClass.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gencodeIntron.o -c gencodeIntron.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genMapDb.o -c genMapDb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneBands.o -c geneBands.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneCheck.o -c geneCheck.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneCheckDetails.o -c geneCheckDetails.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneCheckWidget.o -c geneCheckWidget.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneGraph.o -c geneGraph.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genePred.o -c genePred.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genePredReader.o -c genePredReader.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geneSimilarities.o -c geneSimilarities.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genoLay.o -c genoLay.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genomeRangeTreeFile.o -c genomeRangeTreeFile.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genomicDups.o -c genomicDups.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o genomicSuperDups.o -c genomicSuperDups.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o geoMirror.o -c geoMirror.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggCluster.o -c ggCluster.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggDbIo.o -c ggDbIo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggDump.o -c ggDump.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -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] int totalWithDupes = 0; ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggMrnaAli.o -c ggMrnaAli.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ggTypes.o -c ggTypes.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o glDbRep.o -c glDbRep.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o goa.o -c goa.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o goaPart.o -c goaPart.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o googleAnalytics.o -c googleAnalytics.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gpFx.o -c gpFx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o growthCondition.o -c growthCondition.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o grp.o -c grp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexAse.o -c gtexAse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexBoxplot.o -c gtexBoxplot.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexEqtlCluster.o -c gtexEqtlCluster.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexInfo.o -c gtexInfo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexDonor.o -c gtexDonor.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexGeneBed.o -c gtexGeneBed.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexSample.o -c gtexSample.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexSampleData.o -c gtexSampleData.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexTissue.o -c gtexTissue.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexTissueData.o -c gtexTissueData.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexTissueMedian.o -c gtexTissueMedian.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gtexUi.o -c gtexUi.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o gwasCatalog.o -c gwasCatalog.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hAnno.o -c hAnno.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o haplotypes.o -c haplotypes.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapAllelesOrtho.o -c hapmapAllelesOrtho.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapAllelesSummary.o -c hapmapAllelesSummary.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapPhaseIIISummary.o -c hapmapPhaseIIISummary.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapSnps.o -c hapmapSnps.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hapmapSnpsCombined.o -c hapmapSnpsCombined.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hashJoin.o -c hashJoin.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hCommon.o -c hCommon.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hCytoBand.o -c hCytoBand.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hdb.o -c hdb.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgColors.o -c hgColors.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgConfig.o -c hgConfig.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgExp.o -c hgExp.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgFind.o -c hgFind.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgFindSpec.o -c hgFindSpec.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgFindSpecCustom.o -c hgFindSpecCustom.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgHgvs.o -c hgHgvs.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgHgvsParse.o -c hgHgvsParse.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgGene.o -c hgGene.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hic.o -c hic.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hicUi.o -c hicUi.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgMaf.o -c hgMaf.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgRelate.o -c hgRelate.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgSeq.o -c hgSeq.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hgdpGeo.o -c hgdpGeo.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hPrint.o -c hPrint.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hVarSubst.o -c hVarSubst.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hvGfx.o -c hvGfx.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o HInv.o -c HInv.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hubConnect.o -c hubConnect.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hubSearchText.o -c hubSearchText.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hui.o -c hui.c hui.c:2387:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] { ^ hui.c:2383:1: note: previous statement is here if (selectedName == NULL) ^ 1 warning generated. cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o humanParalog.o -c humanParalog.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o hubPublic.o -c hubPublic.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o imageClone.o -c imageClone.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o indelShift.o -c indelShift.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o interact.o -c interact.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o interactUi.o -c interactUi.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o isochores.o -c isochores.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o ispyTables.o -c ispyTables.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o itemAttr.o -c itemAttr.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o itemConf.o -c itemConf.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o itemDetailsHtml.o -c itemDetailsHtml.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jalview.o -c jalview.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jaxOrtholog.o -c jaxOrtholog.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jaxQTL.o -c jaxQTL.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jaxQTL3.o -c jaxQTL3.c cc -O -g -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_amd64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/local/include/libpng16 -I/usr/local/include/mysql -o jksql.o -c jksql.c jksql.c:1119:5: error: use of undeclared identifier 'my_bool' my_bool flag = TRUE; ^ jksql.c:1120:25: error: use of undeclared identifier 'MYSQL_OPT_SSL_VERIFY_SERVER_CERT' mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag); ^ jksql.c:1120:60: error: use of undeclared identifier 'flag' mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag); ^ 3 errors generated. gmake: *** [makefile:140: jksql.o] Error 1 *** Error code 2 Stop. make: stopped in /usr/ports/biology/ucsc-userapps =>> Cleaning up wrkdir ===> Cleaning for ucsc-userapps-414_1 build of biology/ucsc-userapps | ucsc-userapps-414_1 ended at Sun Apr 7 12:02:40 BST 2024 build time: 02:35:53 !!! build failure encountered !!!