=>> Building biology/wise build started at Mon May 5 01:40:20 BST 2025 port directory: /usr/ports/biology/wise package name: wise-2.4.1_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2350 Dec 29 14:16 /usr/ports/biology/wise/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for wise-2.4.1_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/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 -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing " 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-- PORTDOCS="" PORTEXAMPLES="" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/wise" EXAMPLESDIR="share/examples/wise" DATADIR="share/wise" WWWDIR="www/wise" ETCDIR="etc/wise" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/wise DOCSDIR=/usr/local/share/doc/wise EXAMPLESDIR=/usr/local/share/examples/wise WWWDIR=/usr/local/www/wise ETCDIR=/usr/local/etc/wise --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of wise-2.4.1_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by wise-2.4.1_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by wise-2.4.1_1 for building => SHA256 Checksum OK for wise2.4.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by wise-2.4.1_1 for building ===> Extracting for wise-2.4.1_1 => SHA256 Checksum OK for wise2.4.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for wise-2.4.1_1 ===> Applying FreeBSD patches for wise-2.4.1_1 from /usr/ports/biology/wise/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wise-2.4.1_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.3.0_1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.3.0_1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.3.0_1,1: .......... done ===> wise-2.4.1_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of wise-2.4.1_1 ===> wise-2.4.1_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> wise-2.4.1_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of wise-2.4.1_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wise-2.4.1_1 depends on shared library: libglib-2.0.so - not found ===> Installing existing package /packages/All/glib-2.84.1_2,2.pkg [pkg-builder.dan.net.uk] Installing glib-2.84.1_2,2... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libinotify-20240724_1... [pkg-builder.dan.net.uk] `-- Extracting libinotify-20240724_1: .......... done [pkg-builder.dan.net.uk] `-- Installing pcre2-10.45_1... [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting pcre2-10.45_1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-packaging-24.2... [pkg-builder.dan.net.uk] | `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-packaging-24.2: .......... done [pkg-builder.dan.net.uk] Extracting glib-2.84.1_2,2: .......... done ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from libinotify-20240724_1: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> wise-2.4.1_1 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> Returning to build of wise-2.4.1_1 ===> wise-2.4.1_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for wise-2.4.1_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for wise-2.4.1_1 (cd base ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisebase.a ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiseconfig.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisestring.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiseerror.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisememman.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisefile.c wisefile.dy:72:33: warning: format specifies type 'int' but the argument has type 'FILE *' (aka 'struct __sFILE *') [-Wformat] 72 | fprintf(stderr,"Closing %d\n",ofp); | ~~ ^~~ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiserandom.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisetime.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiseoverlay.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisestreaminterface.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include commandline.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: warning: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libhmmer.a ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c alphabet.c alphabet.c:237:9: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^ ~ alphabet.c:237:9: note: add parentheses after the '!' to evaluate the bitwise operator first 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^ | ( ) alphabet.c:237:9: note: add parentheses around left hand side expression to silence this warning 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^ | ( ) 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c core_algorithms.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c debug.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c emit.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c emulation.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c histogram.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c hmmio.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c mathsupport.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c masks.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c misc.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c modelmakers.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c plan7.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c plan9.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c prior.c prior.c:102:12: warning: call to undeclared library function 'strcmp' with type 'int (const char *, const char *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^ prior.c:102:12: note: include the header or explicitly provide a declaration for 'strcmp' 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c tophits.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c trace.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c aligneval.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c alignio.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c cluster.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c dayhoff.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c file.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c getopt.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c gnuregex.c gnuregex.c:795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 795 | re_set_syntax (syntax) | ^ gnuregex.c:1175:37: warning: passing arguments to 'at_begline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1175 | || at_begline_loc_p (pattern, p, syntax)) | ^ gnuregex.c:1190:37: warning: passing arguments to 'at_endline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1190 | || at_endline_loc_p (p, pend, syntax)) | ^ gnuregex.c:1296:21: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1296 | STORE_JUMP (jump, b, laststart); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1301:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1301 | STORE_JUMP (maybe_pop_jump, b, laststart - 3); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1310:13: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1310 | INSERT_JUMP (keep_string_p ? on_failure_keep_string_jump | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1324:17: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1324 | INSERT_JUMP (dummy_failure_jump, laststart, laststart + 6); | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1407:39: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1407 | = compile_range (&p, pend, translate, syntax, b); | ^ gnuregex.c:1418:41: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1418 | ret = compile_range (&p, pend, translate, syntax, b); | ^ gnuregex.c:1616:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] 1616 | else | ^ gnuregex.c:1629:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1629 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b - 1); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1636:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] 1636 | else | ^ gnuregex.c:1686:15: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1686 | INSERT_JUMP (on_failure_jump, begalt, b + 6); | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1707:17: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1707 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1801:22: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1801 | INSERT_JUMP (jump, laststart, b + 3); | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1826:22: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1826 | INSERT_JUMP2 (succeed_n, laststart, | ^ gnuregex.c:915:14: note: expanded from macro 'INSERT_JUMP2' 915 | insert_op2 (op, loc, (to) - (loc) - 3, arg, b) | ^ gnuregex.c:1835:33: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1835 | insert_op2 (set_number_at, laststart, 5, lower_bound, b); | ^ gnuregex.c:1846:26: warning: passing arguments to 'store_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1846 | STORE_JUMP2 (jump_n, b, laststart + 5, | ^ gnuregex.c:907:13: note: expanded from macro 'STORE_JUMP2' 907 | store_op2 (op, loc, (to) - (loc) - 3, arg) | ^ gnuregex.c:1864:37: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1864 | insert_op2 (set_number_at, laststart, b - laststart, | ^ gnuregex.c:1958:42: warning: passing arguments to 'group_in_compile_stack' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1958 | if (group_in_compile_stack (compile_stack, c1)) | ^ gnuregex.c:2024:5: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1049:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1049 | regex_compile (pattern, size, syntax, bufp) | ^ gnuregex.c:2050:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2050 | store_op1 (op, loc, arg) | ^ gnuregex.c:829:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 829 | static void store_op1 (), store_op2 (); | ^ gnuregex.c:2063:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2063 | store_op2 (op, loc, arg1, arg2) | ^ gnuregex.c:829:27: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 829 | static void store_op1 (), store_op2 (); | ^ gnuregex.c:2078:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2078 | insert_op1 (op, loc, arg, end) | ^ gnuregex.c:830:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 830 | static void insert_op1 (), insert_op2 (); | ^ gnuregex.c:2097:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2097 | insert_op2 (op, loc, arg1, arg2, end) | ^ gnuregex.c:830:28: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 830 | static void insert_op1 (), insert_op2 (); | ^ gnuregex.c:2118:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2118 | at_begline_loc_p (pattern, p, syntax) | ^ gnuregex.c:831:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 831 | static boolean at_begline_loc_p (), at_endline_loc_p (); | ^ gnuregex.c:2137:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2137 | at_endline_loc_p (p, pend, syntax) | ^ gnuregex.c:831:37: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 831 | static boolean at_begline_loc_p (), at_endline_loc_p (); | ^ gnuregex.c:2159:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2159 | group_in_compile_stack (compile_stack, regnum) | ^ gnuregex.c:832:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 832 | static boolean group_in_compile_stack (); | ^ gnuregex.c:2187:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2187 | compile_range (p_ptr, pend, translate, syntax, b) | ^ gnuregex.c:833:22: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 833 | static reg_errcode_t compile_range (); | ^ gnuregex.c:2519:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2519 | re_compile_fastmap (bufp) | ^ gnuregex.c:2804:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2804 | re_set_registers (bufp, regs, num_regs, starts, ends) | ^ gnuregex.c:2821:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'regoff_t *' (aka 'int *') [-Wnon-literal-null-conversion] 2821 | regs->start = regs->end = (regoff_t) 0; | ^~~~~~~~~~~~ gnuregex.c:2831:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2831 | re_search (bufp, string, size, startpos, range, regs) | ^ gnuregex.c:2864:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2864 | re_search_2 (bufp, string1, size1, string2, size2, startpos, range, regs, stop) | ^ gnuregex.c:3123:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3123 | re_match (bufp, string, size, pos, regs) | ^ gnuregex.c:3148:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3148 | re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) | ^ gnuregex.c:3604:43: warning: passing arguments to 'group_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3604 | = group_match_null_string_p (&p1, pend, reg_info); | ^ gnuregex.c:3752:31: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^~~~~~~~~~~~~~~~~~~ gnuregex.c:3752:54: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3822:38: warning: passing arguments to 'bcmp_translate' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3822 | ? bcmp_translate (d, d2, mcnt, translate) | ^ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4065 | dummy_low_reg, dummy_high_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4066 | reg_dummy, reg_dummy, reg_info_dummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4065 | dummy_low_reg, dummy_high_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4066 | reg_dummy, reg_dummy, reg_info_dummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~~~~~~~~ 4279 | lowest_active_reg, highest_active_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4280 | regstart, regend, reg_info); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~~~~~~~~ 4279 | lowest_active_reg, highest_active_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4280 | regstart, regend, reg_info); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4394:48: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4394 | if (!alt_match_null_string_p (p1, p1 + mcnt - 3, | ^ gnuregex.c:4424:44: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4424 | if (!alt_match_null_string_p (p1, p1 + mcnt, reg_info)) | ^ gnuregex.c:4439:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4439 | if (!common_op_match_null_string_p (&p1, end, reg_info)) | ^ gnuregex.c:4344:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4344 | group_match_null_string_p (p, end, reg_info) | ^ gnuregex.c:2984:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2984 | group_match_null_string_p (); | ^ gnuregex.c:4475:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4475 | if (!common_op_match_null_string_p (&p1, end, reg_info)) | ^ gnuregex.c:4453:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4453 | alt_match_null_string_p (p, end, reg_info) | ^ gnuregex.c:2982:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2982 | static boolean alt_match_null_string_p (), | ^ gnuregex.c:4490:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4490 | common_op_match_null_string_p (p, end, reg_info) | ^ gnuregex.c:2983:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2983 | common_op_match_null_string_p (), | ^ gnuregex.c:4578:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4578 | bcmp_translate (s1, s2, len, translate) | ^ gnuregex.c:2981:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2981 | static int bcmp_translate (); | ^ gnuregex.c:4634:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4634 | re_comp (s) | ^ gnuregex.c:4672:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4672 | re_exec (s) | ^ gnuregex.c:4720:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4720 | regcomp (preg, pattern, cflags) | ^ gnuregex.c:4795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4795 | regexec (preg, string, nmatch, pmatch, eflags) | ^ gnuregex.c:4860:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4860 | regerror (errcode, preg, errbuf, errbuf_size) | ^ gnuregex.c:4904:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4904 | regfree (preg) | ^ 81 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c interleaved.c interleaved.c:165:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] 165 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:165:32: note: did you mean to compare the result of 'strncmp' instead? 165 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ ~ | ) interleaved.c:165:60: note: explicitly cast the argument to size_t to silence this warning 165 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ | (size_t)( ) interleaved.c:240:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] 240 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:240:32: note: did you mean to compare the result of 'strncmp' instead? 240 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ ~ | ) interleaved.c:240:60: note: explicitly cast the argument to size_t to silence this warning 240 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ | (size_t)( ) 2 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c iupac.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c msf.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c revcomp.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c selex.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sqerror.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sqio.c sqio.c:1033:9: warning: comparison of array 'sp' equal to a null pointer is always false [-Wtautological-pointer-compare] 1033 | if (sp==NULL || *sp=='\0') | ^~ ~~~~ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sre_ctype.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sre_math.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sre_string.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c stack.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c translate.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c types.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c weight.c ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libdyna.a ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ packaln.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ aln.c aln.dy:867:65: warning: data argument not used by format string [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ~~~~~~~~~~~~ ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dnamatrix.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ probability.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ alnrange.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ alnconvert.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ basematrix.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shattermatrix.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ matrixdebug.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dpenvelope.c dpenvelope.dy:68:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 68 | } | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dbsearchimpl.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dprunimpl.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ complexsequence.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ complexevalset.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ complexconsensi.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ sequence.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ sequencestream.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ seqalign.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hitlist.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsp.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspstream.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ codon.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ compmat.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ codonmatrix.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ codonmapper.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ sequencedb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hscore.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ seqlookup.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ arrayseqlookup.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genericindexresult.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ linkedlist_lookpos.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ singlenumberspace.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ histogram.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ searchstatinterface.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ searchstatlookup.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteindb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ protein.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ pairbase.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ pairbaseseq.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genomicdb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ randommodel.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ randomdb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genomic.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ cdna.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ cdnadb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dna.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ embl.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genomicregion.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ gene.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ transcript.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ translation.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ btcanvas.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ asciibtcanvas.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: warning: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libdyna_glib.a ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ subseqhash.c subseqhash.dy:111:29: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:128:85: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:160:54: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:161:29: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^~~~~~~~~~~~~~~~~~~~ subseqhash.dy:188:52: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:189:27: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^~~~~~~~~~~~~~~~~~~~ 6 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ intallocator.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteinstreamedindex.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shadowseq.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shadowseqindex.c shadowseqindex.dy:285:59: warning: format specifies type 'double' but the argument has type 'unsigned long' [-Wformat] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | %.2lu 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsphandler.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspscaninterface.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsp2hitscan.c hsp2hitscan.dy:210:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~ | %ld 210 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:211:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~~~ | %03ld 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:212:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~ | %ld 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, 212 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:213:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~~~ | %03ld 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, 212 | use.ru_stime.tv_sec, 213 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:274:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~ | %ld 274 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:275:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:276:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~ | %ld 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, 276 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:277:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, 276 | use.ru_stime.tv_sec, 277 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:287:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~ | %ld 287 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:288:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~~~ | %03ld 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:289:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~ | %ld 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, 289 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:290:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~~~ | %03ld 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, 289 | use.ru_stime.tv_sec, 290 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:303:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~ | %ld 303 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:304:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:305:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~ | %ld 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, 305 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:306:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, 305 | use.ru_stime.tv_sec, 306 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ 16 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsplookupscan.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsplookupthreaded.c hsplookupthreaded.dy:263:55: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ~~ ^~~~~~~~~~~ | %ld hsplookupthreaded.dy:567:1: warning: non-void function does not return a value [-Wreturn-type] 567 | } | ^ 2 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspthreadeddb.c hspthreadeddb.dy:154:77: warning: cast to smaller integer type 'int' from 'Wise2_LinearHSPmanager *' (aka 'struct Wise2_LinearHSPmanager *') [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~ hspthreadeddb.dy:154:73: warning: format specifies type 'int' but the argument has type 'Wise2_HSPDatabaseSegment *' (aka 'struct Wise2_HSPDatabaseSegment *') [-Wformat] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ~~ ^~~ 2 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspscanruntime.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsptwohitscan.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteinindexcons.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dnaindexcons.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: warning: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi (cd external ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) (cd mott; make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include" all) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c mott_api.c -o mott_api.o mott_api.c:64:3: warning: call to undeclared library function 'free' with type 'void (void *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 64 | free(freq0); | ^ mott_api.c:64:3: note: include the header or explicitly provide a declaration for 'free' mott_api.c:179:16: warning: call to undeclared library function 'calloc' with type 'void *(unsigned long, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^ mott_api.c:179:16: note: include the header or explicitly provide a declaration for 'calloc' mott_api.c:207:12: warning: call to undeclared library function 'toupper' with type 'int (int)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^ mott_api.c:207:12: note: include the header or explicitly provide a declaration for 'toupper' 3 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c gaplib.c -o gaplib.o cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: warning: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi (cd socket ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisesocket.a ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionserver.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionclient.c functionclient.dy:193:24: warning: incompatible pointer types passing 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ /usr/include/sys/socket.h:697:41: note: passing argument to parameter here 697 | int connect(int, const struct sockaddr *, socklen_t); | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ anonobj.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ transferinterface.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: warning: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy:296:44: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly.dy:302:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly.dy:309:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ~~~ ^~~ kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ~^ 5 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy:318:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ~~~~~~ ^~~~~~~~~~~~~ | %016llx kmer_hash.dy:319:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ~~~~~~ ^~~~~~~~~~~~~ | %016llx 2 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy:52:65: warning: cast to smaller integer type 'int' from 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:120:80: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:141:71: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:141:99: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:157:73: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:159:69: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:444:89: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ~~~ ^~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing 'long[10000]' to parameter of type 'int *' [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ ./kmer_assembly_untangler.h:174:116: note: passing argument to parameter 'start_label' here 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ^ kmer_assembly_untangler.dy:746:149: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:746:182: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld 10 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy:93:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_error.dy:105:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ~~ ^~~~~~~~~~~~ 3 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy:223:10: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'boolean' (aka 'int') [-Wint-conversion] 223 | return NULL; | ^~~~ /usr/include/sys/_null.h:32:14: note: expanded from macro 'NULL' 32 | #define NULL ((void *)0) | ^~~~~~~~~~~ 1 warning generated. (cd network ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` -pthread cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c client_multihspscan.dy:128:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 128 | } | ^ 1 warning generated. (cd models ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dnal.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ psw.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ abc.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pba.c cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pswdb.c cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dbac.c dbac.c:413:45: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~~ ^~~~~~~~~~~ | %lu 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dba.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ slimdba.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ bigdba.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genestats.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneutil.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise4.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise6.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise21.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genephase6.c genephase6.c:873:1: warning: non-void function does not return a value [-Wreturn-type] 873 | } | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwlite.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwrap.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ matchsum.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estwrap.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ phasemodel.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ cdparser.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy:493:37: warning: data argument not used by format string [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ~~~~~~~~~~~~~~~~ ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estwise3.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estslim3.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estloop3.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwquickdb.c gwquickdb.dy:46:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 46 | } | ^ gwquickdb.dy:65:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 65 | } | ^ 2 warnings generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ seqhit.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ standardout.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estquick3.c cc -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genomewise.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genomewise9.c genomewise9.c:745:1: warning: non-void function does not return a value [-Wreturn-type] 745 | } | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genome_evidence.c genome_evidence.dy:61:1: warning: non-void function does not return a value [-Wreturn-type] 61 | } | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy:142:16: warning: incompatible function pointer types assigning to 'int (*)(void *)' from 'Wise2_EstEvidence *(Wise2_EstEvidence *)' (aka 'struct Wise2_EstEvidence *(struct Wise2_EstEvidence *)') [-Wincompatible-function-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ ~~~~~~~~~~~~~~~~ 1 warning generated. cc -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ sywise.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ sywise20.c sywise20.c:764:1: warning: non-void function does not return a value [-Wreturn-type] 764 | } | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pseudowise7.c cc -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` promoterwise.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ localdba.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` localcishit.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ localcispara.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c:408:24: warning: incompatible pointer to integer conversion assigning to 'char' from 'void *' [-Wint-conversion] 408 | out->mat[i][j] = NULL; | ^ ~~~~ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ transfactor.c transfactor.dy:339:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 339 | } | ^ 1 warning generated. cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c cc -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -pthread cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` hsp2aln_sw.c cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -pthread ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o ar: warning: creating libmodel.a /usr/bin/make bin mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for wise-2.4.1_1 ===> Generating temporary packing list (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/bin && install -s -m 555 dba dnal estwise estwisedb genewise genewisedb promoterwise psw pswdb scanwise scanwise_server /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/bin) (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/wisecfg && install -m 0644 BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd cb.tmf codon.table gene.stat gon120.bla gon160.bla gon200.bla gon250.bla gon350.bla human.gf human.gp human.stats idenity.bla methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/share/wise) (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/docs && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/share/doc/wise) (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/test_data && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/share/examples/wise) ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-05T00:40:20+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for wise-2.4.1_1 ===> Building wise-2.4.1_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for wise-2.4.1_1 build of biology/wise | wise-2.4.1_1 ended at Mon May 5 01:42:12 BST 2025 build time: 00:01:52