=>> Building biology/fasta3 build started at Mon Apr 1 02:27:46 BST 2024 port directory: /usr/ports/biology/fasta3 package name: fasta3-36.3.8_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: wendell@bsd.com.br Makefile datestamp: -rw-r--r-- 1 root wheel 2348 Jan 11 20:37 /usr/ports/biology/fasta3/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 1b819e4869 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 14 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/14/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for fasta3-36.3.8_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-- wendell@bsd.com.br --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fasta3/work/.cache HOME=/wrkdirs/usr/ports/biology/fasta3/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/fasta3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fasta3/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- THR_LIBS="-pthread" XDIR="/wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/bin" FASTA_HOST="$(/usr/bin/uname -n)" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fasta3/work/.cache HOME=/wrkdirs/usr/ports/biology/fasta3/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/fasta3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fasta3/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 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- VER="36" PORTDOCS="" PORTEXAMPLES="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fasta3" EXAMPLESDIR="share/examples/fasta3" DATADIR="share/fasta3" WWWDIR="www/fasta3" ETCDIR="etc/fasta3" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fasta3 DOCSDIR=/usr/local/share/doc/fasta3 EXAMPLESDIR=/usr/local/share/examples/fasta3 WWWDIR=/usr/local/www/fasta3 ETCDIR=/usr/local/etc/fasta3 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fasta3-36.3.8_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> fasta3-36.3.8_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fasta3-36.3.8_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasta3-36.3.8_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasta3-36.3.8_1 for building => SHA256 Checksum OK for fasta3/2014-01-29/fasta-36.3.8.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasta3-36.3.8_1 for building ===> Extracting for fasta3-36.3.8_1 => SHA256 Checksum OK for fasta3/2014-01-29/fasta-36.3.8.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 fasta3-36.3.8_1 ===> Applying FreeBSD patches for fasta3-36.3.8_1 from /usr/ports/biology/fasta3/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fasta3-36.3.8_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fasta3-36.3.8_1 cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c work_thr2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c pthr_subs2.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -DCOMP_MLIB -c compacc2e.c -o compacc2_t.o compacc2e.c:2502:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); ^~~~~~~~~~~~~~~~~~~~ compacc2e.c:2686:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); ^~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mshowbest.c -o showbest.o mshowbest.c:404:11: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] if (!bbp->have_ares & 0x1) { ^ ~ mshowbest.c:404:11: note: add parentheses after the '!' to evaluate the bitwise operator first if (!bbp->have_ares & 0x1) { ^ ( ) mshowbest.c:404:11: note: add parentheses around left hand side expression to silence this warning if (!bbp->have_ares & 0x1) { ^ ( ) 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c build_ares.c -o build_ares.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c re_getlib.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c htime.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c apam.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c doinit.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTA initfa.c -o init_fa.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DLOCAL_SCORE -c scaleswn.c -o scale_se.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c karlin.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnfa.c -o drop_nfa.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c wm_align.c -o wm_align.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTA -c cal_cons2.c -o calcons_fa.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c nmgetlib.c -o lgetlib.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mmgetaa.c -o lgetaa_m.o mmgetaa.c:166:87: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); ~~~~ ^~~~~~ %ld mmgetaa.c:205:14: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] bname,statbuf.st_size,f_size); ^~~~~~~~~~~~~~~ mmgetaa.c:205:30: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] bname,statbuf.st_size,f_size); ^~~~~~ mmgetaa.c:296:14: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] sname,statbuf.st_size,f_size); ^~~~~~~~~~~~~~~ mmgetaa.c:296:30: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] sname,statbuf.st_size,f_size); ^~~~~~ mmgetaa.c:1076:10: warning: format specifies type 'long long' but the argument has type 'MM_OFF' (aka 'long') [-Wformat] i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], ^~~~~~~~~~~~~~~~~~ mmgetaa.c:1076:29: warning: format specifies type 'long long' but the argument has type 'MM_OFF' (aka 'long') [-Wformat] i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], ^~~~~~~~~~~~~~~~~~ mmgetaa.c:1077:8: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat] m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c c_dispn.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c ncbl2_mlib.c -o ncbl2_mlib.o ncbl2_mlib.c:1087:8: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] *libpos,tmp,seq_len); ^~~~~~~ ncbl2_mlib.c:1131:60: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); ~~~~ ^~~~~~~ %ld ncbl2_mlib.c:1416:10: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] libstr,*libpos,tmp,seqcnt,*seq); ^~~~~~~ ncbl2_mlib.c:1436:3: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] *libpos,tmp,seqcnt); ^~~~~~~ ncbl2_mlib.c:1659:60: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); ~~~~ ^~~~~~~ %ld 5 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c lib_sel.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c url_subs.c url_subs.c:154:43: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) { ^ ~~ url_subs.c:154:43: note: add parentheses after the '!' to evaluate the comparison first if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) { ^ ( ) url_subs.c:154:43: note: add parentheses around left hand side expression to silence this warning if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) { ^ ( ) 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mrandom.c -o mrandom.o cc -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DSSEARCH initfa.c -o init_sw.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropgsw2.c -o dropgsw2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c wm_align.c -o lwm_align.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DSSEARCH -c cal_cons2.c -o calcons_sw.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c pssm_asn_subs.c cc -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw.o dropgsw2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o compacc2e.c:2502:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); ^~~~~~~~~~~~~~~~~~~~ compacc2e.c:2686:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); ^~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DLALIGN -c mshowalign2.c -o lshowalign.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DLALIGN initfa.c -o init_lal.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c last_thresh.c cc -DLALIGN -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropgsw2.c -o droplal2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c lsim4.c cc -DLALIGN -DLCAL_CONS -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c cal_cons2.c -o calcons_la.o cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS initfa.c -o init_fs.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c scaleswt.c -o scaleswts.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c last_tat.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS tatstats.c -o tatstats_fs.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTS -c dropfs2.c -o drop_fs2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTS -c cal_consf.c -o calcons_fs.o cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTX initfa.c -o init_fx.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c faatran.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropfx2.c -o drop_fx.o cc -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTX -DTFAST initfa.c -o init_tfx.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST dropfx2.c -o drop_tfx.o cc -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTY initfa.c -o init_fy.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropfz3.c -o drop_fz.o cc -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTY -DTFAST initfa.c -o init_tfy.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST dropfz3.c -o drop_tfz.o cc -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS -DTFAST initfa.c -o init_tfs.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o cc -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM initfa.c -o init_fm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM tatstats.c -o tatstats_fm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM dropfs2.c -o drop_fm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTM -c cal_consf.c -o calcons_fm.o cc -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mshowalign2.c -o mshowalign2_s.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM -DTFAST initfa.c -o init_tfm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF initfa.c -o init_ff.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTF -c scaleswt.c -o scaleswtf.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF tatstats.c -o tatstats_ff.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF dropff2.c -o drop_ff2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTF -c cal_consf.c -o calcons_ff.o cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF -DTFAST initfa.c -o init_tf.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF -DTFAST dropff2.c -o drop_tff.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o cc -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -DNORMAL_DIST -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c scaleswn.c -o scale_sn.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DGLSEARCH initfa.c -o init_lnw.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnnw2.c -o droplnw.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DGGSEARCH -c wm_align.c -o gwm_align.o cc -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw.o droplnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DGGSEARCH initfa.c -o init_gnw.o cc -DGLOBAL_GLOBAL -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnnw2.c -o dropgnw.o cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw.o dropgnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -o ../bin/map_db map_db.c =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for fasta3-36.3.8_1 ===> Generating temporary packing list cc -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw.o dropgsw2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw.o droplnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw.o dropgnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg-builder.dan.net.uk' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -o ../bin/map_db map_db.c cd ../bin; cp fasta36 ssearch36 lalign36 fasts36 fastx36 tfastx36 fasty36 tfasty36 tfasts36 fastm36 tfastm36 fastf36 tfastf36 glsearch36 ggsearch36 map_db /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/bin; cd ../src (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/bin && install -s -m 555 * /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/bin) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/conf && install -m 0644 fastlibs /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/etc/fastlibs.sample) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 data/*.mat /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 fastf3.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 fasts3.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 prss3.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 map_db.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 ps_lav.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fastf35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fasts35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fastm35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fastx35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fasty35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/ggsearch35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/lalign35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/ssearch35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfasta35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfastf35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfasts35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfastx35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfasty35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/prfx35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/prss35.1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 COPYRIGHT /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 FASTA_LIST /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 README /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 README.versions /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta_func.doc /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 readme.* /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta.defaults /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta.options /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta_versions.html /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 changes*.html /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.aa /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.lc /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.seq /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.lib /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) ====> 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=2024-04-01T01:27:46+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1b819e4869' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for fasta3-36.3.8_1 ===> Building fasta3-36.3.8_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for fasta3-36.3.8_1 build of biology/fasta3 | fasta3-36.3.8_1 ended at Mon Apr 1 02:28:52 BST 2024 build time: 00:01:07