Diff of the two buildlogs: -- --- b1/build.log 2024-05-01 12:14:39.893054259 +0000 +++ b2/build.log 2024-05-01 12:16:29.500394959 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 3 06:35:33 -12 2025 -I: pbuilder-time-stamp: 1748975733 +I: Current time: Thu May 2 02:14:42 +14 2024 +I: pbuilder-time-stamp: 1714565682 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,51 +30,83 @@ dpkg-source: info: applying adjust-scripts I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3008113/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 1 12:14 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8a204c896b6f479b97f4e60ff05c8fea' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3008113' - PS1='# ' - PS2='> ' + INVOCATION_ID=b0ad207bdac4422a801831d314e7628d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=538490 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eShVmceM/pbuilderrc_1Vpe --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eShVmceM/b1 --logfile b1/build.log fasta3_36.3.8i.14-Nov-2020-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eShVmceM/pbuilderrc_hvM3 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eShVmceM/b2 --logfile b2/build.log fasta3_36.3.8i.14-Nov-2020-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 24 13:34 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3008113/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 23 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -143,7 +175,7 @@ Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.0-1 [458 kB] -Fetched 19.5 MB in 1s (17.2 MB/s) +Fetched 19.5 MB in 0s (87.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19901 files and directories currently installed.) @@ -282,7 +314,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../fasta3_36.3.8i.14-Nov-2020-1_source.changes +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../fasta3_36.3.8i.14-Nov-2020-1_source.changes dpkg-buildpackage: info: source package fasta3 dpkg-buildpackage: info: source version 36.3.8i.14-Nov-2020-1 dpkg-buildpackage: info: source distribution unstable @@ -322,10 +358,7 @@ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c apam.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c compacc2e.c: In function 'save_best': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnfa.c -o drop_nfa.o compacc2e.c:2569:87: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] 2569 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~^ @@ -349,13 +382,63 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnfa.c -o drop_nfa.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTA -c cal_cons2.c -o calcons_fa.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c nmgetlib.c -o lgetlib.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mmgetaa.c -o lgetaa_m.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c c_dispn.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c ncbl2_mlib.c -o ncbl2_mlib.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lib_sel.c +mmgetaa.c: In function 'load_mmap': +mmgetaa.c:167:63: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 167 | fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); + | ~~~^ ~~~~~~ + | | | + | long long int fseek_t {aka long int} + | %ld +mmgetaa.c:205:41: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '__off_t' {aka 'long int'} [-Wformat=] + 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 206 | bname,statbuf.st_size,f_size); + | ~~~~~~~~~~~~~~~ + | | + | __off_t {aka long int} +mmgetaa.c:205:66: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 206 | bname,statbuf.st_size,f_size); + | ~~~~~~ + | | + | fseek_t {aka long int} +mmgetaa.c:296:59: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '__off_t' {aka 'long int'} [-Wformat=] + 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); + | ~~~~~~~~~~~~~~~ + | | + | __off_t {aka long int} +mmgetaa.c:296:84: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); + | ~~~~~~ + | | + | fseek_t {aka long int} +mmgetaa.c: In function 'check_mmap': nmgetlib.c: In function 'agetlib': nmgetlib.c:636:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 636 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); @@ -363,6 +446,16 @@ nmgetlib.c:638:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 638 | fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mmgetaa.c:1077:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} nmgetlib.c:681:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 681 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -370,12 +463,31 @@ 696 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'aranlib': +mmgetaa.c:1077:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} nmgetlib.c:716:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 716 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'qgetlib': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c url_subs.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c +mmgetaa.c:1077:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} nmgetlib.c:778:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 778 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -525,88 +637,6 @@ nmgetlib.c:1674:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1674 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mmgetaa.c: In function 'load_mmap': -mmgetaa.c:167:63: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 167 | fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); - | ~~~^ ~~~~~~ - | | | - | long long int fseek_t {aka long int} - | %ld -mmgetaa.c:205:41: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '__off_t' {aka 'long int'} [-Wformat=] - 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 206 | bname,statbuf.st_size,f_size); - | ~~~~~~~~~~~~~~~ - | | - | __off_t {aka long int} -mmgetaa.c:205:66: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 206 | bname,statbuf.st_size,f_size); - | ~~~~~~ - | | - | fseek_t {aka long int} -mmgetaa.c:296:59: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '__off_t' {aka 'long int'} [-Wformat=] - 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); - | ~~~~~~~~~~~~~~~ - | | - | __off_t {aka long int} -mmgetaa.c:296:84: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); - | ~~~~~~ - | | - | fseek_t {aka long int} -mmgetaa.c: In function 'check_mmap': -mmgetaa.c:1077:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1077:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1077:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c ncbl2_mlib.c: In function 'ncbl2_getliba': ncbl2_mlib.c:1105:78: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] 1105 | fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %lld %ld != %ld\n", @@ -651,8 +681,6 @@ | | | | long long int fseek_t {aka long int} | %ld -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o ncbl2_mlib.c: In function 'load_ncbl2': ncbl2_mlib.c:810:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | fread(title_str,(size_t)1,(size_t)title_len,ifile); @@ -679,7 +707,6 @@ 1856 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function 'src_uint4_read': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pssm_asn_subs.c ncbl2_mlib.c:1869:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1869 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -699,15 +726,17 @@ ncbl2_mlib.c:1916:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1916 | fread(val,(size_t)slen,(size_t)1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lib_sel.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c url_subs.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pssm_asn_subs.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLALIGN -c mshowalign2.c -o lshowalign.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS initfa.c -o init_fs.o compacc2e.c: In function 'save_best': compacc2e.c:2569:87: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] 2569 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", @@ -732,6 +761,13 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLALIGN -c mshowalign2.c -o lshowalign.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS initfa.c -o init_fs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswt.c -o scaleswts.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_tat.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS tatstats.c -o tatstats_fs.o @@ -776,8 +812,6 @@ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -o ../bin/map_db map_db.c 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 -lpthread 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_sse.o dropgsw2_sse.o smith_waterman_sse2.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 -lpthread -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_sse.o smith_waterman_sse2.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 -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 -lpthread map_db.c: In function 'main': map_db.c:370:47: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'fseek_t' {aka 'long int'} [-Wformat=] 370 | fprintf(stderr," wrote %d sequences (tot=%lld, max=%ld) to %s\n", @@ -800,6 +834,9 @@ map_db.c:524:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 524 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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_sse.o smith_waterman_sse2.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 +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 -lpthread +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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -840,7 +877,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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 -lpthread 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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); @@ -899,14 +935,6 @@ compacc2e.c:2313:1: note: type 'long int' should match type 'int' compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] - 236 | process_hist(struct stat_str *sptr, int nstats, - | ^ -scaleswt.c:164:1: note: type mismatch in parameter 7 - 164 | process_hist(struct stat_str *sptr, int nstats, - | ^ -scaleswt.c:164:1: note: 'process_hist' was previously declared here -scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -923,11 +951,10 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ +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 -lpthread nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ @@ -942,6 +969,14 @@ compacc2e.c:2313:1: note: type 'long int' should match type 'int' compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] + 236 | process_hist(struct stat_str *sptr, int nstats, + | ^ +scaleswt.c:164:1: note: type mismatch in parameter 7 + 164 | process_hist(struct stat_str *sptr, int nstats, + | ^ +scaleswt.c:164:1: note: 'process_hist' was previously declared here +scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -958,6 +993,7 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1001,8 +1037,6 @@ compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ -lto-wrapper: warning: using serial compilation of 4 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ @@ -1040,16 +1074,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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 -lpthread -lto-wrapper: warning: using serial compilation of 6 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -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 -lpthread -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -lto-wrapper: warning: using serial compilation of 6 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1131,13 +1155,16 @@ | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used 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 -lpthread +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information 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 -lpthread 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 -lpthread -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: warning: using serial compilation of 6 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 6 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); - | ^ compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1166,19 +1193,15 @@ mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ compacc2e.c:2202:1: note: type mismatch in parameter 4 2202 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2202:1: note: type 'long int' should match type 'int' compacc2e.c:2202:1: note: 'get_annot' was previously declared here compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowalign2.c:85:1: warning: type of 'buf_align_seq' does not match original declaration [-Wlto-type-mismatch] - 85 | buf_align_seq(unsigned char **aa0, int n0, - | ^ -compacc2e.c:3597:1: note: type mismatch in parameter 8 - 3597 | buf_align_seq(unsigned char **aa0, int n0, - | ^ -compacc2e.c:3597:1: note: 'buf_align_seq' was previously declared here comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ @@ -1186,8 +1209,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ @@ -1226,6 +1247,13 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1260,6 +1288,13 @@ compacc2e.c:2202:1: note: type 'long int' should match type 'int' compacc2e.c:2202:1: note: 'get_annot' was previously declared here compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +mshowalign2.c:85:1: warning: type of 'buf_align_seq' does not match original declaration [-Wlto-type-mismatch] + 85 | buf_align_seq(unsigned char **aa0, int n0, + | ^ +compacc2e.c:3597:1: note: type mismatch in parameter 8 + 3597 | buf_align_seq(unsigned char **aa0, int n0, + | ^ +compacc2e.c:3597:1: note: 'buf_align_seq' was previously declared here comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ @@ -1267,12 +1302,7 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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 -lpthread -lto-wrapper: warning: using serial compilation of 4 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -lto-wrapper: warning: using serial compilation of 4 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); @@ -1317,6 +1347,12 @@ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used lto-wrapper: warning: using serial compilation of 4 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information compacc2e.c: In function 'next_annot_entry.constprop': compacc2e.c:2124:55: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2124 | if ((s_tmp_ann_entry_arr = (struct annot_entry **)calloc((n_annot+1),sizeof(struct annot_entry *)))==NULL) { @@ -1359,6 +1395,13 @@ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^ +initfa.c: In function 'get_lambda.constprop': +initfa.c:2225:54: warning: argument 1 value '18446744072709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 2225 | if (max > 1023 || min < -1024 || ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL)) { + | ^ +/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here + 556 | extern void *calloc (size_t __nmemb, size_t __size) + | ^ compacc2e.c: In function 'next_annot_entry.constprop': compacc2e.c:2124:55: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2124 | if ((s_tmp_ann_entry_arr = (struct annot_entry **)calloc((n_annot+1),sizeof(struct annot_entry *)))==NULL) { @@ -1373,13 +1416,6 @@ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^ -initfa.c: In function 'get_lambda.constprop': -initfa.c:2225:54: warning: argument 1 value '18446744072709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 2225 | if (max > 1023 || min < -1024 || ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL)) { - | ^ -/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here - 556 | extern void *calloc (size_t __nmemb, size_t __size) - | ^ compacc2e.c: In function 'next_annot_entry.constprop': compacc2e.c:2124:55: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2124 | if ((s_tmp_ann_entry_arr = (struct annot_entry **)calloc((n_annot+1),sizeof(struct annot_entry *)))==NULL) { @@ -1387,13 +1423,6 @@ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^ -initfa.c: In function 'get_lambda.constprop': -initfa.c:2225:54: warning: argument 1 value '18446744072709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 2225 | if (max > 1023 || min < -1024 || ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL)) { - | ^ -/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here - 556 | extern void *calloc (size_t __nmemb, size_t __size) - | ^ compacc2e.c: In function 'next_annot_entry.constprop': compacc2e.c:2124:55: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2124 | if ((s_tmp_ann_entry_arr = (struct annot_entry **)calloc((n_annot+1),sizeof(struct annot_entry *)))==NULL) { @@ -1408,6 +1437,13 @@ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^ +initfa.c: In function 'get_lambda.constprop': +initfa.c:2225:54: warning: argument 1 value '18446744072709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 2225 | if (max > 1023 || min < -1024 || ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL)) { + | ^ +/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here + 556 | extern void *calloc (size_t __nmemb, size_t __size) + | ^ compacc2e.c: In function 'next_annot_entry.constprop': compacc2e.c:2124:55: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2124 | if ((s_tmp_ann_entry_arr = (struct annot_entry **)calloc((n_annot+1),sizeof(struct annot_entry *)))==NULL) { @@ -1500,9 +1536,9 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +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_sse.o dropgnw_sse.o global_sse2.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 -lpthread lto-wrapper: warning: using serial compilation of 6 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information -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_sse.o dropgnw_sse.o global_sse2.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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1587,21 +1623,21 @@ make[1]: Entering directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020' cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg -STARTING FASTA36 Tue Jun 3 18:36:41 2025 on infom02-amd64 -Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux +STARTING FASTA36 Wed May 1 12:15:42 2024 on i-capture-the-hostname +Linux i-capture-the-hostname 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Tue Jun 3 18:36:41 2025 +starting prss36(ssearch/fastx) Wed May 1 12:15:42 2024 done -starting lalign36 Tue Jun 3 18:36:42 2025 -FINISHED Tue Jun 3 18:36:59 2025 +starting lalign36 Wed May 1 12:15:42 2024 +FINISHED Wed May 1 12:15:59 2024 -STARTING FASTA36 Tue Jun 3 18:36:59 2025 on infom02-amd64 -Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux +STARTING FASTA36 Wed May 1 12:15:59 2024 on i-capture-the-hostname +Linux i-capture-the-hostname 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Tue Jun 3 18:36:59 2025 +starting prss36(ssearch/fastx) Wed May 1 12:15:59 2024 done -starting lalign36 Tue Jun 3 18:36:59 2025 -FINISHED Tue Jun 3 18:37:16 2025 +starting lalign36 Wed May 1 12:15:59 2024 +FINISHED Wed May 1 12:16:16 2024 # ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg FASTA searches a protein or DNA sequence data bank version 36.3.8i Nov, 2022 @@ -1613,29 +1649,29 @@ Library: ../seq/prot_test.lseg 2267 residues in 12 sequences -Statistics: (shuffled [424]) MLE statistics: Lambda= 0.1693; K=0.00601 - statistics sampled from 4 (4) to 424 sequences +Statistics: (shuffled [458]) MLE statistics: Lambda= 0.1615; K=0.00443 + statistics sampled from 4 (4) to 458 sequences Algorithm: FASTA (3.8 Nov 2011) [optimized] Parameters: BL50 matrix (15:-5), open/ext: -10/-2 ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 Scan time: 0.000 The best scores are: opt bits E(12) -sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 312.7 4.3e-89 -sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 67.3 3.2e-15 -sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.9 0.098 -sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.9 0.9 -sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.2 1.2 -sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 17.0 2 +sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 299.1 5.3e-85 +sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 64.9 1.7e-14 +sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.6 0.12 +sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.7 1 +sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.1 1.2 +sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.9 2.1 sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.7 2.3 -sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.7 3.3 -sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.4 3.5 -sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.8 3.8 -sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.8 4.1 -sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.0 6 +sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.7 3.4 +sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.8 3.7 +sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.3 3.8 +sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.8 4 +sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.1 5.9 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) - initn: 1242 init1: 1242 opt: 1242 Z-score: 1651.4 bits: 312.7 E(12): 4.3e-89 + initn: 1242 init1: 1242 opt: 1242 Z-score: 1578.0 bits: 299.1 E(12): 5.3e-85 Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 10 20 30 40 50 60 @@ -1663,7 +1699,7 @@ 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) - initn: 204 init1: 73 opt: 237 Z-score: 325.0 bits: 67.3 E(12): 3.2e-15 + initn: 204 init1: 73 opt: 237 Z-score: 312.3 bits: 64.9 E(12): 1.7e-14 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 @@ -1691,7 +1727,7 @@ 180 190 200 210 220 >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) - initn: 40 init1: 40 opt: 51 Z-score: 83.0 bits: 21.9 E(12): 0.098 + initn: 40 init1: 40 opt: 51 Z-score: 81.5 bits: 21.6 E(12): 0.12 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 @@ -1707,7 +1743,7 @@ 70 80 90 100 110 120 >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) - initn: 43 init1: 43 opt: 43 Z-score: 65.4 bits: 19.9 E(12): 0.9 + initn: 43 init1: 43 opt: 43 Z-score: 64.4 bits: 19.7 E(12): 1 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 @@ -1726,7 +1762,7 @@ 320 330 340 350 >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) - initn: 56 init1: 36 opt: 36 Z-score: 63.4 bits: 18.2 E(12): 1.2 + initn: 56 init1: 36 opt: 36 Z-score: 62.8 bits: 18.1 E(12): 1.2 Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 10 20 30 @@ -1742,7 +1778,7 @@ 80 90 100 110 120 130 >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) - initn: 31 init1: 31 opt: 31 Z-score: 58.7 bits: 17.0 E(12): 2 + initn: 31 init1: 31 opt: 31 Z-score: 58.5 bits: 16.9 E(12): 2.1 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 @@ -1758,7 +1794,7 @@ 50 60 70 80 90 100 >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) - initn: 30 init1: 30 opt: 30 Z-score: 57.6 bits: 16.7 E(12): 2.3 + initn: 30 init1: 30 opt: 30 Z-score: 57.4 bits: 16.7 E(12): 2.3 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 @@ -1777,7 +1813,7 @@ sp|P10 SNK >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) - initn: 30 init1: 30 opt: 30 Z-score: 54.4 bits: 16.7 E(12): 3.3 + initn: 30 init1: 30 opt: 30 Z-score: 54.1 bits: 16.7 E(12): 3.4 Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 20 30 40 50 60 70 @@ -1792,8 +1828,21 @@ sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE 40 50 60 70 80 90 +>>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) + initn: 26 init1: 26 opt: 26 Z-score: 53.2 bits: 15.8 E(12): 3.7 +Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) + + 90 100 110 120 130 140 +sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK + : :: ::.: +sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG + 60 70 80 90 + + 150 160 170 180 190 200 +sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI + >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) - initn: 37 init1: 37 opt: 37 Z-score: 53.7 bits: 18.4 E(12): 3.5 + initn: 37 init1: 37 opt: 37 Z-score: 53.1 bits: 18.3 E(12): 3.8 Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 50 60 70 80 90 100 @@ -1808,21 +1857,8 @@ sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH 430 440 450 460 470 480 ->>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) - initn: 26 init1: 26 opt: 26 Z-score: 53.1 bits: 15.8 E(12): 3.8 -Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) - - 90 100 110 120 130 140 -sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK - : :: ::.: -sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG - 60 70 80 90 - - 150 160 170 180 190 200 -sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI - >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) - initn: 22 init1: 22 opt: 22 Z-score: 52.3 bits: 14.8 E(12): 4.1 + initn: 22 init1: 22 opt: 22 Z-score: 52.5 bits: 14.8 E(12): 4 Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 150 160 170 180 190 200 @@ -1838,7 +1874,7 @@ 50 >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) - initn: 23 init1: 23 opt: 23 Z-score: 48.3 bits: 15.0 E(12): 6 + initn: 23 init1: 23 opt: 23 Z-score: 48.5 bits: 15.1 E(12): 5.9 Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 30 40 50 60 70 80 @@ -1864,8 +1900,8 @@ 218 residues in 1 query sequences 2267 residues in 12 library sequences Tcomplib [36.3.8i Nov, 2022] (12 proc in memory [0G]) - start: Tue Jun 3 18:37:16 2025 done: Tue Jun 3 18:37:16 2025 - Total Scan time: 0.000 Total Display time: 0.000 + start: Wed May 1 12:16:16 2024 done: Wed May 1 12:16:16 2024 + Total Scan time: 0.000 Total Display time: 0.010 Function used was FASTA [36.3.8i Nov, 2022] make[1]: Leaving directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020' @@ -1897,8 +1933,8 @@ dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8i.14-Nov-2020-1_amd64.deb'. -dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-1_all.deb'. dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8i.14-Nov-2020-1_amd64.deb'. +dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-1_all.deb'. dpkg-genbuildinfo --build=binary -O../fasta3_36.3.8i.14-Nov-2020-1_amd64.buildinfo dpkg-genchanges --build=binary -O../fasta3_36.3.8i.14-Nov-2020-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1906,12 +1942,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/538490/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3008113 and its subdirectories -I: Current time: Tue Jun 3 06:37:39 -12 2025 -I: pbuilder-time-stamp: 1748975859 +I: removing directory /srv/workspace/pbuilder/538490 and its subdirectories +I: Current time: Thu May 2 02:16:28 +14 2024 +I: pbuilder-time-stamp: 1714565788