Diff of the two buildlogs: -- --- b1/build.log 2024-10-29 18:12:36.937604352 +0000 +++ b2/build.log 2024-10-29 18:14:46.672995526 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 29 06:10:03 -12 2024 -I: pbuilder-time-stamp: 1730225403 +I: Current time: Tue Dec 2 14:35:36 +14 2025 +I: pbuilder-time-stamp: 1764635736 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying adjust-scripts I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/959672/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/565993/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Dec 2 00:35 /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/565993/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/565993/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='99ad9145c7b84e0fb0f6f3aacd1c3cb3' - 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='959672' - PS1='# ' - PS2='> ' + INVOCATION_ID=e2d64cf1fe2648e7937617faab956aa3 + 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=565993 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.gyW8mf3e/pbuilderrc_LLIs --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gyW8mf3e/b1 --logfile b1/build.log fasta3_36.3.8i.14-Nov-2020-3.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.gyW8mf3e/pbuilderrc_hbpb --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gyW8mf3e/b2 --logfile b2/build.log fasta3_36.3.8i.14-Nov-2020-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/959672/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/565993/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-1 [465 kB] -Fetched 20.3 MB in 0s (76.9 MB/s) +Fetched 20.3 MB in 2s (9611 kB/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 ... 19949 files and directories currently installed.) @@ -277,7 +309,11 @@ 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-2020-3_source.changes +I: user script /srv/workspace/pbuilder/565993/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/565993/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-2020-3_source.changes dpkg-buildpackage: info: source package fasta3 dpkg-buildpackage: info: source version 36.3.8i.14-Nov-2020-3 dpkg-buildpackage: info: source distribution unstable @@ -307,7 +343,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020' dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f "../make/Makefile.linux64" - cd src && make -j20 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64 + cd src && make -j42 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64 make[2]: Entering directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/src' 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_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.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 work_thr2.c @@ -325,35 +361,82 @@ 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 -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", - | ~~~~^ - | | - | long long int - | %8ld -...... - 2577 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | off_t {aka long int} -compacc2e.c: In function 'save_best2': -compacc2e.c:2753:87: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] - 2753 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", - | ~~~~^ - | | - | long long int - | %8ld -...... - 2761 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | 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 -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 +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 +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 +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 -DFASTS -c dropfs2.c -o drop_fs2.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 -DFASTS -c cal_consf.c -o calcons_fs.o +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} +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 -DFASTX initfa.c -o init_fx.o +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} 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); @@ -411,6 +494,7 @@ nmgetlib.c:967:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 967 | fgets(ver,sizeof(ver),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mmgetaa.c: In function 'check_mmap': nmgetlib.c: In function 'lranlib': nmgetlib.c:1041:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1041 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -422,6 +506,16 @@ nmgetlib.c:1086:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1086 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); /* get the extra line */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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:1108:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -438,10 +532,31 @@ nmgetlib.c:1143:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1143 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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: In function 'egetlib': nmgetlib.c:1227:1: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1227 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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: In function 'eranlib': nmgetlib.c:1257:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1257 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -486,6 +601,7 @@ 1470 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'vranlib': +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 faatran.c nmgetlib.c:1497:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1497 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -521,34 +637,8 @@ 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} ncbl2_mlib.c: In function 'ncbl2_getliba': +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 dropfx2.c -o drop_fx.o 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", | ~~~^ @@ -559,26 +649,6 @@ | ~~~~~~~ | | | 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} ncbl2_mlib.c:1150:68: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'fseek_t' {aka 'long int'} [-Wformat=] 1150 | error: fprintf(stderr,"*** ERROR [%s:%d] - error reading %s at %lld\n",__FILE__,__LINE__,libstr,*libpos); | ~~~^ ~~~~~~~ @@ -612,40 +682,35 @@ | | | | 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 lib_sel.c -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 url_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 -c -DFASTX -DTFAST initfa.c -o init_tfx.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", + | ~~~~^ + | | + | long long int + | %8ld +...... + 2577 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); + | ~~~~~~~~~~~~~~~~~~~~ + | | + | 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 -c -DTFAST dropfx2.c -o drop_tfx.o +compacc2e.c: In function 'save_best2': +compacc2e.c:2753:87: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] + 2753 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", + | ~~~~^ + | | + | long long int + | %8ld +...... + 2761 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); + | ~~~~~~~~~~~~~~~~~~~~ + | | + | 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 -c -DFASTY initfa.c -o init_fy.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 dropfz3.c -o drop_fz.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 -DFASTY -DTFAST initfa.c -o init_tfy.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); @@ -656,7 +721,9 @@ ncbl2_mlib.c:831:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 831 | fread(date_str,(size_t)1,(size_t)date_len,ifile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -DTFAST dropfz3.c -o drop_tfz.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 -DTFAST initfa.c -o init_tfs.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 -DTFAST -DFASTS dropfs2.c -o drop_tfs.o ncbl2_mlib.c: In function 'ncbl2_ranlib': ncbl2_mlib.c:1720:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1720 | fread(str,(size_t)1,(size_t)(llen),m_fd->hfile); @@ -673,39 +740,16 @@ 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 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function 'src_long8_read': +compacc2e.c: In function 'save_best': ncbl2_mlib.c:1884:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1884 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function 'ncbi_long8_read': -ncbl2_mlib.c:1904:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1904 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_char_read': -ncbl2_mlib.c:1911:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1911 | fread(val,(size_t)1,(size_t)1,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_fstr_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 -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o -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 -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 -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", | ~~~~^ @@ -717,6 +761,17 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} +ncbl2_mlib.c:1904:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1904 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_char_read': +ncbl2_mlib.c:1911:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1911 | fread(val,(size_t)1,(size_t)1,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_fstr_read': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compacc2e.c: In function 'save_best2': compacc2e.c:2753:87: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] 2753 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", @@ -729,25 +784,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} -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 -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 -DFASTS -c dropfs2.c -o drop_fs2.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 -DFASTS -c cal_consf.c -o calcons_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 -DFASTX initfa.c -o init_fx.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 faatran.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 dropfx2.c -o drop_fx.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 -DFASTX -DTFAST initfa.c -o init_tfx.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 -DTFAST dropfx2.c -o drop_tfx.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 -DFASTY initfa.c -o init_fy.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 dropfz3.c -o drop_fz.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 -DFASTY -DTFAST initfa.c -o init_tfy.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 -DTFAST dropfz3.c -o drop_tfz.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 -DTFAST initfa.c -o init_tfs.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 -DTFAST -DFASTS dropfs2.c -o drop_tfs.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 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.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 -DFASTM initfa.c -o init_fm.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 -DFASTM tatstats.c -o tatstats_fm.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 -DFASTM dropfs2.c -o drop_fm.o @@ -773,9 +809,6 @@ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DGLOBAL_GLOBAL -DSW_SSE2 -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 dropnnw2.c -o dropgnw_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 global_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 -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 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", @@ -798,164 +831,169 @@ 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/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/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 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 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 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 -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 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 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/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/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 +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 -lpthread +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_sse.o droplnw_sse.o glocal_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 +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 +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 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); + | ^ +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) + | ^ 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) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +nmgetlib.c:514:3: note: 're_openlib' was previously declared here mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ 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:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( - | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here -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: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: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 '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 -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, +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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 +compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used 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:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ 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) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +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 mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ +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) + | ^ +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ compacc2e.c:2313:1: note: type 'long int' should match type 'int' +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ 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, - | ^ -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: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 '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 -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, +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 +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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 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); | ^ +initfa.c:2036:1: note: 'last_calc' was previously declared here 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) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: 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, + | ^ +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, + | ^ mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { +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) + | ^ +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, | ^ -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 +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ +compacc2e.c:2202:1: note: type 'long int' should match type 'int' initfa.c:2036:1: note: 'last_calc' was previously declared here +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 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:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ 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' +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ 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 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, | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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/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 -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); - | ^ -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); - | ^ -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) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ 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, | ^ +compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used 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 +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, + | ^ +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, + | ^ 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, | ^ @@ -963,29 +1001,39 @@ 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: 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: 'get_annot' was previously declared here +compacc2e.c:2202:1: note: type 'long int' should match type 'int' +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ +compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used 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 +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 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, | ^ mshowalign2.c:134:6: note: 'showalign' was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, + | ^ +compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { +mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( | ^ -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 +initfa.c:2036:1: note: 'last_calc' was previously declared here +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 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 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, | ^ @@ -998,34 +1046,25 @@ 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, | ^ +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, + | ^ +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, + | ^ mshowalign2.c:134:6: note: 'showalign' was previously declared here 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 -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); - | ^ -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) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ -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:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 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 +scaleswt.c:164:1: note: type mismatch in parameter 7 + 164 | process_hist(struct stat_str *sptr, int nstats, | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here +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, | ^ @@ -1085,35 +1124,71 @@ 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); + | ^ 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) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +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) + | ^ +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ +compacc2e.c:2313:1: note: type 'long int' should match type 'int' 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 +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:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( + | ^ initfa.c:2036:1: note: 'last_calc' was previously declared here 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, | ^ +initfa.c:2036:1: note: 'last_calc' was previously declared here +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: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 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: 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 +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, + | ^ compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used 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, @@ -1121,80 +1196,75 @@ mshowalign2.c:134:6: note: 'showalign' was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 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 mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used 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); + | ^ 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) | ^ +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) + | ^ +nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +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); + | ^ +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ 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, - | ^ -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, - | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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 -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); - | ^ 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) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:2313:1: note: type 'long int' should match type 'int' mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ +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 compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2313:1: note: type 'long int' should match type 'int' +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ 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, +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( | ^ -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 +initfa.c:2036:1: note: 'last_calc' was previously declared here +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ 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, | ^ @@ -1204,38 +1274,28 @@ 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 +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 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, | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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 -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); - | ^ -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) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); +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:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { +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: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 -lto-wrapper: warning: using serial compilation of 4 LTRANS jobs -comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: 'last_calc' was previously declared here +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 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 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, | ^ @@ -1243,9 +1303,14 @@ 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: type 'long int' should match type 'int' +compacc2e.c:2202:1: note: 'get_annot' was previously declared here 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 -lto-wrapper: note: see the '-flto' option documentation for more information +compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +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, + | ^ 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, | ^ @@ -1253,19 +1318,10 @@ 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 4 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 -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 -lto-wrapper: warning: using serial compilation of 6 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 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 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); | ^ @@ -1286,11 +1342,19 @@ 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, | ^ +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); + | ^ +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) + | ^ 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 +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: 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, | ^ @@ -1298,40 +1362,24 @@ 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' +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ 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 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, | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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 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 -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 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); - | ^ -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) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, + | ^ 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 +mshowalign2.c:134:6: 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, | ^ @@ -1356,12 +1404,6 @@ 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/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_sse.o droplnw_sse.o glocal_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 4 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 -lto-wrapper: warning: using serial compilation of 4 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); | ^ @@ -1379,13 +1421,14 @@ 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:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( +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, | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here +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, | ^ @@ -1395,46 +1438,13 @@ 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 -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, - | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 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 -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); - | ^ -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) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ -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:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( - | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here -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, +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: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:3597:1: note: type mismatch in parameter 8 + 3597 | buf_align_seq(unsigned char **aa0, int n0, | ^ -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 +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, | ^ @@ -1443,23 +1453,49 @@ | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used lto-wrapper: warning: using serial compilation of 6 LTRANS jobs +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +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 5 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 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 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 6 LTRANS jobs +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 +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 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 initfa.c: In function 'get_lambda.constprop': +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:675:14: note: in a call to allocation function 'calloc' declared here - 675 | 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:675:14: note: in a call to allocation function 'calloc' declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ +/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here + 675 | 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)) { @@ -1481,21 +1517,21 @@ 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 Oct 29 18:11:21 2024 on ionos11-amd64 -Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux +STARTING FASTA36 Tue Dec 2 00:36:38 2025 on i-capture-the-hostname +Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Tue Oct 29 18:11:21 2024 +starting prss36(ssearch/fastx) Tue Dec 2 00:36:38 2025 done -starting lalign36 Tue Oct 29 18:11:22 2024 -FINISHED Tue Oct 29 18:11:46 2024 +starting lalign36 Tue Dec 2 00:36:39 2025 +FINISHED Tue Dec 2 00:37:02 2025 -STARTING FASTA36 Tue Oct 29 18:11:46 2024 on ionos11-amd64 -Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux +STARTING FASTA36 Tue Dec 2 00:37:02 2025 on i-capture-the-hostname +Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Tue Oct 29 18:11:46 2024 +starting prss36(ssearch/fastx) Tue Dec 2 00:37:02 2025 done -starting lalign36 Tue Oct 29 18:11:47 2024 -FINISHED Tue Oct 29 18:12:12 2024 +starting lalign36 Tue Dec 2 00:37:03 2025 +FINISHED Tue Dec 2 00:37:26 2025 # ../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 @@ -1507,29 +1543,27 @@ Library: ../seq/prot_test.lseg 2267 residues in 12 sequences -Statistics: (shuffled [200]) MLE statistics: Lambda= 0.1137; K=0.001712 - statistics sampled from 4 (4) to 200 sequences +Statistics: (shuffled [139]) MLE statistics: Lambda= 0.1362; K=0.00818 + statistics sampled from 4 (4) to 139 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 + Scan time: 0.030 The best scores are: opt bits E(12) -sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 214.8 1.2e-59 -sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 50.0 5.3e-10 -sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 19.4 0.51 -sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.0 2.5 -sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 18.1 2.8 -sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.2 3.3 -sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.0 3.5 -sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.7 4.3 -sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.3 4.7 -sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.0 4.9 -sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.9 6.5 -sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 17.2 6.9 +sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 252.9 4.3e-71 +sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 55.4 1.3e-11 +sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 18.8 0.78 +sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 17.2 4.7 +sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 15.9 4.8 +sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 14.9 6.5 +sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 14.7 7 +sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 14.7 8.8 +sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 13.1 8.8 +sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 13.9 8.9 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) - initn: 1242 init1: 1242 opt: 1242 Z-score: 1122.5 bits: 214.8 E(12): 1.2e-59 + initn: 1242 init1: 1242 opt: 1242 Z-score: 1328.3 bits: 252.9 E(12): 4.3e-71 Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 10 20 30 40 50 60 @@ -1557,7 +1591,7 @@ 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) - initn: 204 init1: 73 opt: 237 Z-score: 231.4 bits: 50.0 E(12): 5.3e-10 + initn: 204 init1: 73 opt: 237 Z-score: 260.6 bits: 55.4 E(12): 1.3e-11 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 @@ -1585,7 +1619,7 @@ 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: 70.0 bits: 19.4 E(12): 0.51 + initn: 40 init1: 40 opt: 51 Z-score: 66.5 bits: 18.8 E(12): 0.78 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 @@ -1600,24 +1634,8 @@ sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA 70 80 90 100 110 120 ->>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) - initn: 56 init1: 36 opt: 36 Z-score: 56.8 bits: 17.0 E(12): 2.5 -Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) - - 10 20 30 -sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG - ::.. :: -sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP - 20 30 40 50 60 70 - - 40 50 60 70 80 90 -sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR - -sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG - 80 90 100 110 120 130 - >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) - initn: 43 init1: 43 opt: 43 Z-score: 55.8 bits: 18.1 E(12): 2.8 + initn: 43 init1: 43 opt: 43 Z-score: 51.0 bits: 17.2 E(12): 4.7 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 @@ -1635,8 +1653,24 @@ sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 320 330 340 350 +>>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) + initn: 56 init1: 36 opt: 36 Z-score: 50.8 bits: 15.9 E(12): 4.8 +Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) + + 10 20 30 +sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG + ::.. :: +sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP + 20 30 40 50 60 70 + + 40 50 60 70 80 90 +sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR + +sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG + 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: 54.4 bits: 16.2 E(12): 3.3 + initn: 31 init1: 31 opt: 31 Z-score: 47.4 bits: 14.9 E(12): 6.5 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 @@ -1652,7 +1686,7 @@ 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: 53.7 bits: 16.0 E(12): 3.5 + initn: 30 init1: 30 opt: 30 Z-score: 46.6 bits: 14.7 E(12): 7 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 @@ -1670,8 +1704,24 @@ sp|P10 SNK +>>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) + initn: 30 init1: 30 opt: 30 Z-score: 43.3 bits: 14.7 E(12): 8.8 +Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) + + 20 30 40 50 60 70 +sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- + :. . .:: ..:. . ::. :. +sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK + 10 20 30 + + 80 90 100 110 120 +sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL + . ....:.:.. :..::. :: +sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE + 40 50 60 70 80 90 + >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) - initn: 22 init1: 22 opt: 22 Z-score: 51.8 bits: 14.7 E(12): 4.3 + initn: 22 init1: 22 opt: 22 Z-score: 43.3 bits: 13.1 E(12): 8.8 Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 150 160 170 180 190 200 @@ -1687,7 +1737,7 @@ 50 >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) - initn: 26 init1: 26 opt: 26 Z-score: 51.0 bits: 15.3 E(12): 4.7 + initn: 26 init1: 26 opt: 26 Z-score: 43.1 bits: 13.9 E(12): 8.9 Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 90 100 110 120 130 140 @@ -1699,67 +1749,13 @@ 150 160 170 180 190 200 sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI ->>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) - initn: 30 init1: 30 opt: 30 Z-score: 50.4 bits: 16.0 E(12): 4.9 -Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) - - 20 30 40 50 60 70 -sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- - :. . .:: ..:. . ::. :. -sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK - 10 20 30 - - 80 90 100 110 120 -sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL - . ....:.:.. :..::. :: -sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE - 40 50 60 70 80 90 - ->>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) - initn: 23 init1: 23 opt: 23 Z-score: 47.4 bits: 14.9 E(12): 6.5 -Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) - - 30 40 50 60 70 80 -sp|P10 YDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLARKHH - :. : .:. ... .: : . . -sp|P01 TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK - 10 20 30 40 - - 90 100 110 120 130 140 -sp|P10 LDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLG - .:. . . ...:.. :. ..: . . :.::.: -sp|P01 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF - 50 60 70 80 90 100 - - 150 160 170 180 190 200 -sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY - -sp|P01 NRGEC - - ->>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) - initn: 37 init1: 37 opt: 37 Z-score: 46.8 bits: 17.2 E(12): 6.9 -Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) - - 50 60 70 80 90 100 -sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN - : ... .: :... : : . : . .:. -sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK - 370 380 390 400 410 420 - - 110 120 130 140 150 160 -sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD - : ::...: -sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH - 430 440 450 460 470 480 - 218 residues in 1 query sequences 2267 residues in 12 library sequences - Tcomplib [36.3.8i Nov, 2022] (64 proc in memory [0G]) - start: Tue Oct 29 18:12:12 2024 done: Tue Oct 29 18:12:12 2024 - Total Scan time: 0.000 Total Display time: 0.020 + Tcomplib [36.3.8i Nov, 2022] (128 proc in memory [0G]) + start: Tue Dec 2 00:37:26 2025 done: Tue Dec 2 00:37:26 2025 + Total Scan time: 0.030 Total Display time: 0.010 Function used was FASTA [36.3.8i Nov, 2022] rm -rf test/results/test* @@ -1792,8 +1788,8 @@ dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8i.14-Nov-2020-3_amd64.deb'. -dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-3_all.deb'. dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8i.14-Nov-2020-3_amd64.deb'. +dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-3_all.deb'. dpkg-genbuildinfo --build=binary -O../fasta3_36.3.8i.14-Nov-2020-3_amd64.buildinfo dpkg-genchanges --build=binary -O../fasta3_36.3.8i.14-Nov-2020-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1801,12 +1797,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/565993/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/565993/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/959672 and its subdirectories -I: Current time: Tue Oct 29 06:12:36 -12 2024 -I: pbuilder-time-stamp: 1730225556 +I: removing directory /srv/workspace/pbuilder/565993 and its subdirectories +I: Current time: Tue Dec 2 14:37:43 +14 2025 +I: pbuilder-time-stamp: 1764635863