Diff of the two buildlogs: -- --- b1/build.log 2024-12-04 01:16:10.238711060 +0000 +++ b2/build.log 2024-12-04 01:20:49.806079001 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 3 13:08:41 -12 2024 -I: pbuilder-time-stamp: 1733274521 +I: Current time: Tue Jan 6 21:39:12 +14 2026 +I: pbuilder-time-stamp: 1767685152 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,54 +30,86 @@ dpkg-source: info: applying adjust-scripts I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/48341/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/124086/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 Jan 6 07:39 /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/124086/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/124086/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='f2382658c4f841f29a3255c7d817bd87' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='48341' - PS1='# ' - PS2='> ' + INVOCATION_ID=ae22bc763b7a4017b4cb9d6bbfe71757 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=124086 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.rRgVcHZf/pbuilderrc_jISy --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.rRgVcHZf/b1 --logfile b1/build.log fasta3_36.3.8i.14-Nov-2020-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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.rRgVcHZf/pbuilderrc_y3UU --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.rRgVcHZf/b2 --logfile b2/build.log fasta3_36.3.8i.14-Nov-2020-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/48341/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/124086/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -145,7 +177,7 @@ Get: 28 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.2-2 [467 kB] -Fetched 20.6 MB in 0s (71.0 MB/s) +Fetched 20.6 MB in 0s (51.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19955 files and directories currently installed.) @@ -280,7 +312,11 @@ 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/124086/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/124086/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 @@ -310,7 +346,7 @@ 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 -j11 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64 + cd src && make -j21 "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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 @@ -323,6 +359,17 @@ 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 -Wformat -Werror=format-security -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 htime.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 -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c apam.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 mshowalign2.c: In function 'showalign': mshowalign2.c:617:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 617 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n", @@ -344,44 +391,6 @@ | ~~~~~~~~~~~~~ | | | size_t {aka unsigned 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 -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -scaleswn.c: In function 'process_hist': -scaleswn.c:255:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] - 255 | fprintf(stderr," cannot allocate pstat_union: %ld\n",sizeof(struct pstat_str)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 -initfa.c: In function 'alloc_pam2p': -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d -dropnfa.c: In function 'init_work': -dropnfa.c:306:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] - 306 | fprintf (stderr,"*** ERROR [%s:%d] - cannot allocate diagonal arrays: %lu\n", - | ~~^ - | | - | long unsigned int - | %u -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 nmgetlib.c: In function 'open_lib': nmgetlib.c:414:76: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 414 | fprintf(stderr,"\n*** Warning [%s:%d] - cannot allocate lmf_str (%ld) for %s\n", @@ -393,7 +402,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 +scaleswn.c: In function 'process_hist': +scaleswn.c:255:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] + 255 | fprintf(stderr," cannot allocate pstat_union: %ld\n",sizeof(struct pstat_str)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 nmgetlib.c: In function 'sel_hacc_libstr_init': nmgetlib.c:2025:71: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2025 | fprintf(stderr, "*** Warning [%s:%d] - cannot allocate acc_hash[%ld]\n",__FILE__, __LINE__,hash_max*sizeof(int)); @@ -414,6 +432,20 @@ | | | | long int unsigned int | %d +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 -Wformat -Werror=format-security -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 +dropnfa.c: In function 'init_work': +dropnfa.c:306:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] + 306 | fprintf (stderr,"*** ERROR [%s:%d] - cannot allocate diagonal arrays: %lu\n", + | ~~^ + | | + | long unsigned int + | %u +nmgetlib.c:2158:75: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2158 | fprintf(stderr, "*** Warning [%s:%d] - cannot allocate gi_hash_link[%ld]\n",__FILE__, __LINE__,acc_cnt*sizeof(char *)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d ncbl2_mlib.c: In function 'ncbl2_getlibn': ncbl2_mlib.c:1434:80: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1434 | "*** ERROR [%s:%d] - could not read sequence record: %s %lld %ld != %ld: %d\n", @@ -435,12 +467,7 @@ | ~~~ | | | size_t {aka unsigned int} -nmgetlib.c:2158:75: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2158 | fprintf(stderr, "*** Warning [%s:%d] - cannot allocate gi_hash_link[%ld]\n",__FILE__, __LINE__,acc_cnt*sizeof(char *)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d +initfa.c: In function 'alloc_pam2p': ncbl2_mlib.c:1594:72: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 1594 | fprintf(stderr, "*** ERROR [%s:%d] malloc amb table error size %ld\n", | ~~^ @@ -455,6 +482,12 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d nmgetlib.c:638:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 638 | fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -479,16 +512,6 @@ 811 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'qranlib': -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c:820:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 820 | fread(pdb_title_str,(size_t)1,(size_t)pdb_title_len,ifile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:834:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 834 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -518,59 +541,35 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'ncbl2_ranlib': nmgetlib.c: In function 'lranlib': -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c:1735:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1735 | fread(my_buff,(size_t)1,llen,m_fd->hfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1048:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1048 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_int4_read': -ncbl2_mlib.c:1841:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1841 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_long4_read': -ncbl2_mlib.c:1856:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1856 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'pgetlib': -ncbl2_mlib.c: In function 'src_uint4_read': -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_long8_read': -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: 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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:820:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 820 | fread(pdb_title_str,(size_t)1,(size_t)pdb_title_len,ifile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'pranlib': -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 -Wformat -Werror=format-security -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 nmgetlib.c:1132:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1132 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1135:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1135 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -597,23 +596,58 @@ nmgetlib.c:1272:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1272 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'ncbl2_ranlib': nmgetlib.c: In function 'igetlib': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:1735:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1735 | fread(my_buff,(size_t)1,llen,m_fd->hfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1305:19: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1305 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1336:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1336 | fgets(lm_fd->lline,MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_int4_read': +ncbl2_mlib.c:1841:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1841 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_long4_read': nmgetlib.c:1340:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1340 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:1856:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1856 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_uint4_read': +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': nmgetlib.c: In function 'iranlib': +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': nmgetlib.c:1367:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1367 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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': nmgetlib.c:1378:11: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1378 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1387:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1387 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -647,6 +681,7 @@ nmgetlib.c:1575:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1575 | fgets(&lm_fd->lline[strlen(lm_fd->lline)-MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -Wformat -Werror=format-security -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 nmgetlib.c:1595:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1595 | fread((char *)seqp,(size_t)r_block,(size_t)1,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -654,7 +689,6 @@ 1610 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'gcg_ranlib': -initfa.c: In function 'alloc_pam2p': nmgetlib.c:1634:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1634 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -664,23 +698,23 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d +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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -smith_waterman_sse2.c: In function 'smith_waterman_sse2_word': -smith_waterman_sse2.c:69:15: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 69 | v_gapopen = _mm_setzero_si128(); /* Apple Devel */ - | ^ 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 -Wformat -Werror=format-security -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 +initfa.c: In function 'alloc_pam2p': 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 -Wformat -Werror=format-security -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 +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 mshowalign2.c: In function 'showalign': mshowalign2.c:617:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 617 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n", @@ -702,6 +736,7 @@ | ~~~~~~~~~~~~~ | | | size_t {aka unsigned 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 -Wformat -Werror=format-security -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 initfa.c: In function 'alloc_pam2p': initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); @@ -709,9 +744,10 @@ | | | | long int unsigned int | %d -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 +smith_waterman_sse2.c: In function 'smith_waterman_sse2_word': +smith_waterman_sse2.c:69:15: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 69 | v_gapopen = _mm_setzero_si128(); /* Apple Devel */ + | ^ 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 @@ -735,7 +771,6 @@ | long int size_t {aka unsigned int} | %d 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 scaleswt.c: In function 'process_hist': scaleswt.c:184:72: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 184 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate rs_snion: %ld\n",__FILE__, __LINE__, sizeof(struct pstat_str)); @@ -743,6 +778,7 @@ | | | | long int unsigned int | %d +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 -Wformat -Werror=format-security -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 scaleswt.c: In function 'last_stats': scaleswt.c:1230:67: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 1230 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate rs_s: %ld\n",__FILE__, __LINE__,sizeof(struct pstat_str)); @@ -751,6 +787,20 @@ | long int unsigned int | %d 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 -Wformat -Werror=format-security -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 +initfa.c: In function 'alloc_pam2p': +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d +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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 dropfs2.c: In function 'init_work': dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] 377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n", @@ -762,6 +812,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 initfa.c: In function 'alloc_pam2p': initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); @@ -769,13 +823,6 @@ | | | | long int unsigned int | %d -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 dropfx2.c: In function 'do_walign': dropfx2.c:2660:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 2660 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate a_res [%lu]", @@ -787,7 +834,30 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 +dropfz3.c: In function 'init_work': +dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] + 629 | fprintf (stderr,"*** ERROR [%s:%d] - cannot allocate diagonal arrays: %lu\n", + | ~~^ + | | + | long unsigned int + | %u +initfa.c: In function 'alloc_pam2p': +dropfz3.c: In function 'init_work': +dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] + 629 | fprintf (stderr,"*** ERROR [%s:%d] - cannot allocate diagonal arrays: %lu\n", + | ~~^ + | | + | long unsigned int + | %u +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d +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 -Wformat -Werror=format-security -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 dropfx2.c: In function 'do_walign': dropfx2.c:2660:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 2660 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate a_res [%lu]", @@ -806,44 +876,6 @@ | | | | long int unsigned int | %d -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 -Wformat -Werror=format-security -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 -initfa.c: In function 'alloc_pam2p': -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -initfa.c: In function 'alloc_pam2p': -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d -dropfz3.c: In function 'init_work': -dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] - 629 | fprintf (stderr,"*** ERROR [%s:%d] - cannot allocate diagonal arrays: %lu\n", - | ~~^ - | | - | long unsigned int - | %u -initfa.c: In function 'alloc_pam2p': -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d -dropfz3.c: In function 'init_work': -dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] - 629 | fprintf (stderr,"*** ERROR [%s:%d] - cannot allocate diagonal arrays: %lu\n", - | ~~^ - | | - | long unsigned int - | %u dropfz3.c: In function 'do_walign': dropfz3.c:2672:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 2672 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate a_res [%lu]", @@ -866,31 +898,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned int -dropfs2.c: In function 'init_work': -dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] - 377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n", - | ~~^ - | | - | long int - | %d - 378 | tat_size * sizeof(struct tat_str *)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | unsigned int -initfa.c: In function 'alloc_pam2p': -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 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 -Wformat -Werror=format-security -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 -DFASTM -c cal_consf.c -o calcons_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 -Wformat -Werror=format-security -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 mshowalign2.c -o mshowalign2_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 -Wformat -Werror=format-security -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 -DTFAST initfa.c -o init_tfm.o initfa.c: In function 'alloc_pam2p': initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); @@ -898,7 +908,8 @@ | | | | long int unsigned int | %d -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 -Wformat -Werror=format-security -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 -DFASTM dropfs2.c -o drop_tfm.o +initfa.c: In function 'alloc_pam2p': +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 -Wformat -Werror=format-security -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 -DTFAST initfa.c -o init_tfm.o dropfs2.c: In function 'init_work': dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] 377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n", @@ -910,6 +921,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned int +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d mshowalign2.c: In function 'showalign': mshowalign2.c:617:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 617 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n", @@ -931,7 +948,13 @@ | ~~~~~~~~~~~~~ | | | size_t {aka unsigned 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 -Wformat -Werror=format-security -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 -DFASTM -c cal_consf.c -o calcons_tfm.o +initfa.c: In function 'alloc_pam2p': +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d dropfs2.c: In function 'init_work': dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] 377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n", @@ -943,6 +966,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned 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 -Wformat -Werror=format-security -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 -DFASTM dropfs2.c -o drop_tfm.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 -Wformat -Werror=format-security -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 -DFASTM -c cal_consf.c -o calcons_tfm.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 -Wformat -Werror=format-security -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 -DFASTF initfa.c -o init_ff.o initfa.c: In function 'alloc_pam2p': initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); @@ -950,21 +976,28 @@ | | | | long int unsigned int | %d -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 -Wformat -Werror=format-security -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 -DFASTF initfa.c -o init_ff.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 -Wformat -Werror=format-security -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 -DFASTF -c scaleswt.c -o scaleswtf.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 -Wformat -Werror=format-security -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 -DFASTF tatstats.c -o tatstats_ff.o +dropfs2.c: In function 'init_work': +dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] + 377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n", + | ~~^ + | | + | long int + | %d + 378 | tat_size * sizeof(struct tat_str *)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | unsigned 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 -Wformat -Werror=format-security -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 -DFASTF dropff2.c -o drop_ff2.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 -Wformat -Werror=format-security -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 -DFASTF -c cal_consf.c -o calcons_ff.o initfa.c: In function 'alloc_pam2p': +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 -Wformat -Werror=format-security -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 -DFASTF -c cal_consf.c -o calcons_ff.o initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d -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 -Wformat -Werror=format-security -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 -DFASTF -DTFAST initfa.c -o init_tf.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 -Wformat -Werror=format-security -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 -DFASTF -DTFAST dropff2.c -o drop_tff.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 -Wformat -Werror=format-security -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 -DFASTF -c cal_consf.c -o calcons_tff.o scaleswt.c: In function 'process_hist': scaleswt.c:184:72: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 184 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate rs_snion: %ld\n",__FILE__, __LINE__, sizeof(struct pstat_str)); @@ -972,7 +1005,16 @@ | | | | long int unsigned int | %d +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 -Wformat -Werror=format-security -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 -DFASTF -DTFAST initfa.c -o init_tf.o scaleswt.c: In function 'last_stats': +scaleswt.c:1230:67: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 1230 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate rs_s: %ld\n",__FILE__, __LINE__,sizeof(struct pstat_str)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d +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 -Wformat -Werror=format-security -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 -DFASTF -DTFAST dropff2.c -o drop_tff.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 -Wformat -Werror=format-security -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 -DFASTF -c cal_consf.c -o calcons_tff.o dropff2.c: In function 'init_work': dropff2.c:120:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 120 | fprintf(stderr, "*** ERROR [%s:%d] - cannot calloc f_str [%lu]\n", @@ -984,12 +1026,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned int -scaleswt.c:1230:67: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 1230 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate rs_s: %ld\n",__FILE__, __LINE__,sizeof(struct pstat_str)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 scaleswn.c -o scale_sn.o dropff2.c: In function 'do_walign': dropff2.c:1176:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 1176 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate a_res [%lu]", @@ -1001,7 +1038,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned int -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 scaleswn.c -o scale_sn.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 -Wformat -Werror=format-security -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 -DGLSEARCH initfa.c -o init_lnw_sse.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 droplnw_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 -Wformat -Werror=format-security -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 glocal_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 -Wformat -Werror=format-security -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 -DGGSEARCH -c wm_align.c -o gwm_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 -Wformat -Werror=format-security -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 -DGGSEARCH initfa.c -o init_gnw_sse.o dropff2.c: In function 'init_work': dropff2.c:120:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 120 | fprintf(stderr, "*** ERROR [%s:%d] - cannot calloc f_str [%lu]\n", @@ -1013,6 +1054,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned int +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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 dropff2.c: In function 'do_walign': dropff2.c:1176:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] 1176 | fprintf(stderr,"*** ERROR [%s:%d] - cannot allocate a_res [%lu]", @@ -1025,7 +1068,6 @@ | | | unsigned int initfa.c: In function 'alloc_pam2p': -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 -Wformat -Werror=format-security -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 -DGLSEARCH initfa.c -o init_lnw_sse.o initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ @@ -1040,22 +1082,10 @@ | | unsigned int | long int | %d -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -Wformat -Werror=format-security -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 droplnw_sse.o -initfa.c: In function 'alloc_pam2p': -initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] - 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d -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 -Wformat -Werror=format-security -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 glocal_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 -Wformat -Werror=format-security -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 -DGGSEARCH -c wm_align.c -o gwm_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 -Wformat -Werror=format-security -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 -DGGSEARCH initfa.c -o init_gnw_sse.o -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 initfa.c: In function 'alloc_pam2p': initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); @@ -1063,11 +1093,12 @@ | | | | long int unsigned int | %d -cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2_sse.o smith_waterman_sse2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm +cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread map_db.c: In function 'main': map_db.c:149:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | fgets(lname,sizeof(lname),stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 map_db.c: In function 'gbf_get_ent': map_db.c:512:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 512 | fgets(lline,MAXLINE,libf); @@ -1076,16 +1107,18 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -glocal_sse2.c: In function 'max_epu16': -glocal_sse2.c:33:1: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 33 | { - | ^ -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 -global_sse2.c: In function 'max_epu16': -global_sse2.c:34:1: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 34 | { - | ^ -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 +initfa.c: In function 'alloc_pam2p': +initfa.c:2001:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] + 2001 | "*** Warning [%s:%d] - Cannot reallocate pam2p[0]: %ld\n", __FILE__, __LINE__, (nsq+1)*len*sizeof(int)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d +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/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/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 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); | ^ @@ -1102,6 +1135,13 @@ | ^ 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, | ^ @@ -1117,6 +1157,7 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +cc -o ../bin/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); | ^ @@ -1155,6 +1196,10 @@ 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 +glocal_sse2.c: In function 'max_epu16': +glocal_sse2.c:33:1: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 33 | { + | ^ 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); | ^ @@ -1171,13 +1216,6 @@ | ^ 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, | ^ @@ -1193,15 +1231,6 @@ 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/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/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/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 -lto-wrapper: warning: using serial compilation of 6 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1218,15 +1247,14 @@ | ^ 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, - | ^ -lto-wrapper: warning: using serial compilation of 6 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -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, | ^ @@ -1242,8 +1270,9 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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); +global_sse2.c: In function 'max_epu16': +global_sse2.c:34:1: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 34 | { | ^ 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); @@ -1253,14 +1282,6 @@ | ^ 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); | ^ @@ -1269,22 +1290,13 @@ | ^ 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 2 - 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, - | ^ 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, | ^ -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 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, | ^ @@ -1296,14 +1308,33 @@ 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, | ^ -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 +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 2 + 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: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, | ^ @@ -1395,6 +1426,7 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread 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); | ^ @@ -1473,7 +1505,9 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread +lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +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); | ^ @@ -1520,97 +1554,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -lto-wrapper: warning: using serial compilation of 5 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -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 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 -initfa.c: In function 'get_lambda.constprop': -initfa.c: In function 'get_lambda.constprop': -initfa.c:2225:54: warning: argument 1 value '3294967297' exceeds maximum object size 2147483647 [-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:2225:54: warning: argument 1 value '3294967297' exceeds maximum object size 2147483647 [-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) - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1650,40 +1593,8 @@ 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 -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ -lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information -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 -url_subs.c: In function 'showalign.isra': -url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); - | ^ -In function 'do_url1', - inlined from 'do_show' at mshowalign2.c:867:7, - inlined from 'showalign.isra' at mshowalign2.c:764:7: -url_subs.c:219:37: note: length computed here - 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; - | ^ 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); | ^ @@ -1700,13 +1611,17 @@ | ^ 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 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information 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, | ^ +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs 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 +lto-wrapper: note: see the '-flto' option documentation for more information 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, @@ -1723,9 +1638,20 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread lto-wrapper: warning: using serial compilation of 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 6 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +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 +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 5 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1764,6 +1690,12 @@ 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 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information +lto-wrapper: warning: using serial compilation of 4 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1802,6 +1734,31 @@ 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 6 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:2225:54: warning: argument 1 value '3294967297' exceeds maximum object size 2147483647 [-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 '3294967297' exceeds maximum object size 2147483647 [-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 '3294967297' exceeds maximum object size 2147483647 [-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) + | ^ url_subs.c: In function 'showalign.isra': url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); @@ -1812,10 +1769,6 @@ url_subs.c:219:37: note: length computed here 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; | ^ -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 6 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information url_subs.c: In function 'showalign.isra': url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); @@ -1826,13 +1779,20 @@ url_subs.c:219:37: note: length computed here 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; | ^ -initfa.c: In function 'get_lambda.constprop': -initfa.c:2225:54: warning: argument 1 value '3294967297' exceeds maximum object size 2147483647 [-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) - | ^ +glocal_sse2.c: In function 'max_epu16': +glocal_sse2.c:188:10: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 188 | vF = max_epu16 (vF, vTemp); + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ initfa.c: In function 'get_lambda.constprop': initfa.c:2225:54: warning: argument 1 value '3294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2225 | if (max > 1023 || min < -1024 || ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL)) { @@ -1860,10 +1820,26 @@ url_subs.c:219:37: note: length computed here 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; | ^ -glocal_sse2.c: In function 'max_epu16': -glocal_sse2.c:188:10: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 188 | vF = max_epu16 (vF, vTemp); - | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ global_sse2.c: In function 'max_epu16': global_sse2.c:177:10: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 177 | vF = max_epu16 (vF, vTemp); @@ -1888,6 +1864,66 @@ url_subs.c:219:37: note: length computed here 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ +url_subs.c: In function 'showalign.isra': +url_subs.c:229:25: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 229 | if (q_domain_s) SAFE_STRNCAT(tmp_domain_s, q_domain_s, n_tmp_domain); + | ^ +In function 'do_url1', + inlined from 'do_show' at mshowalign2.c:867:7, + inlined from 'showalign.isra' at mshowalign2.c:764:7: +url_subs.c:219:37: note: length computed here + 219 | if (q_domain_s) n_tmp_domain += strlen(q_domain_s)+1; + | ^ make[2]: Leaving directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/src' # convoluted, but necessary to allow cross builds make[1]: Leaving directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020' @@ -1895,21 +1931,21 @@ 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 Wed Dec 4 01:10:21 2024 on ionos2-i386 -Linux ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux +STARTING FASTA36 Tue Jan 6 07:39:58 2026 on i-capture-the-hostname +Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Wed Dec 4 01:10:21 2024 +starting prss36(ssearch/fastx) Tue Jan 6 07:39:58 2026 done -starting lalign36 Wed Dec 4 01:10:21 2024 -FINISHED Wed Dec 4 01:13:03 2024 +starting lalign36 Tue Jan 6 07:39:59 2026 +FINISHED Tue Jan 6 07:41:50 2026 -STARTING FASTA36 Wed Dec 4 01:13:03 2024 on ionos2-i386 -Linux ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux +STARTING FASTA36 Tue Jan 6 07:41:50 2026 on i-capture-the-hostname +Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Wed Dec 4 01:13:03 2024 +starting prss36(ssearch/fastx) Tue Jan 6 07:41:50 2026 done -starting lalign36 Wed Dec 4 01:13:04 2024 -FINISHED Wed Dec 4 01:15:50 2024 +starting lalign36 Tue Jan 6 07:41:50 2026 +FINISHED Tue Jan 6 07:43:38 2026 # ../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 @@ -1921,29 +1957,28 @@ Library: ../seq/prot_test.lseg 2267 residues in 12 sequences -Statistics: (shuffled [240]) MLE statistics: Lambda= 0.1194; K=0.001609 - statistics sampled from 4 (4) to 240 sequences +Statistics: (shuffled [133]) MLE statistics: Lambda= 0.1355; K=0.00801 + statistics sampled from 4 (4) to 133 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: 0.040 The best scores are: opt bits E(12) -sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 224.9 1.1e-62 -sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 51.9 1.4e-10 -sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 19.8 0.39 -sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.3 2.1 -sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 18.5 2.3 -sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.4 2.8 -sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.2 3.1 -sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.9 3.9 -sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.5 4.2 -sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.2 4.4 -sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.0 6 -sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 17.4 6 +sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 251.7 9.5e-71 +sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 55.2 1.4e-11 +sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 18.8 0.76 +sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 17.3 4.6 +sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 15.9 4.6 +sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 14.9 6.3 +sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 14.7 6.8 +sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 13.2 8.6 +sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 14.7 8.6 +sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 14.0 8.7 +sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 16.1 9.9 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) - initn: 1242 init1: 1242 opt: 1242 Z-score: 1177.2 bits: 224.9 E(12): 1.1e-62 + initn: 1242 init1: 1242 opt: 1242 Z-score: 1322.0 bits: 251.7 E(12): 9.5e-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 @@ -1971,7 +2006,7 @@ 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) - initn: 204 init1: 73 opt: 237 Z-score: 241.8 bits: 51.9 E(12): 1.4e-10 + initn: 204 init1: 73 opt: 237 Z-score: 259.8 bits: 55.2 E(12): 1.4e-11 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 @@ -1999,7 +2034,7 @@ 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: 72.2 bits: 19.8 E(12): 0.39 + initn: 40 init1: 40 opt: 51 Z-score: 66.7 bits: 18.8 E(12): 0.76 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 @@ -2014,24 +2049,8 @@ 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: 58.4 bits: 17.3 E(12): 2.1 -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: 57.7 bits: 18.5 E(12): 2.3 + initn: 43 init1: 43 opt: 43 Z-score: 51.2 bits: 17.3 E(12): 4.6 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 @@ -2049,8 +2068,24 @@ sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 320 330 340 350 +>>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) + initn: 56 init1: 36 opt: 36 Z-score: 51.1 bits: 15.9 E(12): 4.6 +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: 55.7 bits: 16.4 E(12): 2.8 + initn: 31 init1: 31 opt: 31 Z-score: 47.7 bits: 14.9 E(12): 6.3 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 @@ -2066,7 +2101,7 @@ 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: 55.0 bits: 16.2 E(12): 3.1 + initn: 30 init1: 30 opt: 30 Z-score: 46.9 bits: 14.7 E(12): 6.8 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 @@ -2085,7 +2120,7 @@ sp|P10 SNK >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) - initn: 22 init1: 22 opt: 22 Z-score: 52.7 bits: 14.9 E(12): 3.9 + initn: 22 init1: 22 opt: 22 Z-score: 43.6 bits: 13.2 E(12): 8.6 Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 150 160 170 180 190 200 @@ -2100,21 +2135,8 @@ sp|P00 CPVGAPNPED 50 ->>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) - initn: 26 init1: 26 opt: 26 Z-score: 52.0 bits: 15.5 E(12): 4.2 -Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) - - 90 100 110 120 130 140 -sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK - : :: ::.: -sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG - 60 70 80 90 - - 150 160 170 180 190 200 -sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI - >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) - initn: 30 init1: 30 opt: 30 Z-score: 51.7 bits: 16.2 E(12): 4.4 + initn: 30 init1: 30 opt: 30 Z-score: 43.6 bits: 14.7 E(12): 8.6 Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 20 30 40 50 60 70 @@ -2129,30 +2151,21 @@ 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: 48.4 bits: 15.0 E(12): 6 -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 +>>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) + initn: 26 init1: 26 opt: 26 Z-score: 43.5 bits: 14.0 E(12): 8.7 +Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) + + 90 100 110 120 130 140 +sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK + : :: ::.: +sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG + 60 70 80 90 - 150 160 170 180 190 200 -sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY - -sp|P01 NRGEC - + 150 160 170 180 190 200 +sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) - initn: 37 init1: 37 opt: 37 Z-score: 48.3 bits: 17.4 E(12): 6 + initn: 37 init1: 37 opt: 37 Z-score: 41.2 bits: 16.1 E(12): 9.9 Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 50 60 70 80 90 100 @@ -2171,9 +2184,9 @@ 218 residues in 1 query sequences 2267 residues in 12 library sequences - Tcomplib [36.3.8i Nov, 2022] (64 proc in memory [0G]) - start: Wed Dec 4 01:15:50 2024 done: Wed Dec 4 01:15:50 2024 - Total Scan time: 0.000 Total Display time: 0.020 + Tcomplib [36.3.8i Nov, 2022] (128 proc in memory [0G]) + start: Tue Jan 6 07:43:38 2026 done: Tue Jan 6 07:43:38 2026 + Total Scan time: 0.040 Total Display time: 0.000 Function used was FASTA [36.3.8i Nov, 2022] rm -rf test/results/test* @@ -2205,9 +2218,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -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_i386.deb'. dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8i.14-Nov-2020-3_i386.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_i386.buildinfo dpkg-genchanges --build=binary -O../fasta3_36.3.8i.14-Nov-2020-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2215,12 +2228,14 @@ 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/124086/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/124086/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/48341 and its subdirectories -I: Current time: Tue Dec 3 13:16:08 -12 2024 -I: pbuilder-time-stamp: 1733274968 +I: removing directory /srv/workspace/pbuilder/124086 and its subdirectories +I: Current time: Tue Jan 6 21:43:48 +14 2026 +I: pbuilder-time-stamp: 1767685428