I: pbuilder: network access will be disabled during build I: Current time: Mon May 13 16:08:18 +14 2024 I: pbuilder-time-stamp: 1715566098 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mafft_7.505-1.dsc] I: copying [./mafft_7.505.orig.tar.gz] I: copying [./mafft_7.505-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jun 25 19:18:48 2022 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mafft_7.505-1.dsc: no acceptable signature found dpkg-source: info: extracting mafft in mafft-7.505 dpkg-source: info: unpacking mafft_7.505.orig.tar.gz dpkg-source: info: unpacking mafft_7.505-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1885553/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 13 02:08 /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/1885553/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1885553/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=e9565940d77c4c1995ffe9f437c76774 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=1885553 PS4='+ ' 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.lok45NUv/pbuilderrc_Fiv3 --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.lok45NUv/b2 --logfile b2/build.log mafft_7.505-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1885553/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After unpacking 75.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Fetched 18.7 MB in 0s (112 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 ... 19744 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1885553/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1885553/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mafft-7.505/ && 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 > ../mafft_7.505-1_source.changes dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.505-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core cd core && make -j12 clean make[1]: Entering directory '/build/reproducible-path/mafft-7.505/core' rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno make[1]: Leaving directory '/build/reproducible-path/mafft-7.505/core' dh_autoreconf_clean -O--sourcedirectory=core debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/mafft-7.505' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory '/build/reproducible-path/mafft-7.505' debian/rules binary dh binary --sourcedirectory=core dh_update_autotools_config -O--sourcedirectory=core dh_autoreconf -O--sourcedirectory=core dh_auto_configure -O--sourcedirectory=core debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/mafft-7.505' dh_auto_build -- \ PREFIX=/usr/lib/mafft \ ENABLE_MULTITHREAD=-Denablemultithread \ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd core && make -j12 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/mafft-7.505/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c io.c: In function 'PreRead': io.c:1120:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1120 | fgets( b, B-1, fp ); *locnjob = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c:1125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1125 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1129:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1129 | fgets( b, B-1, fp ); nleni = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'FRead': io.c:1165:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1165 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1255:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1255 | fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ | ^~~~~~~~~~~~~~~~~~~ rna.c: In function 'rnaalifoldcall': rna.c:225:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | system( cmd ); | ^~~~~~~~~~~~~ rna.c:245:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 245 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 285 | system( cmd ); | ^~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_part_pointer': io.c:2707:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2707 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2709:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2709 | fgets( b, B, fp ); nseq0 = atoi( b ); // 2020/Oct/23 | ^~~~~~~~~~~~~~~~~ io.c:2715:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2715 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_pointer': io.c:2745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2745 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2746:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2746 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) | ^~~~~~~~~~~~~~~~~ io.c:2751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2751 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf': io.c:2779:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2779 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2780 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2781:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2781 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_double': io.c:2809:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2809 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2810:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2810 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2811 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_int': io.c:2839:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2839 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2840 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2841:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2841 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_pointer': io.c:2870:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2870 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2871:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2871 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2872:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2872 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2': io.c:2900:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2900 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2901:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2901 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2902:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2902 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta_sub': io.c:3102:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3102 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3117:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3117 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadSsearch': io.c:3136:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3136 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_avscore': io.c:3264:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3264 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3271:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3271 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3272:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3272 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_scoreonly': io.c:3387:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3387 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3394:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3394 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3395:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3395 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7': io.c:3505:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3505 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3512:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3512 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3513:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3513 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34noalign': io.c:3537:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3537 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_nuc': io.c:3574:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3574 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3600:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3600 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10': io.c:3713:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3713 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3737:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3737 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nucbk': io.c:3840:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3840 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nuc': io.c:3890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3890 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly': io.c:3951:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3951 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34': io.c:4007:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4007 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:4033:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4033 | fgets( b, B-1, fp ); // initn: | ^~~~~~~~~~~~~~~~~~~ io.c:4036:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4036 | fgets( b, B-1, fp ); // Smith-Waterman score | ^~~~~~~~~~~~~~~~~~~ io.c:4048:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4048 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta3': io.c:4070:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4070 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta': io.c:4095:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4095 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt': io.c:4132:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4132 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt2': io.c:4153:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4153 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readOtherOptions': io.c:4249:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4249 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'check_guidetreefile': mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2850 | fgets( string, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'loadaamtx': io.c:5507:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5507 | fgets( inorder, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5539:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5539 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5562:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5562 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readsubalignmentstable': io.c:5718:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5718 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5739:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5739 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readmccaskill': io.c:5793:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5793 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5803:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5803 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readpairfoldalign': io.c:5862:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5862 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5875:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5875 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5882:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5882 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5896:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5896 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5902:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5902 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readexternalanchors': io.c:6340:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 6340 | fgets( buf, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from constants.c:7: blosum.c: In function 'overridematrix': blosum.c:370:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 370 | fgets( buf, 499, fp ); | ^~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': mltaln9.c:15685:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15685 | fread( &size, sizeof( int ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15686:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15686 | fread( &opt, sizeof( double ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15689:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15689 | fread( m, size*sizeof( int ), 3, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15725:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15725 | fread( &c, sizeof( char ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'check_guidetreefile': mltaln9.c:2850:9: warning: 'fgets' writing 999 bytes into a region of size 100 overflows the destination [-Wstringop-overflow=] 2850 | fgets( string, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:2834:14: note: destination object 'string' of size 100 2834 | char string[100]; | ^~~~~~ In file included from /usr/include/stdio.h:964, from mltaln.h:12, from mltaln9.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:195:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 195 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o dvtditr.c: In function 'main': dvtditr.c:1020:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1020 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c mltaln9.c: In function 'createchain': mltaln9.c:2113:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2113 | instanttree = calloc( treelen, sizeof( char ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mltaln.h:13: /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) | ^~~~~~ mltaln9.c:2124:17: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2124 | order = calloc( nseq, sizeof( int ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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) | ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c In function 'fgets', inlined from 'check_guidetreefile' at mltaln9.c:2850:2: /usr/include/aarch64-linux-gnu/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 201 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dndfast7.c: In function 'main': dndfast7.c:326:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c dndblast.c: In function 'main': dndblast.c:201:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | system( com ); | ^~~~~~~~~~~~~ dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c pairlocalalign.c: In function 'calllast_once': pairlocalalign.c:1056:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1056 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1092:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1092 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx': pairlocalalign.c:608:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 608 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calllast_fast': pairlocalalign.c:981:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 981 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'lastcallthread': pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 872 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx_singleq': pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 374 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readhat4': pairlocalalign.c:1532:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1532 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1544:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1544 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'recalllara': pairlocalalign.c:1245:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1245 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'callmxscarna_giving_bpp': pairlocalalign.c:1408:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1408 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1410:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1410 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1430:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1430 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1451:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1451 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1465:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1465 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1485:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1485 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1487:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1487 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calldafs_giving_bpp': pairlocalalign.c:1291:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1291 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1293:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1293 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1313:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1313 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1334:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1334 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1344:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1344 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1364:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1364 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1366:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1366 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1368:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1368 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'pairalign_node': pairlocalalign.c:3467:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3467 | system( "rm -rf hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3468:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3468 | system( "mkdir hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3473:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3473 | system( fn ); | ^~~~~~~~~~~~ pairash.c: In function 'prepareash': pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 639 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 681 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash': pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 485 | system( com ); | ^~~~~~~~~~~~~ pairash.c: In function 'readrash': pairash.c:277:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 294 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'preparetmalign': pairash.c:530:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 576 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 587 | system( command ); | ^~~~~~~~~~~~~~~~~ pairash.c: In function 'checkcbeta': pairash.c:321:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 321 | fgets( linec, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'calltmalign': pairash.c:347:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | system( com ); | ^~~~~~~~~~~~~ pairash.c:356:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 356 | fgets( com, 100, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'readtmalign': pairash.c:228:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 228 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 238 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c maffttext2hex.c: In function 'main': maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets( (char *)buf, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash.isra': pairash.c:428:43: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 428 | sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); | ^ In file included from /usr/include/stdio.h:964, from mltaln.h:12, from pairash.c:1: In function 'sprintf', inlined from 'callrash.isra' at pairash.c:428:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash.isra': pairash.c:484:36: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=] 484 | sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); | ^~ ~~~~~~~~~ In function 'sprintf', inlined from 'callrash.isra' at pairash.c:484:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ splittbfast.c: In function 'main': splittbfast.c:3218:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3218 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c pairash.c: In function 'calltmalign.isra': pairash.c:346:41: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] 346 | sprintf( com, "mkdir -p %s", cachedir ); | ^~ ~~~~~~~~ In function 'sprintf', inlined from 'calltmalign.isra' at pairash.c:346:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pairash.c: In function 'calltmalign.isra': pairash.c:349:45: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 349 | sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); | ^ In function 'sprintf', inlined from 'calltmalign.isra' at pairash.c:349:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave': mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 6494 | int *mem = calloc( sizeof( int ), nseq ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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) | ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c disttbfast.c: In function 'disttbfast': disttbfast.c:4583:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 4583 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c tbfast.c: In function 'main': tbfast.c:3254:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3254 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f2cl.c: In function 'main': f2cl.c:287:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 287 | fgets( gett, B-1, orderfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function 'main': mccaskillwrap.c:372:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 372 | system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function 'athread': mccaskillwrap.c:115:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:117:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 117 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:129:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ mccaskillwrap.c:155:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c: In function 'readrawmccaskill': mccaskillwrap.c:46:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 46 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c contrafoldwrap.c: In function 'readcontrafold': contrafoldwrap.c:57:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c regtable2seq.c: In function 'readereg': regtable2seq.c:69:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c regtable2seq.c: In function 'readreg': regtable2seq.c:120:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft setdirection.c: In function 'main': setdirection.c:132:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 132 | fgets( line, 99, difp ); | ^~~~~~~~~~~~~~~~~~~~~~~ restoreu.c: In function 'main': restoreu.c:185:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fgets( gett, 999, dlfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. make[2]: Leaving directory '/build/reproducible-path/mafft-7.505/core' make[1]: Leaving directory '/build/reproducible-path/mafft-7.505' dh_auto_test -O--sourcedirectory=core create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=core dh_prep -O--sourcedirectory=core debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/mafft-7.505' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft cd core && make -j12 install DESTDIR=/build/reproducible-path/mafft-7.505/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft make[2]: Entering directory '/build/reproducible-path/mafft-7.505/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. mkdir -p /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/bin chmod 755 /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/bin chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb install --strip-program=true mafft mafft-homologs.rb mafft-sparsecore.rb /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/bin install: WARNING: ignoring --strip-program option as -s option was not specified chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ||: # in MinGW, it's ok if this fails strip dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ||: # may fail for dash_client on mac. install --strip-program=true dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified ( cd /build/reproducible-path/mafft-7.505/debian/mafft/usr/lib/mafft/bin; \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-distance . ) mkdir -p /build/reproducible-path/mafft-7.505/debian/mafft/usr/share/man/man1 chmod 755 /build/reproducible-path/mafft-7.505/debian/mafft/usr/share/man/man1 install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/reproducible-path/mafft-7.505/debian/mafft/usr/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/reproducible-path/mafft-7.505/core' rm debian/mafft/usr/lib/mafft/lib/mafft/*.1 make[1]: Leaving directory '/build/reproducible-path/mafft-7.505' dh_installdocs -O--sourcedirectory=core dh_installchangelogs -O--sourcedirectory=core dh_installman -O--sourcedirectory=core dh_installsystemduser -O--sourcedirectory=core dh_perl -O--sourcedirectory=core dh_link -O--sourcedirectory=core dh_strip_nondeterminism -O--sourcedirectory=core debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/mafft-7.505' dh_compress -X test/sample make[1]: Leaving directory '/build/reproducible-path/mafft-7.505' dh_fixperms -O--sourcedirectory=core dh_missing -O--sourcedirectory=core dh_dwz -a -O--sourcedirectory=core dwz: debian/mafft/usr/lib/mafft/lib/mafft/addsingle: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/contrafoldwrap: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/countlen: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/disttbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndblast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndfast7: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndpre: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dvtditr: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/f2cl: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/filter: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/getlag: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/hex2maffttext: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/maffttext2hex: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/makedirectionlist: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mccaskillwrap: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/multi2hat3s: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/nodepair: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairash: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairlocalalign: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/regtable2seq: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/replaceu: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/restoreu: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/score: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/seq2regtable: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/setcore: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/setdirection: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/sextet5: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/splittbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/tbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/version: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a -O--sourcedirectory=core dh_makeshlibs -a -O--sourcedirectory=core dh_shlibdeps -a -O--sourcedirectory=core dh_installdeb -O--sourcedirectory=core dh_gencontrol -O--sourcedirectory=core dh_md5sums -O--sourcedirectory=core dh_builddeb -O--sourcedirectory=core dpkg-deb: building package 'mafft' in '../mafft_7.505-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../mafft_7.505-1_arm64.buildinfo dpkg-genchanges --build=binary -O../mafft_7.505-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1885553/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1885553/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/1885553 and its subdirectories I: Current time: Mon May 13 16:08:54 +14 2024 I: pbuilder-time-stamp: 1715566134