I: pbuilder: network access will be disabled during build I: Current time: Sat May 1 23:43:04 -12 2021 I: pbuilder-time-stamp: 1619955784 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [mafft_7.407-2.dsc] I: copying [./mafft_7.407.orig.tar.gz] I: copying [./mafft_7.407-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 1 22:43:32 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mafft_7.407-2.dsc dpkg-source: info: extracting mafft in mafft-7.407 dpkg-source: info: unpacking mafft_7.407.orig.tar.gz dpkg-source: info: unpacking mafft_7.407-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_bashism.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 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 (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 70.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Fetched 19.4 MB in 0s (71.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6_i386.deb ... Unpacking libicu63:i386 (63.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/mafft-7.407/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.407-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core cd core && make -j18 clean make[1]: Entering directory '/build/mafft-7.407/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 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/mafft-7.407/core' dh_autoreconf_clean -O--sourcedirectory=core debian/rules override_dh_clean make[1]: Entering directory '/build/mafft-7.407' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory '/build/mafft-7.407' debian/rules build dh build --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/mafft-7.407' dh_auto_build -- \ PREFIX=/usr/lib/mafft \ ENABLE_MULTITHREAD=-Denablemultithread \ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd core && make -j18 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/mafft-7.407/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mltaln9.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from io.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from nj.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from tddis.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from constants.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from partSalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from rna.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Lalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Salignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Dalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Galign11.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Falign_localhom.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Lalign11.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Falign.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from genalign11.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from MSalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ rna.c: In function 'rnaalifoldcall': rna.c:225:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( cmd ); ^~~~~~~~~~~~~ rna.c:245:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( cmd ); ^~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from fftFunctions.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ io.c: In function 'PreRead': io.c:1065:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); *locnjob = atoi( b ); ^~~~~~~~~~~~~~~~~~~ io.c:1070:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:1074:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); nleni = atoi( b ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'FRead': io.c:1110:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:1200:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_part_pointer': io.c:2635:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2636:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ^~~~~~~~~~~~~~~~~ io.c:2641:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_pointer': io.c:2671:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2672:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ^~~~~~~~~~~~~~~~~ io.c:2677:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf': io.c:2705:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2706:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2707:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_double': io.c:2735:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2736:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2737:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_int': io.c:2765:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2766:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2767:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_pointer': io.c:2796:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2797:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2798:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2': io.c:2826:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2827:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2828:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta_sub': io.c:3028:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3043:13: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadSsearch': io.c:3062:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_avscore': io.c:3190:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3197:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3198:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_scoreonly': io.c:3313:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3320:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3321:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7': io.c:3431:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3438:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3439:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34noalign': io.c:3463:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_nuc': io.c:3500:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3526:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10': io.c:3639:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3663:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nucbk': io.c:3766:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nuc': io.c:3816:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly': io.c:3877:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34': io.c:3933:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3959:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); // initn: ^~~~~~~~~~~~~~~~~~~ io.c:3962:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); // Smith-Waterman score ^~~~~~~~~~~~~~~~~~~ io.c:3974:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta3': io.c:3996:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta': io.c:4021:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt': io.c:4058:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt2': io.c:4079:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readOtherOptions': io.c:4175:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'check_guidetreefile': mltaln9.c:2802:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( string, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'loadaamtx': io.c:5431:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( inorder, 999, mf ); ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5463:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, mf ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5485:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, mf ); ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readsubalignmentstable': io.c:5631:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, linelen-1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5652:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, linelen-1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readmccaskill': io.c:5706:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5716:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readpairfoldalign': io.c:5775:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5788:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5795:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5809:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5815:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ In file included from constants.c:7: blosum.c: In function 'overridematrix': blosum.c:342:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( buf, 499, fp ); ^~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': mltaln9.c:15152:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &size, sizeof( int ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15153:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &opt, sizeof( double ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15156:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( m, size*sizeof( int ), 3, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15192:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &c, sizeof( char ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from fft.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dvtditr.c:4: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from tditeration.c:9: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from defs.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ dvtditr.c: In function 'main': dvtditr.c:1020:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "cp infile.tree GuideTree" ); // tekitou ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from SAalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from treeOperation.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from addfunctions.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dndfast7.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dndblast.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from sextet5.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ dndfast7.c: In function 'main': dndfast7.c:328:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ dndblast.c: In function 'main': dndblast.c:203:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ dndblast.c:384:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mafft-distance.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from MSalign11.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from suboptalign11.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from pairlocalalignmain.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from pairlocalalign.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from multi2hat3s.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from pairash.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from addsingle.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread pairlocalalign.c: In function 'calllast_once': pairlocalalign.c:1055:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1091:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx': pairlocalalign.c:607:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calllast_fast': pairlocalalign.c:980:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'lastcallthread': pairlocalalign.c:871:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx_singleq': pairlocalalign.c:373:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readhat4': pairlocalalign.c:1531:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( oneline, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1543:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( oneline, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'recalllara': pairlocalalign.c:1244:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'callmxscarna_giving_bpp': pairlocalalign.c:1407:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1409:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1429:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1450:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1464:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1484:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1486:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calldafs_giving_bpp': pairlocalalign.c:1290:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1292:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1312:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1333:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1343:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1363:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1365:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1367:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'pairalign_node': pairlocalalign.c:3438:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "rm -rf hat3dir" ); // toriaezu ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3439:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "mkdir hat3dir" ); // toriaezu ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3444:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( fn ); ^~~~~~~~~~~~ maffttext2hex.c: In function 'main': maffttext2hex.c:55:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( (char *)buf, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'prepareash': pairash.c:639:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash': pairash.c:485:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairash.c: In function 'readrash': pairash.c:277:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'preparetmalign': pairash.c:530:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairash.c: In function 'checkcbeta': pairash.c:321:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( linec, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'calltmalign': pairash.c:347:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairash.c:356:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 100, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'readtmalign': pairash.c:228:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c pairash.c: In function 'callrash.isra.1': pairash.c:428:29: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); ^ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:484:22: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=] sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from splittbfast.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from disttbfast.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from tbfast.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from nodepair.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ pairash.c: In function 'calltmalign.isra.2': pairash.c:346:27: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] sprintf( com, "mkdir -p %s", cachedir ); ^~ ~~~~~~~~ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:349:31: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); ^ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mafft-profile.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ disttbfast.c: In function 'disttbfast': disttbfast.c:3638:6: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "cp infile.tree GuideTree" ); // tekitou ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tbfast.c: In function 'main': tbfast.c:3181:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "cp infile.tree GuideTree" ); // tekitou ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ splittbfast.c: In function 'main': splittbfast.c:3218:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from f2cl.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ pairash.c: In function 'preparetmalign.constprop': pairash.c:586:29: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf( command, "cp %s %s.pdb", sline, fname ); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 9 or more bytes (assuming 1008) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:588:44: warning: '%s' directive writing up to 999 bytes into a region of size 983 [-Wformat-overflow=] sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname ); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 22 or more bytes (assuming 1021) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mccaskillwrap.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ f2cl.c: In function 'main': f2cl.c:283:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, B-1, orderfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function 'main': mccaskillwrap.c:372:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function 'athread': mccaskillwrap.c:115:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mccaskillwrap.c:117:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mccaskillwrap.c:129:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ mccaskillwrap.c:155:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mccaskillwrap.c: In function 'readrawmccaskill': mccaskillwrap.c:46:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from contrafoldwrap.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c contrafoldwrap.c: In function 'readcontrafold': contrafoldwrap.c:57:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from countlen.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c mltaln9.c: In function 'createchain': mltaln9.c:2065:17: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] instanttree = calloc( treelen, sizeof( char ) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mltaln.h:14, from mltaln9.c:1: /usr/include/stdlib.h:541:14: note: in a call to allocation function 'calloc' declared here extern void *calloc (size_t __nmemb, size_t __size) ^~~~~~ mltaln9.c:2076:10: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] order = calloc( nseq, sizeof( int ) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mltaln.h:14, from mltaln9.c:1: /usr/include/stdlib.h:541:14: note: in a call to allocation function 'calloc' declared here extern void *calloc (size_t __nmemb, size_t __size) ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from seq2regtable.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from regtable2seq.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from score.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from getlag.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ regtable2seq.c: In function 'readereg': regtable2seq.c:69:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, regfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, regfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c: In function 'readreg': regtable2seq.c:120:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, regfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dndpre.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from setcore.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from restoreu.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from replaceu.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/stdio.h:873, from mltaln.h:13, from mltaln9.c:1: In function 'fgets', inlined from 'check_guidetreefile' at mltaln9.c:2802:2: /usr/include/i386-linux-gnu/bits/stdio2.h:263:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from setdirection.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from makedirectionlist.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ restoreu.c: In function 'main': restoreu.c:177:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, dlfp ); ^~~~~~~~~~~~~~~~~~~~~~~~ setdirection.c: In function 'main': setdirection.c:132:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 99, difp ); ^~~~~~~~~~~~~~~~~~~~~~~ gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread In file included from /usr/include/i386-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from version.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft 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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -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 replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. make[2]: Leaving directory '/build/mafft-7.407/core' make[1]: Leaving directory '/build/mafft-7.407' dh_auto_test -O--sourcedirectory=core create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=core dh_testroot -O--sourcedirectory=core dh_prep -O--sourcedirectory=core debian/rules override_dh_auto_install make[1]: Entering directory '/build/mafft-7.407' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft cd core && make -j18 install DESTDIR=/build/mafft-7.407/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/mafft-7.407/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 replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. mkdir -p /build/mafft-7.407/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /build/mafft-7.407/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /build/mafft-7.407/debian/mafft/usr/lib/mafft/bin chmod 755 /build/mafft-7.407/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/mafft-7.407/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 replaceu restoreu setdirection makedirectionlist version ||: # in MinGW, it's ok if this fails install --strip-program=true -s 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 replaceu restoreu setdirection makedirectionlist version /build/mafft-7.407/debian/mafft/usr/lib/mafft/lib/mafft install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /build/mafft-7.407/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/mafft-7.407/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified ( cd /build/mafft-7.407/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/mafft-7.407/debian/mafft/usr/share/man/man1 chmod 755 /build/mafft-7.407/debian/mafft/usr/share/man/man1 install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/mafft-7.407/debian/mafft/usr/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/mafft-7.407/core' rm debian/mafft/usr/lib/mafft/lib/mafft/*.1 make[1]: Leaving directory '/build/mafft-7.407' dh_installdocs -O--sourcedirectory=core dh_installchangelogs -O--sourcedirectory=core dh_installman -O--sourcedirectory=core dh_installinit -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/mafft-7.407' dh_compress -X test/sample make[1]: Leaving directory '/build/mafft-7.407' dh_fixperms -O--sourcedirectory=core dh_missing -O--sourcedirectory=core dh_strip -O--sourcedirectory=core dh_makeshlibs -O--sourcedirectory=core dh_shlibdeps -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-dbgsym' in '../mafft-dbgsym_7.407-2_i386.deb'. dpkg-deb: building package 'mafft' in '../mafft_7.407-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mafft_7.407-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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/51925 and its subdirectories I: Current time: Sat May 1 23:43:34 -12 2021 I: pbuilder-time-stamp: 1619955814