I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 9 20:52:45 -12 2020 I: pbuilder-time-stamp: 1599727965 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: Copying source file I: copying [t-coffee_12.00.7fb08c2-4.dsc] I: copying [./t-coffee_12.00.7fb08c2.orig.tar.gz] I: copying [./t-coffee_12.00.7fb08c2-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 14 18:47:23 2019 -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 ./t-coffee_12.00.7fb08c2-4.dsc dpkg-source: info: extracting t-coffee in t-coffee-12.00.7fb08c2 dpkg-source: info: unpacking t-coffee_12.00.7fb08c2.orig.tar.gz dpkg-source: info: unpacking t-coffee_12.00.7fb08c2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying ncbi-blast++_has_dropped_pl_extension.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying stable-linking-inputs.patch dpkg-source: info: applying clustalw2.patch dpkg-source: info: applying fix_tempfile_name_sharing.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31654/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='31654' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.fTbvcfKFoP/pbuilderrc_UeU4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.fTbvcfKFoP/b1 --logfile b1/build.log t-coffee_12.00.7fb08c2-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled10-arm64 4.4.0-189-generic #219-Ubuntu SMP Tue Aug 11 12:24:40 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 30 20:25 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/31654/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 (>= 12~); 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 18.6 MB of archives. After unpacking 69.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Fetched 18.6 MB in 1s (17.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.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_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.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_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.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:arm64. Preparing to unpack .../22-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../27-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_arm64.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:arm64 (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:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:arm64 (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:arm64 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (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:arm64 (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/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/t-coffee-12.00.7fb08c2' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/build/t-coffee-12.00.7fb08c2' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules build dh build --sourcedirectory=t_coffee_source dh_update_autotools_config -O--sourcedirectory=t_coffee_source dh_autoreconf -O--sourcedirectory=t_coffee_source dh_auto_configure -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/build/t-coffee-12.00.7fb08c2' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" 'CC=$(CXX)' all cd t_coffee_source && make -j8 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/build/t-coffee-12.00.7fb08c2/t_coffee_source' CC dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate.c CC dp_lib/evaluate_dirichlet.c CC dp_lib/evaluate_for_domain.c CC dp_lib/evaluate_for_struc.c CC dp_lib/fsa_dp.c CC dp_lib/pavie_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_struc.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/fsa_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_dirichlet.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_domain.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dev_lib/dev1.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/pavie_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f\n", &f); ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/showpair.c dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c: In function 'Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)': dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", mat); ~~~~~~~^~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/showpair.c:32: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" CC dp_lib/util_domain_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &res); ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_domain_dp_drivers.c In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:26: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf ( command, "cp %s %s", mat_name[a], latest); ^~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:873, from dp_lib/pavie_dp.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c:1080:26: warning: '%s' directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] sprintf ( command, "cp %s %s", latest, current); ^~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:873, from dp_lib/pavie_dp.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_cdna_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_clean_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_clean_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" CC dp_lib/util_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_est.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_est.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_fasta_nw.c dp_lib/util_dp_drivers.c: In function 'char* seq_file2msa_file(char*, char*, char*)': dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ dp_lib/util_dp_drivers.c:1028:16: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* align_pdb_pair_2(char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1080:10: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* align_pdb_pair(char*, char*, char*, char*, Constraint_list*, Job_TC*)': dp_lib/util_dp_drivers.c:1108:10: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* hh_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1149:8: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:9: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln1); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:9: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln2); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:9: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] tmpnam(hhfile); ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (buf2, 10000, fp); ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1280:6: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", bufname); ~~~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* profile_pair_decomposed(TC_method*, char*, Constraint_list*, char*)': dp_lib/util_dp_drivers.c:1445:7: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* profile_subset_pair_old(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1581:7: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* pdbid_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1717:8: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* pdb_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1774:8: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1906:8: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* lsqman_pair(char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1981:8: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2073:10: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:10: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (get_cache_dir()); ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* rnapdb_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2256:6: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" CC dp_lib/util_dp_fasta_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_sw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_generic_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_gotoh_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" CC dp_lib/util_dp_gotoh_sw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_sw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/util_dp_gotoh_sw.c: In function 'int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)': dp_lib/util_dp_gotoh_sw.c:391:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:382:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); ^~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:373:22: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); ^~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:386:40: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); ^~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_mm_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_mm_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': dp_lib/util_dp_drivers.c:920:22: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_sim.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_sim.c:32: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_ssec_pwaln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1854:22: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 6067) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_suboptimal_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_graph_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_graph_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC fastal/diagonal.c CC fastal/fastal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/diagonal.c:31: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/fastal.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': fastal/diagonal.c:434:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC fastal/fastal_opt_parsing.c fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2115:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2262:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': fastal/fastal.c:3201:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , seq_file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': fastal/fastal.c:3323:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': fastal/fastal.c:3502:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)': fastal/fastal.c:3575:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/iteration.c CC fastal/parttree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/iteration.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/parttree.c:36: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': fastal/iteration.c:310:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command); ~~~~~~^~~~~~~~~ fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': fastal/iteration.c:501:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': fastal/iteration.c:563:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': fastal/parttree.c:848:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)': fastal/parttree.c:891:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'int euclidean_dist_half(FILE*, long int, short int*, short int*, int)': fastal/parttree.c:951:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/scoring.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/scoring.c:37: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(aln_command); ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function 'void make_ref_alignment(char*, char*, char*, int)': fastal/scoring.c:488:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command); ~~~~~~^~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:27: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] sprintf(ref_file_name, "%s/%s",directory, dp->d_name); ^~~~~~~ ~~~~~~~~~ In file included from /usr/include/stdio.h:873, from fastal/scoring.c:28: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 756 bytes into a destination of size 200 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/tree.c CC io_lib/io_func.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/tree.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/io_func.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from io_lib/io_func.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from fastal/tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( dp_mode, "%s", CL->dp_mode); ^~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] if (!A)return NULL; ^~~~ io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/io_func.c: In function 'int** read_matrice(char*)': io_lib/io_func.c:511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': io_lib/io_func.c:971:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC io_lib/pb_util_read_seq_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/pb_util_read_seq_util.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC io_lib/pb_util_read_sequence.c io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': io_lib/pb_util_read_seq_util.c:269:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(outstr, 100, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': io_lib/pb_util_read_seq_util.c:280:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'int getint(char*, int, int, int)': io_lib/pb_util_read_seq_util.c:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/pb_util_read_sequence.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ io_lib/pb_util_read_sequence.c: In function 'void get_clustal_seq(char*, char*, int*, char*, int)': io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for(i=1;idp_mode); ^~~~ In file included from /usr/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC km_coffee/classes.c km_coffee/Vector.c: In function 'void print_vecs(VectorSet*, char*)': km_coffee/Vector.c:869:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] fprintf(out_F, "%i ", i); ^~~~~ ~ CC km_coffee/km_coffee.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from km_coffee/km_coffee.c:43: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ km_coffee/km_coffee.c: In function 'int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)': km_coffee/km_coffee.c:491:7: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(km_tmp_dir); ~~~~~^~~~~~~~~~~~ CC km_coffee/km_util.c CC km_coffee/kmeans.c km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': km_coffee/km_util.c:96:19: warning: format '%s' expects a matching 'char*' argument [-Wformat=] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC t_coffee_lib/t_coffee.c CC util_lib/aln_compare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/aln_compare.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from t_coffee_lib/t_coffee.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" CC util_lib/aln_convertion_util.c CC util_lib/hsearch.c In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/aln_convertion_util.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" In file included from ./io_lib_header.h:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/hsearch.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': t_coffee_lib/t_coffee.c:6544:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': t_coffee_lib/t_coffee.c:7129:61: warning: too many arguments for format [-Wformat-extra-args] else { w=seq2dpa_weight (S, "longuest");fprintf ( stderr, "default longuest\n", dpa_weight);} ^~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)': t_coffee_lib/t_coffee.c:6783:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from ./io_lib_header.h:33, from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/random.c util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ CC util_lib/reformat.c util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': util_lib/aln_convertion_util.c:7697:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/reformat.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': util_lib/aln_convertion_util.c:7459:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7478:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7482:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/reformat_struc.c util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': util_lib/reformat.c:7441:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/reformat_struc.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11290:35: note: in expansion of macro 'ATOI_ACTION' (D1->A)=aln2bootstrap (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11296:32: note: in expansion of macro 'ATOI_ACTION' (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:11529:41: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION (3))D=atof (ACTION(3)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11563:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11662:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11663:34: note: in expansion of macro 'ATOI_ACTION' treelist2lti (D1->S,TS, (int)ATOI_ACTION(1), stdout ); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11670:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11677:35: note: in expansion of macro 'ATOI_ACTION' D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:11705:27: warning: null argument where non-null required (argument 1) [-Wnonnull] ng=atoi(ACTION (2))+1; ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11733:31: note: in expansion of macro 'ATOI_ACTION' tree2bucket (D2->T, D1->S,ATOI_ACTION(1), ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11743:29: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^ util_lib/reformat.c:11754:29: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11880:44: note: in expansion of macro 'ATOI_ACTION' D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11963:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11966:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:11978:77: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11979:77: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:11987:78: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11988:78: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:12022:30: warning: null argument where non-null required (argument 1) [-Wnonnull] radius=atof(ACTION(1)); ^ util_lib/reformat.c:12030:33: warning: null argument where non-null required (argument 1) [-Wnonnull] threshold=atof(ACTION(2)); ^ util_lib/reformat.c:12037:27: warning: null argument where non-null required (argument 1) [-Wnonnull] min=atoi(ACTION(3)); ^ util_lib/reformat.c:12073:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else max=atof(ACTION(na+1)); ^ util_lib/reformat.c:12076:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:12088:77: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:12089:77: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:12097:78: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:12098:78: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12146:44: note: in expansion of macro 'ATOI_ACTION' float results=shuff (D1->S, ACTION (1),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12266:37: note: in expansion of macro 'ATOI_ACTION' D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12390:31: note: in expansion of macro 'ATOI_ACTION' D1->A=shuffle_aln (D1->A, ATOI_ACTION(1), ACTION(2), ACTION (3)); ^~~~~~~~~~~ util_lib/reformat.c:12901:36: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12908:10: note: in expansion of macro 'ATOI_ACTION' F->t=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12909:10: note: in expansion of macro 'ATOI_ACTION' F->f=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12910:11: note: in expansion of macro 'ATOI_ACTION' F->p1=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12911:11: note: in expansion of macro 'ATOI_ACTION' F->p2=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12912:11: note: in expansion of macro 'ATOI_ACTION' F->p3=ATOI_ACTION(6); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12913:11: note: in expansion of macro 'ATOI_ACTION' F->p3=ATOI_ACTION(7); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12936:34: note: in expansion of macro 'ATOI_ACTION' D1->A=unalign_aln (D1->A,SA, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13076:10: note: in expansion of macro 'ATOI_ACTION' if (!ATOI_ACTION(1))myexit(fprintf_error (stderr,"-kmeans ")); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13077:19: note: in expansion of macro 'ATOI_ACTION' km_seq (D1->A,ATOI_ACTION (1),ACTION(2),ACTION(3)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13081:27: note: in expansion of macro 'ATOI_ACTION' D1->A=gap_trim (D1->A,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13088:34: note: in expansion of macro 'ATOI_ACTION' D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13616:7: note: in expansion of macro 'ATOI_ACTION' t=ATOI_ACTION(1); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13617:7: note: in expansion of macro 'ATOI_ACTION' f=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13618:8: note: in expansion of macro 'ATOI_ACTION' p1=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13619:8: note: in expansion of macro 'ATOI_ACTION' p2=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13620:8: note: in expansion of macro 'ATOI_ACTION' p3=ATOI_ACTION(5); ^~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14324:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': util_lib/reformat.c:1321:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': util_lib/reformat.c:1360:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln(char*)': util_lib/reformat.c:1402:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function 'int read_nameseq(char*, char***, char***, char***)': util_lib/reformat.c:1416:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1417:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "# %d\n", &nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1427:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d %d ", &l1, &l2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1430:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1435:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &l1); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1437:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (com[0][nseq],l1, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int read_nameseq_old(char*, char***, char***, char***)': util_lib/reformat.c:1461:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1462:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "# %d\n", &nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1472:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d %d ", &l1, &l2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1475:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1480:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &l1); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1482:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (com[0][nseq],l1, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1779:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d", &result); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'char* get_pdb_id(char*)': util_lib/reformat.c:1817:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int fast_format_determination(char*)': util_lib/reformat.c:2486:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3926:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3933:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3942:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3948:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3950:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3961:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:4234:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4237:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d %d %d %c %c %f\n", &(ST)->list[a][0],&(ST)->list[a][1],&(ST)->list[a][2], &x, &y, &f); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Sequence* get_struc_gor(char*)': util_lib/reformat.c:4464:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d", name, &len); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4485:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4490:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Sequence* get_sequence_dali(char*)': util_lib/reformat.c:4527:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Sequence* get_dialign_sequence(char*)': util_lib/reformat.c:4602:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5636:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_amps_seq_name(char**, char*)': util_lib/reformat.c:5989:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* read_gotoh_aln(char*, Alignment*)': util_lib/reformat.c:6038:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6060:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'float output_maln_pval(char*, Alignment*)': util_lib/reformat.c:6258:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",string); ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* similarities_file2aln(char*)': util_lib/reformat.c:6423:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] fprintf (out, "ATOM ", lw[1]);//ATOM ^~~~~~~~ util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14165:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14178:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14203:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': util_lib/reformat.c:14228:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14245:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14258:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14285:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': util_lib/reformat.c:14396:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util.c:52: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util.c:52: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util.c: In function 'int cherry(int, char**)': util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function 'int dump_nfc(char*, char*)': util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function 'int set_nproc(int)': util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function 'char* vremove3(char*, char*)': util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ CC util_lib/util_aln_analyze.c util_lib/util.c: In function 'FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))': util_lib/util.c:281:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread (ra_j, size, len, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread (ra_j_1, size, len, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))': util_lib/util.c:420:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( key2, el_size, entry_len,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': util_lib/util.c:847:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int quantile(int, char**)': util_lib/util.c:1321:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int** input_array_int(char*)': util_lib/util.c:1805:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &len); ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1809:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &len2); ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1813:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "\n"); ~~~~~~~^~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5621:32: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from t_coffee_lib/t_coffee.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int perl_strstr(char*, char*)': util_lib/util.c:2468:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d", &r); ~~~~~~~^~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_aln_analyze.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': util_lib/util.c:4439:19: warning: control reaches end of non-void function [-Wreturn-type] printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': util_lib/util.c:5760:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",list[n]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stderr(char*)': util_lib/util.c:6300:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] freopen(stderr_file, "w", stderr); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stdout(char*)': util_lib/util.c:6343:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] freopen(stdout_file, "w", stdout); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)': util_lib/util.c:7554:2: warning: second parameter of 'va_start' not last named argument [-Wvarargs] va_start (ap, usage); ^~~~~~~~ CC util_lib/util_analyse_constraints_list.c util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:7821:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': util_lib/util.c:7841:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", string); ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': util_lib/util.c:8228:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8258:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_for_update(char*)': util_lib/util.c:8345:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_internet_connection(int)': util_lib/util.c:8437:10: warning: control reaches end of non-void function [-Wreturn-type] myexit (EXIT_FAILURE); ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function 'int km_main(int, char**)': util_lib/util.c:10370:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_analyse_constraints_list.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ CC util_lib/util_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_constraints_list.c:37: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': util_lib/util_constraints_list.c:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util_constraints_list.c: In function 'Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)': util_lib/util_constraints_list.c:2225:28: warning: too many arguments for format [-Wformat-extra-args] fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Constraint_list* read_constraint_list_file(Constraint_list*, char*)': util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); ^~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (tdir); ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'TC_method* method_file2TC_method(char*)': util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)': util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (line , 200 , fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_declare.c:37: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1287:17: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 4503) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_domain_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_domain_constraints_list.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_domain_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/util_dps.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_dps.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/util_job_handling.c CC util_lib/util_make_tree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_job_handling.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_make_tree.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_make_tree.c: In function 'tnode* redundate(Sequence*, NT_node, char*, char*)': util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util_make_tree.c: In function 'char* seq2co_aln_file(char*, char*)': util_lib/util_make_tree.c:124:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:127:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* seq2mafft_aln_file(char*, char*)': util_lib/util_make_tree.c:157:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:159:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* seq2cw_aln_file(char*, char*)': util_lib/util_make_tree.c:189:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:191:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* prf_pair2cw_aln_file(char*, char*, char*)': util_lib/util_make_tree.c:222:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:225:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns1_dnd(Sequence*)': util_lib/util_make_tree.c:1854:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1867:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns2_dnd(Sequence*)': util_lib/util_make_tree.c:1883:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1896:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2mafft_dnd(Sequence*)': util_lib/util_make_tree.c:1912:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1925:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2parttree_dnd(Sequence*)': util_lib/util_make_tree.c:1942:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1955:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2dpparttree_dnd(Sequence*)': util_lib/util_make_tree.c:1972:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1987:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fastparttree_dnd(Sequence*)': util_lib/util_make_tree.c:2005:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2018:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cwquick_dnd(Sequence*)': util_lib/util_make_tree.c:2034:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2042:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_dnd(Sequence*)': util_lib/util_make_tree.c:2059:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2067:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* aln2cw_tree(Alignment*)': util_lib/util_make_tree.c:2087:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2094:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_tree(Sequence*)': util_lib/util_make_tree.c:2109:9: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2118:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5392:39: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); ^~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_mcoffee_4_tcoffee()': util_lib/util.c:5407:41: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_methods_4_tcoffee()': util_lib/util.c:5420:41: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_plugins_4_tcoffee()': util_lib/util.c:5434:40: warning: '/plugins/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 11 and 1109 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* long_tmpnam_2(char*)': util_lib/util.c:6808:16: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); ^~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10101) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* ultrashort_tmpnam_2(char*)': util_lib/util.c:6840:16: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); ^~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10101) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* short_tmpnam_2(char*)': util_lib/util.c:6871:17: warning: '%s' directive writing up to 99 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s%d%s",root2, file++,set_file2remove_extension (NULL, GET)); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/util.c:32: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10110 bytes into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12082:26: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/aln_convertion_util.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:12076:26: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/aln_convertion_util.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': util_lib/util_constraints_list.c:695:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( aln_mode, "%s", method->aln_mode); ^~~~ In file included from /usr/include/stdio.h:873, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:696:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( out_mode, "%s", method->out_mode); ^~~~ In file included from /usr/include/stdio.h:873, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': util_lib/reformat.c:13510:24: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from util_lib/reformat.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:11528:24: warning: '%s' directive argument is null [-Wformat-overflow=] sprintf (type, "%s", ACTION (2)); ^~~~ Linking... /usr/bin/ld: dp_lib/util_dp_drivers.o: in function `hh_pair(TC_method*, char*, Constraint_list*)': ./t_coffee_source/dp_lib/util_dp_drivers.c:1160: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/build/t-coffee-12.00.7fb08c2/t_coffee_source' make[1]: Leaving directory '/build/t-coffee-12.00.7fb08c2' dh_auto_test -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=t_coffee_source dh_testroot -O--sourcedirectory=t_coffee_source dh_prep -O--sourcedirectory=t_coffee_source dh_auto_install -O--sourcedirectory=t_coffee_source dh_install -O--sourcedirectory=t_coffee_source dh_installdocs -O--sourcedirectory=t_coffee_source dh_installchangelogs -O--sourcedirectory=t_coffee_source debian/rules override_dh_installexamples make[1]: Entering directory '/build/t-coffee-12.00.7fb08c2' dh_installexamples mkdir -p /build/t-coffee-12.00.7fb08c2/debian/t-coffee/usr/share/doc/t-coffee/examples; cp -aR example/* /build/t-coffee-12.00.7fb08c2/debian/t-coffee/usr/share/doc/t-coffee/examples/; make[1]: Leaving directory '/build/t-coffee-12.00.7fb08c2' dh_installman -O--sourcedirectory=t_coffee_source dh_installinit -O--sourcedirectory=t_coffee_source dh_installsystemduser -O--sourcedirectory=t_coffee_source dh_perl -O--sourcedirectory=t_coffee_source dh_link -O--sourcedirectory=t_coffee_source dh_strip_nondeterminism -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory '/build/t-coffee-12.00.7fb08c2' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true make[1]: Leaving directory '/build/t-coffee-12.00.7fb08c2' dh_fixperms -O--sourcedirectory=t_coffee_source dh_missing -O--sourcedirectory=t_coffee_source dh_dwz -O--sourcedirectory=t_coffee_source dh_strip -O--sourcedirectory=t_coffee_source dh_makeshlibs -O--sourcedirectory=t_coffee_source dh_shlibdeps -O--sourcedirectory=t_coffee_source dh_installdeb -O--sourcedirectory=t_coffee_source dh_gencontrol -O--sourcedirectory=t_coffee_source dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source dpkg-deb: building package 't-coffee' in '../t-coffee_12.00.7fb08c2-4_arm64.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb'. dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_12.00.7fb08c2-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../t-coffee_12.00.7fb08c2-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/31654 and its subdirectories I: Current time: Wed Sep 9 20:54:56 -12 2020 I: pbuilder-time-stamp: 1599728096