Running as unit: rb-build-amd64_38-47852.service ==================================================================================== Sat Feb 22 08:55:06 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_38) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Sat Feb 22 08:55:06 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-7crKtnG3" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 08:55:06 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Sat Feb 22 08:55:06 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-C1Wmf7' Sat Feb 22 08:55:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Sat Feb 22 08:55:07 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-IylE4s' ok, let's check if t-coffee is building anywhere yet… ok, t-coffee is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of t-coffee in trixie on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Sat Feb 22 08:55:24 UTC 2025 I: starting to build t-coffee/trixie/amd64 on jenkins on '2025-02-22 08:55' Sat Feb 22 08:55:24 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_38/47852/console.log 1740214524 amd64 trixie t-coffee Sat Feb 22 08:55:24 UTC 2025 I: Downloading source for trixie/t-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 --2025-02-22 08:55:25-- http://deb.debian.org/debian/pool/main/t/t-coffee/t-coffee_13.45.0.4846264%2breally13.41.0.28bdc39%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2391 (2.3K) [text/prs.lines.tag] Saving to: ‘t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc’ 0K .. 100% 306M=0s 2025-02-22 08:55:25 (306 MB/s) - ‘t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc’ saved [2391/2391] --2025-02-22 08:55:25-- http://deb.debian.org/debian/pool/main/t/t-coffee/t-coffee_13.45.0.4846264%2breally13.41.0.28bdc39%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2391 (2.3K) [text/prs.lines.tag] Saving to: ‘t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc’ 0K .. 100% 306M=0s 2025-02-22 08:55:25 (306 MB/s) - ‘t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc’ saved [2391/2391] Sat Feb 22 08:55:25 UTC 2025 I: t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: t-coffee Binary: t-coffee, t-coffee-examples Architecture: any all Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Étienne Mollier Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: t-coffee deb science optional arch=any t-coffee-examples deb science optional arch=all Checksums-Sha1: fab3dbecabca6c0248a8c8a0336f5995be3b4e3f 3229824 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz dc1efbe2dfb5d379e2d04ce1a736f074322be181 18328 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz Checksums-Sha256: a1b37c67caba574ccf53c38279863dffa67d62232e017317754b5eb29db60746 3229824 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz 3e83e95b016af77d28fc7d8315979dd397f12f333bcd4a45be5f471dbd9964ed 18328 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz Files: 74a867b32054875c3ce5f2a11767d610 3229824 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz 13b9ba2309fb654eeb1c4c8017c4cdb7 18328 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOAlj0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG4cw//Qlbaw6pe+7dbaQICdBzx3OMnMJidIS94 0hxonazxybmkqiXvFld5ETsDIyLhqlrCcz3/9pIFLfUyWuyuW7uc7CwFc041BnYY TxT7dRDR7tQ1enXZ3hLjtHLCVwKPHv1M0oVe/6+1JrcpiXIx+ZBQrtSTnmPtur+d Dl0vGvZAwIMjN3AifWvNPI5Noj7hD63bw0QTTVIAD/+sC97xl/TdkV6584b9XMy1 xW8MNaRgFEHWDcL+23X4IA9EfCIsz8wEv78mSA0Y/1fvP6xdKyKQ5ESJ2HwOw3dl S3WUobMn+wKeKbVBAwqTWiKVWIy93rwKIIX8hboX/0sCjAqN4qrtXNyP4k0Nuz6g 1zILk1lUUo21HRs803dCBtw9D3NKtV7ajZ9m1nO3ruzHmJUW7b598ifWPbYw4TEo iOgqNZ/S8O3Ev0idbD6ikfzMlMBfxuk8XUewSaPyOtgaw5BwrNdjEIV0XD0/hgio 6xI/VNkojvyL/3OO7PsIx/X5xQWOfFy5J4aziNNabGmO1KtuYNYHQpMlq0iPLEJI GveIU6JPk2KgUzdhPLo3DD5GsODHoyN83fa6eqV6vYR5x7lfzCZg3ewzcSR5gmYz z7Q6x0bPSenpQpCmcYhHjuPTKS+xD574zjOw/2w/umYCrsVYS4flr9ZJDX1+TQMo vXx4ah4rMEw= =bR2s -----END PGP SIGNATURE----- Sat Feb 22 08:55:25 UTC 2025 I: Checking whether the package is not for us Sat Feb 22 08:55:25 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Sat Feb 22 08:55:25 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Sat Feb 22 08:55:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Sat Feb 22 08:55:25 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-xrkdwN' ==================================================================================== Fri Mar 27 15:18:26 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 t-coffee trixie /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1" as arguments. Fri Mar 27 15:18:26 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-jil2YjPm" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Mar 27 15:18:26 UTC 2026 I: Downloading source for trixie/t-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Reading package lists... NOTICE: 't-coffee' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/t-coffee.git Please use: git clone https://salsa.debian.org/med-team/t-coffee.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3251 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (dsc) [2391 B] Get:2 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (tar) [3230 kB] Get:3 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (diff) [18.3 kB] Fetched 3251 kB in 0s (20.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 't-coffee' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/t-coffee.git Please use: git clone https://salsa.debian.org/med-team/t-coffee.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3251 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (dsc) [2391 B] Get:2 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (tar) [3230 kB] Get:3 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (diff) [18.3 kB] Fetched 3251 kB in 0s (20.2 MB/s) Download complete and in download only mode ============================================================================= Building t-coffee in trixie on amd64 on infom02-amd64 now. Date: Fri Mar 27 15:18:26 UTC 2026 Date UTC: Fri Mar 27 15:18:26 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 27 03:18:26 -12 2026 I: pbuilder-time-stamp: 1774624706 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting t-coffee in t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying bypass_legacy_blast.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 verbose_build dpkg-source: info: applying increase_max_pid.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1959640/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2d953a6b81f74606aef918c2eabdbc3e' 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='1959640' 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/r-b-build.2k9gWSUH/pbuilderrc_Jcqt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1959640/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19858 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.6 MB of archives. After unpacking 77.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Fetched 20.6 MB in 2s (11.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... 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Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/ph_tree_scan.txt 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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules binary dh binary --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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" 'CC=$(CXX)' all cd t_coffee_source && make -j12 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" CC=\$\(CXX\) all make[2]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate_dirichlet.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/pavie_dp.c CC dp_lib/fsa_dp.c CC dp_lib/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c CC dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c CC dp_lib/evaluate_for_domain.c CC dp_lib/util_domain_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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 30 | 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 317 | fscanf(fp, "%f\n", &f); | ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 319 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] 3070 | 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); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:3070:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] 3070 | 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); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:3070:93: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] 3070 | 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); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:3070:109: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] 3070 | 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); | ~~^ ~~~~~~ | | | | int double | %3f dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fscanf (fp, "%s\n",mat_list[nch++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 1079 | 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] 1081 | 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] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ CC dp_lib/util_dp_est.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf (fp, "%d ", &res); | ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c 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 30 | typedef struct ALNcol | ^~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7626:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2051 | register int a; | ^ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:970, from dp_lib/pavie_dp.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1078:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1080:30: warning: '%s' directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] 1080 | sprintf ( command, "cp %s %s", latest, current); | ^~ ~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1080:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_gotoh_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int *p; | ^ 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] 1014 | 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] 1028 | 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:1080:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1080 | 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:1108:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | 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:1149:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1149 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1160 | tmpnam(aln1); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1161 | tmpnam(aln2); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1164 | tmpnam(hhfile); | ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:17: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1211 | 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:1280:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1280 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1363 | 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] 1445 | 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] 1581 | 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:1717:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1717 | 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:1774:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1774 | 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:1906:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1906 | 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:1981:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2073:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:24: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 2121 | getcwd (cdir, sizeof(char)*1000); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:23: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2122 | chdir (get_cache_dir()); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:23: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2142 | 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:2256:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_mm_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | 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:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)': dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 173 | register int d; | ^ dp_lib/util_dp_sim.c: In function 'int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)': dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 248 | vertexptr findmax(); /* return the largest score node */ | ^~ dp_lib/util_dp_sim.c:248:20: note: remove parentheses to default-initialize a variable 248 | vertexptr findmax(); /* return the largest score node */ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:481:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:482:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 482 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:483:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 483 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:484:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 484 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:485:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 485 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:486:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:486:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:487:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:487:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:488:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:488:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:489:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function 'int locate(int*, int*, int)': dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:562:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:563:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 563 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:564:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 564 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:565:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 565 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:566:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 566 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:567:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:567:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:568:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:568:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:569:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:569:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:570:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:570:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 572 | int addnode(); /* function for inserting a node */ | ^~ dp_lib/util_dp_sim.c:572:16: note: remove parentheses to default-initialize a variable 572 | int addnode(); /* function for inserting a node */ | ^~ | -- dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function 'int small_pass(int*, int*, int, int)': dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:786:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:787:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 787 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:788:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 788 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:789:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 789 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:790:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 790 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:791:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:791:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:792:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:792:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:793:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:793:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:794:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function 'SIM_NODE* findmax()': dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c:864:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c: In function 'int no_cross()': dp_lib/util_dp_sim.c:883:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 883 | register int i; | ^ dp_lib/util_dp_sim.c: In function 'int diff_sim(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:911:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:911:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:912:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); | ^~ In file included from /usr/include/stdio.h:970, from dp_lib/util_dp_drivers.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:382:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:373:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:373:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:386:41: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:386:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/util_graph_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Alignment* realign_block(Alignment*, int, int, char*)' at dp_lib/util_dp_drivers.c:921:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC fastal/diagonal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/fastal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 434 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 439 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 440 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | 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 function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)' at dp_lib/util_dp_drivers.c:1854:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 5068) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/parttree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1924 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1929 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1930 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1931 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1976 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1980 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1982 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2115:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2115 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2262:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2262 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': fastal/fastal.c:3201:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3201 | fgets (line, LINE_LENGTH , seq_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': fastal/fastal.c:3323:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3323 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3326 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3329 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3331 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3333 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3352 | fgets(line, LINE_LENGTH , profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': fastal/fastal.c:3502:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3502 | 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:3575:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3575 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3577 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3579 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3581 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 310 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 435 | system(command); | ~~~~~~^~~~~~~~~ fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 565 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 567 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 569 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 757 | register int *p; | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)': io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 68 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 91 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 191 | register int p; | ^ io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 240 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 258 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 356 | register int i; | ^ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 398 | system(aln_command); | ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function 'void make_ref_alignment(char*, char*, char*, int)': fastal/scoring.c:488:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 488 | fgets(line, LINE_LENGTH, seq_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | fgets(outstr, 100, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 584 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': io_lib/pb_util_read_seq_util.c:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | 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:305:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 695 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 701 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': fastal/parttree.c:848:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 859 | 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:891:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 891 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 903 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 906 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 912 | 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:951:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 951 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 1235 | 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] 2076 | } | ^ io_lib/io_func.c: In function 'int** read_matrice(char*)': io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 511 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | 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_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC io_lib/tree_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:970, from fastal/scoring.c:28: In function 'int sprintf(char*, const char*, ...)', inlined from 'int complete_agreement_score(char*, const char*)' at fastal/scoring.c:624:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 756 bytes into a destination of size 200 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC km_coffee/Vector.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC km_coffee/classes.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()': io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 79 | register int i; | ^ io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 80 | register int c; | ^ 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:144:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 144 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | for(i=1;idp_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:491:14: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ CC util_lib/aln_compare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/aln_convertion_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } | ^ t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ CC util_lib/hsearch.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c 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 30 | typedef struct ALNcol | ^~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/reformat_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) | ^~~~ util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ CC util_lib/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 370 | 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] 372 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 378 | 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] 405 | 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] 407 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 416 | 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 output_suchard_aln(char*, Alignment*)': util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ CC util_lib/util_aln_analyze.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/string.h:548, from t_coffee_lib/t_coffee.c:32: In function 'char* strcpy(char*, const char*)', inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' In function 'char* strcpy(char*, const char*)', inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } | ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln(char*)': util_lib/reformat.c:1413:1: warning: control reaches end of non-void function [-Wreturn-type] 1413 | } | ^ util_lib/reformat.c: In function 'int read_nameseq(char*, char***, char***, char***)': util_lib/reformat.c:1427:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1427 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1428:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1428 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1438:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1438 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1441:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1441 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1446:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1446 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1448:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1448 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int read_nameseq_old(char*, char***, char***, char***)': util_lib/reformat.c:1472:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1472 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1473:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1473 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1483:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1483 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1486:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1486 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1491:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1491 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1493:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1788:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'char* get_pdb_id(char*)': util_lib/reformat.c:1826:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int fast_format_determination(char*)': util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3948:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3972:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3972 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3983:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:4256:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4259:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4259 | 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:4486:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4486 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4507:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4512 | 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:4549:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Sequence* get_dialign_sequence(char*)': util_lib/reformat.c:4624:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_next_fasta_sequence(FILE*, char**, char**, char**)': util_lib/reformat.c:5264:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5724:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5724 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_amps_seq_name(char**, char*)': util_lib/reformat.c:6077:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* read_gotoh_aln(char*, Alignment*)': util_lib/reformat.c:6126:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6148:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6148 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'float output_maln_pval(char*, Alignment*)': util_lib/reformat.c:6346:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6346 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* similarities_file2aln(char*)': util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_analyse_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c 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] 713 | } | ^ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 1009 | } | ^ CC util_lib/util_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14307 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14332:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': util_lib/reformat.c:14357:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14374 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14387 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14414 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 4480 | } | ^ util_lib/util.c: In function 'int dump_nfc(char*, char*)': util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] 4456 | } | ^ util_lib/util.c: In function 'int set_nproc(int)': util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] 5489 | } | ^ util_lib/util.c: In function 'char* vremove3(char*, char*)': util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] 6938 | } | ^ 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:281:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 306 | fread (ra_j, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 311 | 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:420:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 420 | 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:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 847 | fscanf ( fp, "%d",&list[n[0]++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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] 1321 | 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] 1805 | 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] 1809 | fscanf(fp, "%d ", &len2); | ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1812 | 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] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ CC util_lib/util_declare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | 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:5761:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stderr(char*)': util_lib/util.c:6301:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stdout(char*)': util_lib/util.c:6344:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6344 | 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:7645:9: warning: second parameter of 'va_start' not last named argument [-Wvarargs] 7645 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:7912:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': util_lib/util.c:7932:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': util_lib/util.c:8319:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8319 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8349:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8349 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_for_update(char*)': util_lib/util.c:8436:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 8436 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_internet_connection(int)': util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ CC util_lib/util_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util.c: In function 'int km_main(int, char**)': util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] 1311 | } | ^ 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:2224:49: warning: too many arguments for format [-Wformat-extra-args] 2224 | 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:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from t_coffee_lib/t_coffee.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_dps.c io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4597 | sprintf (index, "%d", i); | ^~ io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] 4597 | sprintf (index, "%d", i); | ^~~~ In file included from /usr/include/stdio.h:970, from io_lib/tree_util.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 582 | chdir (tdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | chdir (cdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': util_lib/util_constraints_list.c:1150:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1150 | 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:1193:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1193 | 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:2599:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2599 | 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:2917:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2917 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2922:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2954:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2979 | 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:4053:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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] 66 | } | ^ util_lib/util_make_tree.c: In function 'void fast_nj_tree(char**)': util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 853 | register int i; | ^ 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] 124 | 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] 127 | 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] 157 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:160:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* seq2cw_aln_file(char*, char*)': util_lib/util_make_tree.c:190:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:192:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 192 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* prf_pair2cw_aln_file(char*, char*, char*)': util_lib/util_make_tree.c:223:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 223 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:226:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 226 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns1_dnd(Sequence*)': util_lib/util_make_tree.c:1855:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1855 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1868:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1868 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns2_dnd(Sequence*)': util_lib/util_make_tree.c:1884:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1884 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1897:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2mafft_dnd(Sequence*)': util_lib/util_make_tree.c:1913:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1913 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1926:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1926 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2parttree_dnd(Sequence*)': util_lib/util_make_tree.c:1943:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1943 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1956:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1956 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2dpparttree_dnd(Sequence*)': util_lib/util_make_tree.c:1973:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1973 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1988:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1988 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fastparttree_dnd(Sequence*)': util_lib/util_make_tree.c:2006:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2006 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2019:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2019 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cwquick_dnd(Sequence*)': util_lib/util_make_tree.c:2035:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2035 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2043:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2043 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_dnd(Sequence*)': util_lib/util_make_tree.c:2060:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2060 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2068:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2068 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* aln2cw_tree(Alignment*)': util_lib/util_make_tree.c:2088:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2088 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2095:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2095 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_tree(Sequence*)': util_lib/util_make_tree.c:2110:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2110 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1286:28: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | 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:970, from util_lib/util_constraints_list.c:29: In function 'int sprintf(char*, const char*, ...)', inlined from 'char* make_aln_command(TC_method*, char*, char*)' at util_lib/util_constraints_list.c:1286:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 4503) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from util_lib/util_aln_analyze.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4598:11, inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_aln_analyze.c: In function 'Alignment* or_sar(Alignment*, Alignment*, char*, int)': util_lib/util_aln_analyze.c:4599:23: warning: 'COMBINED' directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] 4599 | sprintf ( N->mode, "COMBINED"); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4599:11, inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin_sprintf' output 9 bytes into a destination of size 0 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 695 | sprintf ( out_mode, "%s", method->out_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from util_lib/util.c:32: In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_plugins_4_tcoffee()': util_lib/util.c:5435:43: warning: '/plugins/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5435:20, inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5419:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1109 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/include/stdio.h:970, from util_lib/aln_convertion_util.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_mcoffee_4_tcoffee()': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_methods_4_tcoffee()': util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20, inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5376:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | 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:970, from util_lib/reformat.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] 11638 | sprintf (type, "%s", ACTION (2)); | ^~ util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); | ^~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7, inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10018:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7, inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10019:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Linking... g++ dev_lib/dev1.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/evaluate.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_struc.o dp_lib/fsa_dp.o dp_lib/pavie_dp.o dp_lib/showpair.o dp_lib/util_domain_dp.o dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_drivers.o dp_lib/util_dp_est.o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_sim.o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_graph_maln.o fastal/diagonal.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/iteration.o fastal/parttree.o fastal/scoring.o fastal/tree.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_sequence.o io_lib/tree_util.o km_coffee/Stack.o km_coffee/Vector.o km_coffee/classes.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/kmeans.o t_coffee_lib/t_coffee.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/random.o util_lib/reformat.o util_lib/reformat_struc.o util_lib/util.o util_lib/util_aln_analyze.o util_lib/util_analyse_constraints_list.o util_lib/util_constraints_list.o util_lib/util_declare.o util_lib/util_domain_constraints_list.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_make_tree.o -o t_coffee -lm -Wl,-z,relro -Wl,-z,now /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:(.text+0x29c2): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' make[1]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_test -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp 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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_installexamples for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/share/doc/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_installman -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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' #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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_fixperms -O--sourcedirectory=t_coffee_source dh_missing -O--sourcedirectory=t_coffee_source dh_dwz -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -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-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/1959640 and its subdirectories I: Current time: Fri Mar 27 03:19:53 -12 2026 I: pbuilder-time-stamp: 1774624793 Fri Mar 27 15:19:53 UTC 2026 I: Signing ./b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo as t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc Fri Mar 27 15:19:53 UTC 2026 I: Signed ./b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo as ./b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc Fri Mar 27 15:19:53 UTC 2026 - build #1 for t-coffee/trixie/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Fri Mar 27 15:19:53 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-jil2YjPm, removing. /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 08:56 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 08:55 b2 -rw------- 1 jenkins jenkins 3685 Feb 22 08:55 rbuildlog.uoDuwBe -rw-r--r-- 1 jenkins jenkins 2391 Nov 25 2022 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1: total 9840 -rw-r--r-- 1 jenkins jenkins 197410 Feb 22 08:56 build.log -rw-r--r-- 1 jenkins jenkins 2887988 Feb 22 08:56 t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2651352 Feb 22 08:56 t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 18328 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2391 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5583 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6465 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2810 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1048436 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2576 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 3229824 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2: total 0 Sat Feb 22 08:56:54 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 27 03:18:26 -12 2026 I: pbuilder-time-stamp: 1774624706 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting t-coffee in t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying bypass_legacy_blast.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 verbose_build dpkg-source: info: applying increase_max_pid.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1959640/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2d953a6b81f74606aef918c2eabdbc3e' 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='1959640' 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/r-b-build.2k9gWSUH/pbuilderrc_Jcqt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1959640/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19858 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.6 MB of archives. After unpacking 77.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Fetched 20.6 MB in 2s (11.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/ph_tree_scan.txt 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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules binary dh binary --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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" 'CC=$(CXX)' all cd t_coffee_source && make -j12 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" CC=\$\(CXX\) all make[2]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate_dirichlet.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/pavie_dp.c CC dp_lib/fsa_dp.c CC dp_lib/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c CC dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c CC dp_lib/evaluate_for_domain.c CC dp_lib/util_domain_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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 30 | 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 317 | fscanf(fp, "%f\n", &f); | ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 319 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] 3070 | 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); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:3070:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] 3070 | 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); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:3070:93: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] 3070 | 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); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:3070:109: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] 3070 | 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); | ~~^ ~~~~~~ | | | | int double | %3f dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fscanf (fp, "%s\n",mat_list[nch++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 1079 | 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] 1081 | 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] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ CC dp_lib/util_dp_est.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf (fp, "%d ", &res); | ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c 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 30 | typedef struct ALNcol | ^~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7626:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2051 | register int a; | ^ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:970, from dp_lib/pavie_dp.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1078:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1080:30: warning: '%s' directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] 1080 | sprintf ( command, "cp %s %s", latest, current); | ^~ ~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1080:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_gotoh_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int *p; | ^ 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] 1014 | 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] 1028 | 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:1080:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1080 | 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:1108:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | 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:1149:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1149 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1160 | tmpnam(aln1); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1161 | tmpnam(aln2); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1164 | tmpnam(hhfile); | ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:17: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1211 | 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:1280:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1280 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1363 | 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] 1445 | 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] 1581 | 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:1717:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1717 | 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:1774:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1774 | 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:1906:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1906 | 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:1981:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2073:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:24: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 2121 | getcwd (cdir, sizeof(char)*1000); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:23: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2122 | chdir (get_cache_dir()); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:23: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2142 | 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:2256:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_mm_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | 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:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)': dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 173 | register int d; | ^ dp_lib/util_dp_sim.c: In function 'int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)': dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 248 | vertexptr findmax(); /* return the largest score node */ | ^~ dp_lib/util_dp_sim.c:248:20: note: remove parentheses to default-initialize a variable 248 | vertexptr findmax(); /* return the largest score node */ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:481:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:482:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 482 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:483:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 483 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:484:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 484 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:485:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 485 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:486:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:486:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:487:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:487:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:488:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:488:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:489:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function 'int locate(int*, int*, int)': dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:562:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:563:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 563 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:564:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 564 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:565:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 565 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:566:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 566 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:567:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:567:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:568:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:568:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:569:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:569:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:570:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:570:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 572 | int addnode(); /* function for inserting a node */ | ^~ dp_lib/util_dp_sim.c:572:16: note: remove parentheses to default-initialize a variable 572 | int addnode(); /* function for inserting a node */ | ^~ | -- dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function 'int small_pass(int*, int*, int, int)': dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:786:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:787:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 787 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:788:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 788 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:789:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 789 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:790:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 790 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:791:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:791:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:792:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:792:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:793:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:793:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:794:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function 'SIM_NODE* findmax()': dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c:864:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c: In function 'int no_cross()': dp_lib/util_dp_sim.c:883:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 883 | register int i; | ^ dp_lib/util_dp_sim.c: In function 'int diff_sim(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:911:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:911:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:912:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); | ^~ In file included from /usr/include/stdio.h:970, from dp_lib/util_dp_drivers.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:382:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:373:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:373:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:386:41: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:386:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/util_graph_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Alignment* realign_block(Alignment*, int, int, char*)' at dp_lib/util_dp_drivers.c:921:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC fastal/diagonal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/fastal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 434 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 439 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 440 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | 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 function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)' at dp_lib/util_dp_drivers.c:1854:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 5068) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/parttree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1924 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1929 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1930 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1931 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1976 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1980 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1982 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2115:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2115 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2262:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2262 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': fastal/fastal.c:3201:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3201 | fgets (line, LINE_LENGTH , seq_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': fastal/fastal.c:3323:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3323 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3326 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3329 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3331 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3333 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3352 | fgets(line, LINE_LENGTH , profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': fastal/fastal.c:3502:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3502 | 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:3575:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3575 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3577 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3579 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3581 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 310 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 435 | system(command); | ~~~~~~^~~~~~~~~ fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 565 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 567 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 569 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 757 | register int *p; | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)': io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 68 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 91 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 191 | register int p; | ^ io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 240 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 258 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 356 | register int i; | ^ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 398 | system(aln_command); | ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function 'void make_ref_alignment(char*, char*, char*, int)': fastal/scoring.c:488:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 488 | fgets(line, LINE_LENGTH, seq_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | fgets(outstr, 100, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 584 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': io_lib/pb_util_read_seq_util.c:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | 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:305:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 695 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 701 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': fastal/parttree.c:848:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 859 | 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:891:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 891 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 903 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 906 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 912 | 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:951:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 951 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 1235 | 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] 2076 | } | ^ io_lib/io_func.c: In function 'int** read_matrice(char*)': io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 511 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | 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_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC io_lib/tree_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:970, from fastal/scoring.c:28: In function 'int sprintf(char*, const char*, ...)', inlined from 'int complete_agreement_score(char*, const char*)' at fastal/scoring.c:624:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 756 bytes into a destination of size 200 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC km_coffee/Vector.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC km_coffee/classes.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()': io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 79 | register int i; | ^ io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 80 | register int c; | ^ 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:144:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 144 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | for(i=1;idp_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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:491:14: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ CC util_lib/aln_compare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/aln_convertion_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } | ^ t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ CC util_lib/hsearch.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c 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 30 | typedef struct ALNcol | ^~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/reformat_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) | ^~~~ util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ CC util_lib/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 370 | 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] 372 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 378 | 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] 405 | 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] 407 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 416 | 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 output_suchard_aln(char*, Alignment*)': util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ CC util_lib/util_aln_analyze.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/string.h:548, from t_coffee_lib/t_coffee.c:32: In function 'char* strcpy(char*, const char*)', inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' In function 'char* strcpy(char*, const char*)', inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } | ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln(char*)': util_lib/reformat.c:1413:1: warning: control reaches end of non-void function [-Wreturn-type] 1413 | } | ^ util_lib/reformat.c: In function 'int read_nameseq(char*, char***, char***, char***)': util_lib/reformat.c:1427:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1427 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1428:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1428 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1438:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1438 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1441:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1441 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1446:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1446 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1448:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1448 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int read_nameseq_old(char*, char***, char***, char***)': util_lib/reformat.c:1472:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1472 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1473:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1473 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1483:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1483 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1486:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1486 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1491:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1491 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1493:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1788:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'char* get_pdb_id(char*)': util_lib/reformat.c:1826:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int fast_format_determination(char*)': util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3948:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3972:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3972 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3983:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:4256:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4259:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4259 | 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:4486:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4486 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4507:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4512 | 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:4549:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Sequence* get_dialign_sequence(char*)': util_lib/reformat.c:4624:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_next_fasta_sequence(FILE*, char**, char**, char**)': util_lib/reformat.c:5264:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5724:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5724 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_amps_seq_name(char**, char*)': util_lib/reformat.c:6077:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* read_gotoh_aln(char*, Alignment*)': util_lib/reformat.c:6126:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6148:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6148 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'float output_maln_pval(char*, Alignment*)': util_lib/reformat.c:6346:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6346 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* similarities_file2aln(char*)': util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_analyse_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c 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] 713 | } | ^ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 1009 | } | ^ CC util_lib/util_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14307 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14332:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': util_lib/reformat.c:14357:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14374 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14387 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14414 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 4480 | } | ^ util_lib/util.c: In function 'int dump_nfc(char*, char*)': util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] 4456 | } | ^ util_lib/util.c: In function 'int set_nproc(int)': util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] 5489 | } | ^ util_lib/util.c: In function 'char* vremove3(char*, char*)': util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] 6938 | } | ^ 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:281:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 306 | fread (ra_j, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 311 | 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:420:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 420 | 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:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 847 | fscanf ( fp, "%d",&list[n[0]++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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] 1321 | 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] 1805 | 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] 1809 | fscanf(fp, "%d ", &len2); | ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1812 | 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] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ CC util_lib/util_declare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | 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:5761:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stderr(char*)': util_lib/util.c:6301:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stdout(char*)': util_lib/util.c:6344:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6344 | 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:7645:9: warning: second parameter of 'va_start' not last named argument [-Wvarargs] 7645 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:7912:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': util_lib/util.c:7932:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': util_lib/util.c:8319:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8319 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8349:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8349 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_for_update(char*)': util_lib/util.c:8436:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 8436 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_internet_connection(int)': util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ CC util_lib/util_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util.c: In function 'int km_main(int, char**)': util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] 1311 | } | ^ 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:2224:49: warning: too many arguments for format [-Wformat-extra-args] 2224 | 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:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from t_coffee_lib/t_coffee.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_dps.c io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4597 | sprintf (index, "%d", i); | ^~ io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] 4597 | sprintf (index, "%d", i); | ^~~~ In file included from /usr/include/stdio.h:970, from io_lib/tree_util.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 582 | chdir (tdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | chdir (cdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': util_lib/util_constraints_list.c:1150:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1150 | 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:1193:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1193 | 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:2599:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2599 | 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:2917:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2917 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2922:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2954:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2979 | 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:4053:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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] 66 | } | ^ util_lib/util_make_tree.c: In function 'void fast_nj_tree(char**)': util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 853 | register int i; | ^ 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] 124 | 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] 127 | 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] 157 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:160:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* seq2cw_aln_file(char*, char*)': util_lib/util_make_tree.c:190:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:192:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 192 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* prf_pair2cw_aln_file(char*, char*, char*)': util_lib/util_make_tree.c:223:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 223 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:226:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 226 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns1_dnd(Sequence*)': util_lib/util_make_tree.c:1855:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1855 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1868:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1868 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns2_dnd(Sequence*)': util_lib/util_make_tree.c:1884:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1884 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1897:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2mafft_dnd(Sequence*)': util_lib/util_make_tree.c:1913:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1913 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1926:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1926 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2parttree_dnd(Sequence*)': util_lib/util_make_tree.c:1943:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1943 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1956:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1956 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2dpparttree_dnd(Sequence*)': util_lib/util_make_tree.c:1973:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1973 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1988:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1988 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fastparttree_dnd(Sequence*)': util_lib/util_make_tree.c:2006:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2006 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2019:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2019 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cwquick_dnd(Sequence*)': util_lib/util_make_tree.c:2035:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2035 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2043:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2043 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_dnd(Sequence*)': util_lib/util_make_tree.c:2060:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2060 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2068:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2068 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* aln2cw_tree(Alignment*)': util_lib/util_make_tree.c:2088:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2088 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2095:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2095 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_tree(Sequence*)': util_lib/util_make_tree.c:2110:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2110 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1286:28: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | 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:970, from util_lib/util_constraints_list.c:29: In function 'int sprintf(char*, const char*, ...)', inlined from 'char* make_aln_command(TC_method*, char*, char*)' at util_lib/util_constraints_list.c:1286:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 4503) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from util_lib/util_aln_analyze.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4598:11, inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_aln_analyze.c: In function 'Alignment* or_sar(Alignment*, Alignment*, char*, int)': util_lib/util_aln_analyze.c:4599:23: warning: 'COMBINED' directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] 4599 | sprintf ( N->mode, "COMBINED"); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4599:11, inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin_sprintf' output 9 bytes into a destination of size 0 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 695 | sprintf ( out_mode, "%s", method->out_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from util_lib/util.c:32: In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_plugins_4_tcoffee()': util_lib/util.c:5435:43: warning: '/plugins/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5435:20, inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5419:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1109 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/include/stdio.h:970, from util_lib/aln_convertion_util.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_mcoffee_4_tcoffee()': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_methods_4_tcoffee()': util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20, inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5376:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | 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:970, from util_lib/reformat.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] 11638 | sprintf (type, "%s", ACTION (2)); | ^~ util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); | ^~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7, inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10018:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7, inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10019:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Linking... g++ dev_lib/dev1.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/evaluate.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_struc.o dp_lib/fsa_dp.o dp_lib/pavie_dp.o dp_lib/showpair.o dp_lib/util_domain_dp.o dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_drivers.o dp_lib/util_dp_est.o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_sim.o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_graph_maln.o fastal/diagonal.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/iteration.o fastal/parttree.o fastal/scoring.o fastal/tree.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_sequence.o io_lib/tree_util.o km_coffee/Stack.o km_coffee/Vector.o km_coffee/classes.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/kmeans.o t_coffee_lib/t_coffee.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/random.o util_lib/reformat.o util_lib/reformat_struc.o util_lib/util.o util_lib/util_aln_analyze.o util_lib/util_analyse_constraints_list.o util_lib/util_constraints_list.o util_lib/util_declare.o util_lib/util_domain_constraints_list.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_make_tree.o -o t_coffee -lm -Wl,-z,relro -Wl,-z,now /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:(.text+0x29c2): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' make[1]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_test -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp 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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_installexamples for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/share/doc/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_installman -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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' #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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_fixperms -O--sourcedirectory=t_coffee_source dh_missing -O--sourcedirectory=t_coffee_source dh_dwz -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -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-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/1959640 and its subdirectories I: Current time: Fri Mar 27 03:19:53 -12 2026 I: pbuilder-time-stamp: 1774624793 Sat Feb 22 08:56:55 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Sat Feb 22 08:56:55 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Sat Feb 22 08:56:55 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Sat Feb 22 08:56:55 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-utvodH' ==================================================================================== Sat Feb 22 08:56:56 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 t-coffee trixie /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1" as arguments. Sat Feb 22 08:56:56 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-q7Hr2ENb" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 08:56:56 UTC 2025 I: Downloading source for trixie/t-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Reading package lists... NOTICE: 't-coffee' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/t-coffee.git Please use: git clone https://salsa.debian.org/med-team/t-coffee.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3251 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (dsc) [2391 B] Get:2 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (tar) [3230 kB] Get:3 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (diff) [18.3 kB] Fetched 3251 kB in 0s (37.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 't-coffee' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/t-coffee.git Please use: git clone https://salsa.debian.org/med-team/t-coffee.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3251 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (dsc) [2391 B] Get:2 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (tar) [3230 kB] Get:3 http://deb.debian.org/debian trixie/main t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (diff) [18.3 kB] Fetched 3251 kB in 0s (37.3 MB/s) Download complete and in download only mode ============================================================================= Re-Building t-coffee in trixie on amd64 on infom01-amd64 now. Date: Sat Feb 22 08:56:56 UTC 2025 Date UTC: Sat Feb 22 08:56:56 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/pbuilderrc_zEXm + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' t-coffee = debian-installer -o t-coffee = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' t-coffee = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/pbuilderrc_zEXm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 22 22:56:56 +14 2025 I: pbuilder-time-stamp: 1740214616 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting t-coffee in t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying bypass_legacy_blast.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 verbose_build dpkg-source: info: applying increase_max_pid.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 22 08:57 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=b18f828c2ef5414f8a5731eba72e37b8 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2436871 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/pbuilderrc_zEXm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2436871/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19858 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.6 MB of archives. After unpacking 77.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Fetched 20.6 MB in 1s (18.0 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/ph_tree_scan.txt 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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules binary dh binary --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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" 'CC=$(CXX)' all cd t_coffee_source && make -j12 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" CC=\$\(CXX\) all make[2]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate_dirichlet.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c CC dp_lib/evaluate_for_domain.c CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c CC dp_lib/pavie_dp.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c CC dp_lib/showpair.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_domain_dp.c CC dp_lib/util_domain_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_cdna_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | 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 30 | 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 317 | fscanf(fp, "%f\n", &f); | ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 319 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] 3070 | 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); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:3070:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] 3070 | 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); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:3070:93: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] 3070 | 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); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:3070:109: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] 3070 | 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); | ~~^ ~~~~~~ | | | | int double | %3f 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fscanf (fp, "%s\n",mat_list[nch++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 1079 | 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] 1081 | 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] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf (fp, "%d ", &res); | ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 819 | 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7626:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:970, from dp_lib/pavie_dp.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1078:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1080:30: warning: '%s' directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] 1080 | sprintf ( command, "cp %s %s", latest, current); | ^~ ~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1080:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_est.c CC dp_lib/util_dp_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_fasta_sw.c CC dp_lib/util_dp_generic_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_gotoh_nw.c CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_mm_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2051 | register int a; | ^ dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int *p; | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ 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] 1014 | 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] 1028 | 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:1080:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1080 | 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:1108:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | 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:1149:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1149 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1160 | tmpnam(aln1); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1161 | tmpnam(aln2); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:23: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1164 | tmpnam(hhfile); | ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:17: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1211 | 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:1280:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1280 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1363 | 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] 1445 | 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] 1581 | 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:1717:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1717 | 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:1774:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1774 | 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:1906:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1906 | 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:1981:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | 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:2073:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:24: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 2121 | getcwd (cdir, sizeof(char)*1000); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:23: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2122 | chdir (get_cache_dir()); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:23: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2142 | 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:2256:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_graph_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/diagonal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)': dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 173 | register int d; | ^ dp_lib/util_dp_sim.c: In function 'int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)': dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 248 | vertexptr findmax(); /* return the largest score node */ | ^~ dp_lib/util_dp_sim.c:248:20: note: remove parentheses to default-initialize a variable 248 | vertexptr findmax(); /* return the largest score node */ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable 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 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:481:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:482:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 482 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:483:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 483 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:484:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 484 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:485:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 485 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:486:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:486:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:487:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:487:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:488:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:488:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:489:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function 'int locate(int*, int*, int)': dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:562:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:563:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 563 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:564:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 564 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:565:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 565 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:566:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 566 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:567:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:567:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:568:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:568:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:569:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:569:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:570:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:570:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 572 | int addnode(); /* function for inserting a node */ | ^~ dp_lib/util_dp_sim.c:572:16: note: remove parentheses to default-initialize a variable 572 | int addnode(); /* function for inserting a node */ | ^~ | -- dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function 'int small_pass(int*, int*, int, int)': dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:786:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:787:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 787 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:788:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 788 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:789:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 789 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:790:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 790 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:791:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:791:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:792:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:792:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:793:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:793:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:794:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function 'SIM_NODE* findmax()': dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c:864:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c: In function 'int no_cross()': dp_lib/util_dp_sim.c:883:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 883 | register int i; | ^ dp_lib/util_dp_sim.c: In function 'int diff_sim(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:911:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:911:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:912:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); | ^~ In file included from /usr/include/stdio.h:970, from dp_lib/util_dp_drivers.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:382:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:373:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:373:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:386:41: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:386:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 434 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 439 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 440 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ CC fastal/fastal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Alignment* realign_block(Alignment*, int, int, char*)' at dp_lib/util_dp_drivers.c:921:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/parttree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | 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 function 'int sprintf(char*, const char*, ...)', inlined from 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)' at dp_lib/util_dp_drivers.c:1854:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 5068) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1924 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1929 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1930 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1931 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1976 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1980 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1982 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2115:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2115 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2262:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2262 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': fastal/fastal.c:3201:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3201 | fgets (line, LINE_LENGTH , seq_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': fastal/fastal.c:3323:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3323 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3326 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3329 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3331 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3333 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3352 | fgets(line, LINE_LENGTH , profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': fastal/fastal.c:3502:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3502 | 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:3575:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3575 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3577 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3579 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3581 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 310 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 435 | system(command); | ~~~~~~^~~~~~~~~ fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 565 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 567 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 569 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 757 | register int *p; | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 398 | system(aln_command); | ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function 'void make_ref_alignment(char*, char*, char*, int)': fastal/scoring.c:488:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 488 | fgets(line, LINE_LENGTH, seq_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 584 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 695 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 701 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': fastal/parttree.c:848:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 859 | 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:891:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 891 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 903 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 906 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 912 | 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:951:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 951 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC io_lib/io_func.c CC io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:970, from fastal/scoring.c:28: In function 'int sprintf(char*, const char*, ...)', inlined from 'int complete_agreement_score(char*, const char*)' at fastal/scoring.c:624:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 756 bytes into a destination of size 200 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/pb_util_read_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)': io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 68 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 91 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 191 | register int p; | ^ io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 240 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 258 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 356 | register int i; | ^ io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | 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:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | 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:305:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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] 1235 | 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] 2076 | } | ^ io_lib/io_func.c: In function 'int** read_matrice(char*)': io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 511 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/tree_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()': io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 79 | register int i; | ^ io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 80 | register int c; | ^ 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:144:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 144 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | for(i=1;idp_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': km_coffee/km_util.c:96:69: warning: format '%s' expects a matching 'char*' argument [-Wformat=] 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); | ~^ | | | char* 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:491:14: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ CC km_coffee/kmeans.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC t_coffee_lib/t_coffee.c CC util_lib/aln_compare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/aln_convertion_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } | ^ t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ CC util_lib/hsearch.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) | ^~~~ util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } | ^ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/reformat_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/string.h:548, from t_coffee_lib/t_coffee.c:32: In function 'char* strcpy(char*, const char*)', inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' In function 'char* strcpy(char*, const char*)', inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_aln_analyze.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 370 | 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] 372 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 378 | 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] 405 | 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] 407 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 416 | fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ 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] 1009 | } | ^ util_lib/util.c: In function 'int dump_nfc(char*, char*)': util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] 4456 | } | ^ CC util_lib/util_analyse_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c util_lib/util.c: In function 'int set_nproc(int)': util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] 5489 | } | ^ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util.c: In function 'char* vremove3(char*, char*)': util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] 6938 | } | ^ CC util_lib/util_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/util_declare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } | ^ util_lib/reformat.c: In function 'Alignment* quick_read_aln(char*)': util_lib/reformat.c:1413:1: warning: control reaches end of non-void function [-Wreturn-type] 1413 | } | ^ util_lib/reformat.c: In function 'int read_nameseq(char*, char***, char***, char***)': util_lib/reformat.c:1427:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1427 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1428:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1428 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1438:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1438 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1441:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1441 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1446:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1446 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1448:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1448 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int read_nameseq_old(char*, char***, char***, char***)': util_lib/reformat.c:1472:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1472 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1473:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1473 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1483:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1483 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1486:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1486 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1491:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1491 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1493:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1788:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'char* get_pdb_id(char*)': util_lib/reformat.c:1826:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int fast_format_determination(char*)': util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3948:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ 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:281:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 306 | fread (ra_j, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 311 | fread (ra_j_1, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3972:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3972 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3983:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ 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:420:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 420 | fread ( key2, el_size, entry_len,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:4256:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4259:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4259 | 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:4486:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4486 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4507:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': util_lib/util.c:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 847 | fscanf ( fp, "%d",&list[n[0]++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4512 | 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:4549:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Sequence* get_dialign_sequence(char*)': util_lib/reformat.c:4624:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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] 1321 | fscanf ( fp, "%s %s\n", s1, s2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_next_fasta_sequence(FILE*, char**, char**, char**)': util_lib/reformat.c:5264:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ 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] 1805 | 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] 1809 | fscanf(fp, "%d ", &len2); | ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1812 | 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] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5724:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5724 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_amps_seq_name(char**, char*)': util_lib/reformat.c:6077:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* read_gotoh_aln(char*, Alignment*)': util_lib/reformat.c:6126:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6148:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6148 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'float output_maln_pval(char*, Alignment*)': util_lib/reformat.c:6346:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6346 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* similarities_file2aln(char*)': util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 713 | } | ^ util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': util_lib/util.c:5761:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stderr(char*)': util_lib/util.c:6301:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stdout(char*)': util_lib/util.c:6344:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6344 | 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:7645:9: warning: second parameter of 'va_start' not last named argument [-Wvarargs] 7645 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:7912:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': util_lib/util.c:7932:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': util_lib/util.c:8319:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8319 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8349:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8349 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_for_update(char*)': util_lib/util.c:8436:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 8436 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int check_internet_connection(int)': util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function 'int km_main(int, char**)': util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14307 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14332:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': util_lib/reformat.c:14357:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14374 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14387 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14414 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 4480 | } | ^ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from t_coffee_lib/t_coffee.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] 1311 | } | ^ 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:2224:49: warning: too many arguments for format [-Wformat-extra-args] 2224 | 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:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ CC util_lib/util_dps.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 582 | chdir (tdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | chdir (cdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': util_lib/util_constraints_list.c:1150:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1150 | 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:1193:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1193 | 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:2599:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2599 | 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:2917:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2917 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2922:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2954:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2979 | fgets (line , 200 , fp); | ~~~~~~^~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': util_lib/util_constraints_list.c:4053:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/util_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 30 | 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] 66 | } | ^ util_lib/util_make_tree.c: In function 'void fast_nj_tree(char**)': util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 853 | register int i; | ^ 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] 124 | 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] 127 | 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] 157 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:160:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* seq2cw_aln_file(char*, char*)': util_lib/util_make_tree.c:190:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:192:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 192 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'char* prf_pair2cw_aln_file(char*, char*, char*)': util_lib/util_make_tree.c:223:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 223 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:226:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 226 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns1_dnd(Sequence*)': util_lib/util_make_tree.c:1855:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1855 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1868:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1868 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fftns2_dnd(Sequence*)': util_lib/util_make_tree.c:1884:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1884 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1897:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2mafft_dnd(Sequence*)': util_lib/util_make_tree.c:1913:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1913 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1926:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1926 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2parttree_dnd(Sequence*)': util_lib/util_make_tree.c:1943:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1943 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1956:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1956 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2dpparttree_dnd(Sequence*)': util_lib/util_make_tree.c:1973:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1973 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1988:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1988 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2fastparttree_dnd(Sequence*)': util_lib/util_make_tree.c:2006:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2006 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2019:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2019 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cwquick_dnd(Sequence*)': util_lib/util_make_tree.c:2035:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2035 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2043:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2043 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_dnd(Sequence*)': util_lib/util_make_tree.c:2060:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2060 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2068:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2068 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* aln2cw_tree(Alignment*)': util_lib/util_make_tree.c:2088:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2088 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2095:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2095 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function 'tnode* seq2cw_tree(Sequence*)': util_lib/util_make_tree.c:2110:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2110 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4597 | sprintf (index, "%d", i); | ^~ io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] 4597 | sprintf (index, "%d", i); | ^~~~ In file included from /usr/include/stdio.h:970, from io_lib/tree_util.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1286:28: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | 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:970, from util_lib/util_constraints_list.c:29: In function 'int sprintf(char*, const char*, ...)', inlined from 'char* make_aln_command(TC_method*, char*, char*)' at util_lib/util_constraints_list.c:1286:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 4503) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from util_lib/util_aln_analyze.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4598:11, inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_aln_analyze.c: In function 'Alignment* or_sar(Alignment*, Alignment*, char*, int)': util_lib/util_aln_analyze.c:4599:23: warning: 'COMBINED' directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] 4599 | sprintf ( N->mode, "COMBINED"); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4599:11, inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin_sprintf' output 9 bytes into a destination of size 0 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from util_lib/util.c:32: In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_plugins_4_tcoffee()': util_lib/util.c:5435:43: warning: '/plugins/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5435:20, inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5419:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1109 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 695 | sprintf ( out_mode, "%s", method->out_mode); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_mcoffee_4_tcoffee()': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_methods_4_tcoffee()': util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20, inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5376:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/include/stdio.h:970, from util_lib/aln_convertion_util.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | 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:970, from util_lib/reformat.c:27: In function 'int sprintf(char*, const char*, ...)', inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] 11638 | sprintf (type, "%s", ACTION (2)); | ^~ util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); | ^~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7, inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10018:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7, inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10019:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Linking... g++ dev_lib/dev1.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/evaluate.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_struc.o dp_lib/fsa_dp.o dp_lib/pavie_dp.o dp_lib/showpair.o dp_lib/util_domain_dp.o dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_drivers.o dp_lib/util_dp_est.o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_sim.o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_graph_maln.o fastal/diagonal.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/iteration.o fastal/parttree.o fastal/scoring.o fastal/tree.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_sequence.o io_lib/tree_util.o km_coffee/Stack.o km_coffee/Vector.o km_coffee/classes.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/kmeans.o t_coffee_lib/t_coffee.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/random.o util_lib/reformat.o util_lib/reformat_struc.o util_lib/util.o util_lib/util_aln_analyze.o util_lib/util_analyse_constraints_list.o util_lib/util_constraints_list.o util_lib/util_declare.o util_lib/util_domain_constraints_list.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_make_tree.o -o t_coffee -lm -Wl,-z,relro -Wl,-z,now /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:(.text+0x29c2): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' make[1]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_test -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp 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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_installexamples for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/share/doc/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_installman -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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' #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/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_fixperms -O--sourcedirectory=t_coffee_source dh_missing -O--sourcedirectory=t_coffee_source dh_dwz -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -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-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2436871 and its subdirectories I: Current time: Sat Feb 22 22:58:24 +14 2025 I: pbuilder-time-stamp: 1740214704 + false + set +x Sat Feb 22 08:58:24 UTC 2025 I: Signing ./b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo as t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc Sat Feb 22 08:58:24 UTC 2025 I: Signed ./b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo as ./b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc Sat Feb 22 08:58:24 UTC 2025 - build #2 for t-coffee/trixie/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Sat Feb 22 08:58:24 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-q7Hr2ENb, removing. /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH: total 216 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 08:56 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 08:58 b2 -rw------- 1 jenkins jenkins 201384 Feb 22 08:56 rbuildlog.uoDuwBe -rw-r--r-- 1 jenkins jenkins 2391 Nov 25 2022 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1: total 9860 -rw-r--r-- 1 jenkins jenkins 197410 Feb 22 08:56 build.log -rw-r--r-- 1 jenkins jenkins 2887988 Feb 22 08:56 t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2651352 Feb 22 08:56 t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 18328 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2391 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5583 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6465 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2810 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1048436 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2576 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 3229824 Feb 22 08:56 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2: total 9840 -rw-r--r-- 1 jenkins jenkins 199339 Feb 22 08:58 build.log -rw-r--r-- 1 jenkins jenkins 2887988 Feb 22 08:58 t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2651352 Feb 22 08:58 t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb -rw-r--r-- 1 jenkins jenkins 18328 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2391 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5580 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6462 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2810 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1048436 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2576 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 3229824 Feb 22 08:58 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz Sat Feb 22 08:58:25 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. Sat Feb 22 08:58:25 UTC 2025 I: t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 25 Nov 2022 11:13:19 +0100 Source: t-coffee Binary: t-coffee t-coffee-dbgsym t-coffee-examples Architecture: amd64 all Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Closes: 1022570 1023230 Changes: t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) unstable; urgency=medium . [ Étienne Mollier ] * d/t/run-unit-test: don't meddle with user's home. * d/rules: build with -fsigned-char. This fixes infinite loops on CPU architectures defaulting to the char type being unsigned, such as on arm*, ppc* and s390*. (Closes: #1023230) * d/control: add myself to uploaders. . [ Andreas Tille ] * Revert version bump to latest upstream version until https://github.com/cbcrg/tcoffee/issues/56 is closed. Closes: #1022570 * Keep updated patches in debian/patches dir with suffix .13.45.0.4846264 to ease upgrading to the new version once it is ready Checksums-Sha1: e9646a76b077ff6f89308efbb587972942f267ba 2887988 t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb 7c50c05b136b2a6ae14ece728ce140ad18322d71 2651352 t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb d2265a7b28f9ba3766e7e324a7730af208accd52 5583 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo 02ce09840afaf7343f56565851efd68de72b5a33 1048436 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb Checksums-Sha256: 00ce55583f134314b1d119f89513f4f691852cfd31b086cc84dc3b20694babf1 2887988 t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb 9b6462e3e8fb149f003c15ef13ee50efe251445385c462b1a837aa4d8a4fcfae 2651352 t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb bc9de58f388cc535e186e833eb8d0f60c39edfcde463a3b70520b6c614763467 5583 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo c1bdc09fc1ebb0ed8ebce379bae8d3505f193a1779dc69e5cc07c29c74197e7b 1048436 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb Files: b1bdf1ba49e8ff85970081051b2a06ea 2887988 debug optional t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb 6a13c09e62ffdc89de3c89cae9ae1243 2651352 science optional t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb e388c1b5056f9853bc8e405bca5e2509 5583 science optional t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo fe30a38daa3143bc0e6d33a0407f3a6f 1048436 science optional t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-02-22 08:56:54.305142913 +0000 +++ b2/build.log 2025-02-22 08:58:24.869060022 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 27 03:18:26 -12 2026 -I: pbuilder-time-stamp: 1774624706 +I: Current time: Sat Feb 22 22:56:56 +14 2025 +I: pbuilder-time-stamp: 1740214616 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,51 +33,83 @@ dpkg-source: info: applying increase_max_pid.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1959640/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 22 08:57 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2d953a6b81f74606aef918c2eabdbc3e' - 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='1959640' - PS1='# ' - PS2='> ' + INVOCATION_ID=b18f828c2ef5414f8a5731eba72e37b8 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2436871 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/pbuilderrc_Jcqt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/pbuilderrc_zEXm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1959640/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -143,7 +175,7 @@ Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.6 MB in 2s (11.4 MB/s) +Fetched 20.6 MB in 1s (18.0 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 files and directories currently installed.) @@ -278,7 +310,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -310,114 +346,64 @@ CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate_dirichlet.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c + CC dp_lib/evaluate_for_domain.c + CC dp_lib/evaluate_for_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/pavie_dp.c CC dp_lib/fsa_dp.c - CC dp_lib/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c - CC dp_lib/util_dp_cdna_fasta_nw.c - CC dp_lib/util_domain_dp.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c - CC dp_lib/evaluate_for_domain.c - CC dp_lib/util_domain_dp_drivers.c + CC dp_lib/pavie_dp.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c + CC dp_lib/showpair.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_domain_dp.c + CC dp_lib/util_domain_dp_drivers.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_cdna_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ -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 - 30 | 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 - 30 | typedef struct ALNcol - | ^~~~~~~ -dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': -dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] - 89 | fprintf (stdout, "Process positions\n", i); - | ^~~~~~~~~~~~~~~~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ -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 - 30 | 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 30 | typedef struct ALNcol | ^~~~~~~ - CC dp_lib/util_dp_clean_maln.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ 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 - 30 | 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 30 | 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 - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/pavie_dp.c:33: + from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_clean_maln.c:33: + from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC dp_lib/util_dp_drivers.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 317 | fscanf(fp, "%f\n", &f); @@ -431,6 +417,15 @@ dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': +dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] + 89 | fprintf (stdout, "Process positions\n", i); + | ^~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] 3070 | 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); @@ -456,6 +451,26 @@ | | | | int double | %3f +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 + 30 | 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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fscanf (fp, "%s\n",mat_list[nch++]); @@ -471,12 +486,6 @@ 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] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ - CC dp_lib/util_dp_est.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_dp_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf (fp, "%d ", &res); @@ -487,25 +496,23 @@ dp_lib/evaluate.c:819:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_fasta_sw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_drivers.c:33: + from dp_lib/showpair.c:32: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +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 30 | typedef struct ALNcol | ^~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7626:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_generic_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c + CC dp_lib/util_dp_clean_maln.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': -dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2051 | register int a; - | ^ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); @@ -535,15 +542,36 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_generic_fasta_nw.c:34: + from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC dp_lib/util_dp_drivers.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_est.c + CC dp_lib/util_dp_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_fasta_sw.c + CC dp_lib/util_dp_generic_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_gotoh_nw.c + CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_mm_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_nw.c:34: + from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -552,10 +580,34 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': +dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2051 | register int a; + | ^ dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int *p; | ^ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ 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] 1014 | chdir (dir); @@ -618,8 +670,6 @@ dp_lib/util_dp_drivers.c:1981:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_gotoh_sw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2073:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); @@ -637,45 +687,52 @@ dp_lib/util_dp_drivers.c:2256:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_dp_mm_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_sw.c:33: + from dp_lib/util_dp_gotoh_sw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +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 30 | 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:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_suboptimal_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_graph_maln.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_nw.c:34: + from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_sw.c:33: + from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC dp_lib/util_dp_suboptimal_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_sim.c:32: + from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | 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:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC fastal/diagonal.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_mm_nw.c:33: + from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -692,6 +749,11 @@ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable +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 + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ @@ -859,16 +921,6 @@ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); @@ -910,9 +962,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC dp_lib/util_graph_maln.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': +fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 434 | system(blast_command); + | ~~~~~~^~~~~~~~~~~~~~~ +fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 439 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 440 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 441 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ + CC fastal/fastal.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); @@ -926,38 +990,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC fastal/diagonal.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ - CC fastal/fastal.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c + CC fastal/fastal_opt_parsing.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC fastal/iteration.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': -fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 434 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ -fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 439 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 440 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 441 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_graph_maln.c:33: + from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/fastal_opt_parsing.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC fastal/parttree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | 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); @@ -971,16 +1017,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC fastal/iteration.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ - CC fastal/parttree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c @@ -1061,17 +1097,14 @@ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC fastal/tree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/tree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC io_lib/io_func.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); @@ -1116,20 +1149,12 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC io_lib/pb_util_read_seq_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 757 | register int *p; | ^ 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 - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from io_lib/pb_util_read_seq_util.c:34: + from fastal/tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -1143,30 +1168,6 @@ fastal/scoring.c:82:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)': -io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 68 | register void *ret; - | ^~~ -io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': -io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 91 | register void *ret; - | ^~~ -io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': -io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 191 | register int p; - | ^ -io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': -io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 240 | register char *s = str; - | ^ -io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': -io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 258 | register char *s = str; - | ^ -io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': -io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 356 | register int i; - | ^ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); @@ -1181,10 +1182,6 @@ fastal/scoring.c:502:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': -io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 269 | fgets(outstr, 100, stdin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); @@ -1195,19 +1192,6 @@ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': -io_lib/pb_util_read_seq_util.c:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 280 | 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:305:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 305 | fgets(line, MAXLINE, stdin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 695 | fgets(line, 500, aln_f); @@ -1242,30 +1226,10 @@ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 1235 | 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] - 2076 | } - | ^ -io_lib/io_func.c: In function 'int** read_matrice(char*)': -io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 511 | fscanf ( fp, "\n"); - | ~~~~~~~^~~~~~~~~~~ -io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': -io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 971 | 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_sequence.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC io_lib/tree_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c - CC km_coffee/Stack.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC io_lib/io_func.c + CC io_lib/pb_util_read_seq_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] @@ -1282,17 +1246,82 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC km_coffee/Vector.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ + CC io_lib/pb_util_read_sequence.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)': +io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 68 | register void *ret; + | ^~~ +io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': +io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 91 | register void *ret; + | ^~~ +io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': +io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 191 | register int p; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': +io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 240 | register char *s = str; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': +io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 258 | register char *s = str; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': +io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 356 | register int i; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': +io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 269 | 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:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 280 | 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:305:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 305 | fgets(line, MAXLINE, stdin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +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] + 1235 | 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] + 2076 | } + | ^ +io_lib/io_func.c: In function 'int** read_matrice(char*)': +io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 511 | fscanf ( fp, "\n"); + | ~~~~~~~^~~~~~~~~~~ +io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': +io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 30 | typedef struct ALNcol | ^~~~~~~ - CC km_coffee/classes.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c + CC io_lib/tree_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/Stack.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()': io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 79 | register int i; @@ -1330,6 +1359,10 @@ io_lib/pb_util_read_sequence.c:280:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fgets(line,MAXLINE+1,fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/Vector.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1399,6 +1432,15 @@ io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ + CC km_coffee/classes.c + CC km_coffee/km_coffee.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/km_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ km_coffee/Vector.c: In function 'void print_vecs(VectorSet*, char*)': km_coffee/Vector.c:869:34: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 869 | fprintf(out_F, "%i ", i); @@ -1406,26 +1448,6 @@ | | | | int size_t {aka long unsigned int} | %li - CC km_coffee/km_coffee.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC km_coffee/km_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c - CC km_coffee/kmeans.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': -km_coffee/km_util.c:96:69: warning: format '%s' expects a matching 'char*' argument [-Wformat=] - 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); - | ~^ - | | - | char* -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 - 30 | 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:3717:25: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); @@ -1439,24 +1461,43 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC t_coffee_lib/t_coffee.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': +km_coffee/km_util.c:96:69: warning: format '%s' expects a matching 'char*' argument [-Wformat=] + 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); + | ~^ + | | + | char* 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:491:14: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ + CC km_coffee/kmeans.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC t_coffee_lib/t_coffee.c CC util_lib/aln_compare.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/aln_convertion_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ - CC util_lib/aln_convertion_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 + 30 | typedef struct ALNcol + | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } @@ -1465,11 +1506,8 @@ t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ + CC util_lib/hsearch.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); @@ -1478,23 +1516,15 @@ t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ - CC util_lib/hsearch.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC util_lib/reformat.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 30 | typedef struct ALNcol | ^~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC util_lib/reformat_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) @@ -1512,16 +1542,11 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ + CC util_lib/reformat.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/reformat_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); @@ -1532,12 +1557,40 @@ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from /usr/include/string.h:548, + from t_coffee_lib/t_coffee.c:32: +In function 'char* strcpy(char*, const char*)', + inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] + 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' +In function 'char* strcpy(char*, const char*)', + inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] + 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ + CC util_lib/util_aln_analyze.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ - CC util_lib/util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] @@ -1558,31 +1611,43 @@ util_lib/reformat_struc.c:416:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 416 | fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ - CC util_lib/util_aln_analyze.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c +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] + 1009 | } + | ^ +util_lib/util.c: In function 'int dump_nfc(char*, char*)': +util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4456 | } + | ^ + CC util_lib/util_analyse_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c +util_lib/util.c: In function 'int set_nproc(int)': +util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] + 5489 | } + | ^ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from /usr/include/string.h:548, - from t_coffee_lib/t_coffee.c:32: -In function 'char* strcpy(char*, const char*)', - inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] - 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' -In function 'char* strcpy(char*, const char*)', - inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] - 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' +util_lib/util.c: In function 'char* vremove3(char*, char*)': +util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] + 6938 | } + | ^ + CC util_lib/util_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/util_declare.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } @@ -1645,21 +1710,33 @@ util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3948:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ +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:281:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 306 | fread (ra_j, size, len, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 311 | fread (ra_j_1, size, len, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1669,6 +1746,10 @@ util_lib/reformat.c:3983:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ +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:420:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 420 | fread ( key2, el_size, entry_len,fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:4256:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); @@ -1683,6 +1764,10 @@ util_lib/reformat.c:4507:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': +util_lib/util.c:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 847 | fscanf ( fp, "%d",&list[n[0]++]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4512 | fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1694,15 +1779,32 @@ util_lib/reformat.c:4624:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ -util_lib/reformat.c: In function 'int get_next_fasta_sequence(FILE*, char**, char**, char**)': -util_lib/reformat.c:5264:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 5264 | fgets (line, ml,fp); - | ~~~~~~^~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util.c:52: + from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +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] + 1321 | fscanf ( fp, "%s %s\n", s1, s2); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c: In function 'int get_next_fasta_sequence(FILE*, char**, char**, char**)': +util_lib/reformat.c:5264:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 5264 | fgets (line, ml,fp); + | ~~~~~~^~~~~~~~~~~~~ +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] + 1805 | 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] + 1809 | fscanf(fp, "%d ", &len2); + | ~~~~~~^~~~~~~~~~~~~~~~~~ +util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1812 | 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] + 1813 | fscanf (fp, "\n"); + | ~~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5724:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5724 | fscanf (fp, "%s", name); @@ -1726,125 +1828,18 @@ util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/util_analyse_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c -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] - 713 | } - | ^ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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] - 1009 | } - | ^ - CC util_lib/util_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': -util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14294 | fscanf ( fp, "%s ", buf); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14307 | fscanf ( fp, "%d ", &value); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14332:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14332 | fscanf(fp, "\n"); - | ~~~~~~^~~~~~~~~~ -util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': -util_lib/reformat.c:14357:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] -14357 | fgets ( sbuf, VERY_LONG_STRING, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14374 | fscanf ( fp, "%s ", buf); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14387 | fscanf ( fp, "%d ", &value); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14414 | fscanf(fp, "\n"); - | ~~~~~~^~~~~~~~~~ -util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': -util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] -14525 | fgets ( sbuf, VERY_LONG_STRING, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 4480 | } - | ^ -util_lib/util.c: In function 'int dump_nfc(char*, char*)': -util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] - 4456 | } - | ^ -util_lib/util.c: In function 'int set_nproc(int)': -util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] - 5489 | } - | ^ -util_lib/util.c: In function 'char* vremove3(char*, char*)': -util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] - 6938 | } - | ^ -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:281:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 306 | fread (ra_j, size, len, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 311 | 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:420:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 420 | 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:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 847 | fscanf ( fp, "%d",&list[n[0]++]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ -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] - 1321 | 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] - 1805 | 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] - 1809 | fscanf(fp, "%d ", &len2); - | ~~~~~~^~~~~~~~~~~~~~~~~~ -util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1812 | 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] - 1813 | fscanf (fp, "\n"); - | ~~~~~~~^~~~~~~~~~ - CC util_lib/util_declare.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 713 | } + | ^ util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': util_lib/util.c:5761:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); @@ -1884,25 +1879,41 @@ util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ - CC util_lib/util_domain_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util.c: In function 'int km_main(int, char**)': util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ -util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': -util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] - 1311 | } +util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': +util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14294 | fscanf ( fp, "%s ", buf); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14307 | fscanf ( fp, "%d ", &value); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14332:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14332 | fscanf(fp, "\n"); + | ~~~~~~^~~~~~~~~~ +util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': +util_lib/reformat.c:14357:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] +14357 | fgets ( sbuf, VERY_LONG_STRING, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14374 | fscanf ( fp, "%s ", buf); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14387 | fscanf ( fp, "%d ", &value); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14414 | fscanf(fp, "\n"); + | ~~~~~~^~~~~~~~~~ +util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': +util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] +14525 | fgets ( sbuf, VERY_LONG_STRING, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 4480 | } | ^ -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:2224:49: warning: too many arguments for format [-Wformat-extra-args] - 2224 | 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:2851:40: warning: too many arguments for format [-Wformat-extra-args] - 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); - | ^~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); @@ -1923,25 +1934,32 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ + CC util_lib/util_domain_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': +util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] + 1311 | } + | ^ +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:2224:49: warning: too many arguments for format [-Wformat-extra-args] + 2224 | 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:2851:40: warning: too many arguments for format [-Wformat-extra-args] + 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); + | ^~~~~~~~~~~~~~~~~~~ CC util_lib/util_dps.c -io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': -io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 4597 | sprintf (index, "%d", i); - | ^~ -io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] - 4597 | sprintf (index, "%d", i); - | ^~~~ -In file included from /usr/include/stdio.h:970, - from io_lib/tree_util.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': @@ -1976,33 +1994,33 @@ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2979 | fgets (line , 200 , fp); | ~~~~~~^~~~~~~~~~~~~~~~~ +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 + 30 | typedef struct ALNcol + | ^~~~~~~ util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': util_lib/util_constraints_list.c:4053:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util_domain_constraints_list.c:33: + from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 - 30 | typedef struct ALNcol - | ^~~~~~~ CC util_lib/util_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from util_lib/util_job_handling.c:33: + from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util_make_tree.c:33: + from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -2112,6 +2130,24 @@ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ +io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': +io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 4597 | sprintf (index, "%d", i); + | ^~ +io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] + 4597 | sprintf (index, "%d", i); + | ^~~~ +In file included from /usr/include/stdio.h:970, + from io_lib/tree_util.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1286:28: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | 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); @@ -2179,32 +2215,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 694 | sprintf ( aln_mode, "%s", method->aln_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __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:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 695 | sprintf ( out_mode, "%s", method->out_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); @@ -2234,28 +2244,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': -util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] -12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); - | ^~~~ -In file included from /usr/include/stdio.h:970, - from util_lib/aln_convertion_util.c:27: +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:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 694 | sprintf ( aln_mode, "%s", method->aln_mode); + | ^~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 + inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': -util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] -12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); - | ^~~~ +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:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 695 | sprintf ( out_mode, "%s", method->out_mode); + | ^~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 + inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, @@ -2304,6 +2312,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': +util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] +12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); + | ^~~~ +In file included from /usr/include/stdio.h:970, + from util_lib/aln_convertion_util.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': +util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] +12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); + | ^~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __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:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | 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); @@ -2402,8 +2438,8 @@ dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. -dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. +dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2411,12 +2447,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1959640 and its subdirectories -I: Current time: Fri Mar 27 03:19:53 -12 2026 -I: pbuilder-time-stamp: 1774624793 +I: removing directory /srv/workspace/pbuilder/2436871 and its subdirectories +I: Current time: Sat Feb 22 22:58:24 +14 2025 +I: pbuilder-time-stamp: 1740214704 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diff: 90.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diff.gz b2/build.log: 89.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 89.3% -- replaced with stdout Sat Feb 22 08:58:26 UTC 2025 I: diffoscope 289 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_t-coffee_trixie_amd64_1740214706 + touch /var/log/reproducible-builds/diffoscope_stamp_t-coffee_trixie_amd64_1740214706 + RESULT=0 + systemd-run '--description=diffoscope on t-coffee/13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_38-47852 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH --run-session -c jenkins-reproducible-trixie-diffoscope-54fb2292-0897-49ae-b255-f20d30566af8 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/dbd-tmp-oGtBx5G ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_38-47852.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 257ms CPU time consumed: 257ms _ __ __ | |_ ___ ___ / _|/ _| ___ ___ | __|____ / __/ _ \| |_| |_ / _ \/ _ \ | ||_____| (_| (_) | _| _| __/ __/ \__| \___\___/|_| |_| \___|\___| Sat Feb 22 08:58:27 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sat Feb 22 08:58:27 UTC 2025 I: t-coffee from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-22 08:58:27] INFO: Starting at 2025-02-22 08:58:27.741700 [2025-02-22 08:58:27] INFO: Generating the pages of 1 package(s) [2025-02-22 08:58:28] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/t-coffee didn't produce a buildlog, even though it has been built. [2025-02-22 08:58:28] INFO: Finished at 2025-02-22 08:58:28.173898, took: 0:00:00.432204 Sat Feb 22 08:58:28 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/t-coffee.html Sat Feb 22 08:58:28 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Feb 22 08:58:28 UTC 2025 I: Submitting 8.0K b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc https://buildinfo.debian.net/d2265a7b28f9ba3766e7e324a7730af208accd52/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all Sat Feb 22 08:58:29 UTC 2025 I: Submitting 8.0K b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc https://buildinfo.debian.net/d108e066f58e12305d1218e07b63ac187c7966fb/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all Sat Feb 22 08:58:29 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Feb 22 08:58:29 UTC 2025 I: Done submitting .buildinfo files. Sat Feb 22 08:58:29 UTC 2025 I: Removing signed t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc files: removed './b1/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc' removed './b2/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo.asc' 1740214709 amd64 trixie t-coffee Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.rbuild.log: 88.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.rbuild.log.gz [2025-02-22 08:58:30] INFO: Starting at 2025-02-22 08:58:30.030712 [2025-02-22 08:58:30] INFO: Generating the pages of 1 package(s) [2025-02-22 08:58:30] INFO: Finished at 2025-02-22 08:58:30.456905, took: 0:00:00.426205 All cleanup done. Sat Feb 22 08:58:30 UTC 2025 - total duration: 0h 3m 21s. Sat Feb 22 08:58:30 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-7crKtnG3, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 23.822s CPU time consumed: 7.210s