I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 4 12:07:00 -12 2025 I: pbuilder-time-stamp: 1757030820 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [biococoa_2.2.2-5.dsc] I: copying [./biococoa_2.2.2.orig.tar.gz] I: copying [./biococoa_2.2.2-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.lwXKMrgR/trustedkeys.kbx': General error gpgv: Signature made Wed Nov 25 01:12:07 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biococoa_2.2.2-5.dsc dpkg-source: info: extracting biococoa in biococoa-2.2.2 dpkg-source: info: unpacking biococoa_2.2.2.orig.tar.gz dpkg-source: info: unpacking biococoa_2.2.2-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4148400/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,-fixfilepath parallel=42 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='40ecf17494504b79b52f6dc91abcd9f0' 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='4148400' 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.qcTMy0Ej/pbuilderrc_aTEp --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qcTMy0Ej/b1 --logfile b1/build.log biococoa_2.2.2-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.9.7+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1~bpo12+1 (2024-07-03) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Mar 27 2024 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Mar 27 2024 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Mar 27 2024 more -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount -rwxr-xr-x 1 root root 18664 Mar 27 2024 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 9 03:46 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Mar 27 2024 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Mar 27 2024 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/4148400/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: cdbs, gnustep-make, debhelper (>= 11~), libgnustep-base-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19711 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 cdbs; however: Package cdbs is not installed. pbuilder-satisfydepends-dummy depends on gnustep-make; however: Package gnustep-make is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libgnustep-base-dev; however: Package libgnustep-base-dev 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} ca-certificates{a} cdbs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gnustep-base-common{a} gnustep-base-runtime{a} gnustep-common{a} gnustep-make{a} gobjc{a} gobjc-10{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libdbus-1-3{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgc1{a} libgnustep-base-dev{a} libgnustep-base1.27{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libobjc-10-dev{a} libobjc4{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libxslt1.1{a} m4{a} man-db{a} openssl{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 33.8 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u2 [146 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 cdbs all 0.4.163 [82.6 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 gnustep-common amd64 2.8.0-1 [118 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 gnustep-base-common all 1.27.0-3 [297 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libgc1 amd64 1:8.0.4-3 [239 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libobjc4 amd64 10.2.1-6 [41.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libxslt1.1 amd64 1.1.34-4+deb11u1 [240 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libgnustep-base1.27 amd64 1.27.0-3 [1636 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 gnustep-base-runtime amd64 1.27.0-3 [432 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libobjc-10-dev amd64 10.2.1-6 [170 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 gobjc-10 amd64 10.2.1-6 [8442 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 gobjc amd64 4:10.2.1-1 [1004 B] Get: 49 http://deb.debian.org/debian bullseye/main amd64 gnustep-make all 2.8.0-1 [216 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libgnustep-base-dev amd64 1.27.0-3 [2095 kB] Fetched 33.8 MB in 3s (9791 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19711 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u2_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../06-openssl_1.1.1w-0+deb11u1_amd64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../07-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../09-libmagic1_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cdbs. Preparing to unpack .../18-cdbs_0.4.163_all.deb ... Unpacking cdbs (0.4.163) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../23-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../24-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../25-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../26-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../28-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../29-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/biococoa-2.2.2/ && 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 > ../biococoa_2.2.2-5_source.changes dpkg-buildpackage: info: source package biococoa dpkg-buildpackage: info: source version 2.2.2-5 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 test -x debian/rules rm -f debian/stamp-makefile-build debian/stamp-makefile-install GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 -k clean make[1]: Entering directory '/build/reproducible-path/biococoa-2.2.2' This is gnustep-make 2.8.0. Type 'make print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' make[2]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory '/build/reproducible-path/biococoa-2.2.2' dh_clean rm -f debian/libbiococoa2.install rm -f debian/libbiococoa-dev.install debian/rules binary test -x debian/rules dh_testroot dh_prep dh_installdirs -A sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworklib.install.in > debian/libbiococoa2.install sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworkdev.install.in > debian/libbiococoa-dev.install mkdir -p "." GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 make[1]: Entering directory '/build/reproducible-path/biococoa-2.2.2' This is gnustep-make 2.8.0. Type 'make print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... /usr/share/GNUstep/Makefiles/mkinstalldirs ../../BioCocoa.framework/Versions/2/Headers /usr/bin/install -c -p -m 644 BCPairwiseAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h /usr/bin/install -c -p -m 644 BCScoreMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h /usr/bin/install -c -p -m 644 BCSequenceAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... /usr/bin/install -c -p -m 644 BCMCP.h ../../BioCocoa.framework/Versions/2/Headers/BCMCP.h /usr/bin/install -c -p -m 644 BCSuffixArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... /usr/bin/install -c -p -m 644 BCSeries.h ../../BioCocoa.framework/Versions/2/Headers/BCSeries.h /usr/bin/install -c -p -m 644 BCSample.h ../../BioCocoa.framework/Versions/2/Headers/BCSample.h /usr/bin/install -c -p -m 644 BCPlatform.h ../../BioCocoa.framework/Versions/2/Headers/BCPlatform.h /usr/bin/install -c -p -m 644 BCParseSOFT.h ../../BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... /usr/bin/install -c -p -m 644 BCCodonDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h /usr/bin/install -c -p -m 644 BCCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCCodon.h /usr/bin/install -c -p -m 644 BCCodonRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h /usr/bin/install -c -p -m 644 BCGeneticCode.h ../../BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... /usr/bin/install -c -p -m 644 BCAtom.h ../../BioCocoa.framework/Versions/2/Headers/BCAtom.h /usr/bin/install -c -p -m 644 BCProteinStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h /usr/bin/install -c -p -m 644 BCSecondaryStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h /usr/bin/install -c -p -m 644 BCChain.h ../../BioCocoa.framework/Versions/2/Headers/BCChain.h /usr/bin/install -c -p -m 644 BCResidue.h ../../BioCocoa.framework/Versions/2/Headers/BCResidue.h /usr/bin/install -c -p -m 644 BCSequenceStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... /usr/bin/install -c -p -m 644 BCAnnotation.h ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h /usr/bin/install -c -p -m 644 BCSequence.h ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h /usr/bin/install -c -p -m 644 BCSequenceArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h /usr/bin/install -c -p -m 644 BCSequenceCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... /usr/bin/install -c -p -m 644 BCSequenceReader.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h /usr/bin/install -c -p -m 644 BCSequenceWriter.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h /usr/bin/install -c -p -m 644 BCCachedSequenceFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h /usr/bin/install -c -p -m 644 BCCachedFastaFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... /usr/bin/install -c -p -m 644 BCAminoAcid.h ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h /usr/bin/install -c -p -m 644 BCNucleotide.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h /usr/bin/install -c -p -m 644 BCSymbol.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h /usr/bin/install -c -p -m 644 BCNucleotideDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h /usr/bin/install -c -p -m 644 BCNucleotideRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h /usr/bin/install -c -p -m 644 BCSymbolSet.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... /usr/bin/install -c -p -m 644 BCSequenceTool.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h /usr/bin/install -c -p -m 644 BCToolDigest.h ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h /usr/bin/install -c -p -m 644 BCToolHydropathyCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h /usr/bin/install -c -p -m 644 BCToolMassCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h /usr/bin/install -c -p -m 644 BCToolComplement.h ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h /usr/bin/install -c -p -m 644 BCToolSequenceFinder.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h /usr/bin/install -c -p -m 644 BCToolSymbolCounter.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h /usr/bin/install -c -p -m 644 BCToolTranslator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h /usr/bin/install -c -p -m 644 BCToolTranslatorDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... /usr/bin/install -c -p -m 644 BCDataMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h /usr/bin/install -c -p -m 644 BCUtilData.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h /usr/bin/install -c -p -m 644 BCUtilStrings.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... /usr/bin/install -c -p -m 644 BCFoundation.h ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h /usr/bin/install -c -p -m 644 BCFoundationDefines.h ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h /usr/bin/install -c -p -m 644 BCStringDefinitions.h ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h /usr/bin/install -c -p -m 644 BCPreferences.h ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h make[2]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs ./derived_src; \ touch derived_src/.stamp /usr/share/GNUstep/Makefiles/mkinstalldirs BioCocoa.framework/Versions/2/Resources cd ./BioCocoa.framework/Versions; \ rm -f Current; \ ln -s 2 Current cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of framework BioCocoa... make[2]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAlignment... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAlignment.obj/ gcc BCPairwiseAlignment.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAlignment.obj/BCPairwiseAlignment.m.o gcc BCScoreMatrix.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAlignment.obj/BCScoreMatrix.m.o gcc BCSequenceAlignment.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAlignment.obj/BCSequenceAlignment.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCAlignment.obj/BCPairwiseAlignment.m.o obj/BCAlignment.obj/BCScoreMatrix.m.o obj/BCAlignment.obj/BCSequenceAlignment.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAnalysis... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAnalysis.obj/ gcc BCMCP.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAnalysis.obj/BCMCP.m.o BCMCP.m: In function '+[BCMCP mcpToFile:suffixArray:withSuffixArray:lowerBound:]': BCMCP.m:160:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | fread(&sa1Offset, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:161:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 161 | fread(&sa1File, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:163:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 163 | fread(&sa2Offset, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:164:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 164 | fread(&sa2File, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:334:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 334 | fread(&sa2Offset, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(&sa2File, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:352:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 352 | fread(&sa1Offset, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:353:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 353 | fread(&sa1File, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:358:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&sa2Offset, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:359:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 359 | fread(&sa2File, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:366:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(&sa2Offset, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:367:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | fread(&sa2File, sizeof(int), 1, sa2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m: In function '-[BCMCP intersectToFile:withMCP:]': BCMCP.m:486:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fread(&mcp1Length, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:487:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fread(&mcp1NumFiles, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:489:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 489 | fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:490:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 490 | fread(&(mcp1File[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:514:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 514 | fread(&mcp2Length, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:515:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 515 | fread(&mcp2NumFiles, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:517:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 517 | fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:518:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fread(&(mcp2File[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:735:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 735 | fread(&mcp1Length, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:736:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 736 | fread(&mcp1NumFiles, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:738:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 738 | fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:739:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 739 | fread(&(mcp1File[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 762 | fread(&mcp2Length, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 763 | fread(&mcp2NumFiles, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:765:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 765 | fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:766:11: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 766 | fread(&(mcp2File[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m: In function '-[BCMCP unionToFile:withMCP:]': BCMCP.m:910:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 910 | fread(&mcp1Length, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:911:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 911 | fread(&mcp1NumFiles, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:913:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 913 | fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:914:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 914 | fread(&(mcp1File[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:936:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 936 | fread(&mcp2Length, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:937:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 937 | fread(&mcp2NumFiles, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:939:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 939 | fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:940:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 940 | fread(&(mcp2File[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1093:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1093 | fread(&mcp1Length, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1094:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1094 | fread(&mcp1NumFiles, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1096:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1096 | fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1097:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1097 | fread(&(mcp1File[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1123:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1123 | fread(&mcp2Length, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1124:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1124 | fread(&mcp2NumFiles, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1126:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1126 | fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1127:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1127 | fread(&(mcp2File[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1167:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1167 | fread(&mcp1Length, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1168:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1168 | fread(&mcp1NumFiles, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1170:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1170 | fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1171:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1171 | fread(&(mcp1File[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1186:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1186 | fread(&mcp2Length, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1187:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1187 | fread(&mcp2NumFiles, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1189:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1189 | fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1190:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1190 | fread(&(mcp2File[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1222:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1222 | fread(&mcp2Length, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1223:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1223 | fread(&mcp2NumFiles, sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1225:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1225 | fread(&(mcp2Offset[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1226:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1226 | fread(&(mcp2File[i]), sizeof(int), 1, mcp2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1239:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1239 | fread(&mcp1Length, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1240:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1240 | fread(&mcp1NumFiles, sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1242:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1242 | fread(&(mcp1Offset[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1243:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1243 | fread(&(mcp1File[i]), sizeof(int), 1, mcp1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m: In function '-[BCMCP trimToFile:]': BCMCP.m:1272:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1272 | fread(&mcpLength, sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1273:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1273 | fread(&mcpNumFiles, sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1275:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1275 | fread(&(mcpOffset[i]), sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1276:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1276 | fread(&(mcpFile[i]), sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m: In function '-[BCMCP outputFormat:withMinimumLength:]': BCMCP.m:1481:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1481 | fread(&mcpLength, sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1482:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1482 | fread(&mcpNumFiles, sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1485:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1485 | fread(&(mcpOffset[i]), sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1486:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1486 | fread(&(mcpFile[i]), sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1603:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1603 | fread(&mcpLength, sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1604:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1604 | fread(&mcpNumFiles, sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1606 | fread(&(mcpOffset[i]), sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1607 | fread(&(mcpFile[i]), sizeof(int), 1, mcp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc BCSuffixArray.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCAnalysis.obj/BCSuffixArray.m.o BCSuffixArray.m: In function '-[BCSuffixArray dumpSuffixArray]': BCSuffixArray.m:896:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 896 | fread(&sa1Offset, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:897:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 897 | fread(&sa1File, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:932:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 932 | fread(&sa1Offset, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:933:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 933 | fread(&sa1File, sizeof(int), 1, sa1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m: In function '-[BCSuffixArrayUnionEnumerator nextSuffixPosition:sequence:suffixArray:]': BCSuffixArray.m:1464:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1464 | fread(&(suffixPositions[i]), sizeof(int), 1, arrayFiles[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:1465:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1465 | fread(&(suffixSequences[i]), sizeof(int), 1, arrayFiles[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:1598:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1598 | fread(&(suffixPositions[currentSuffix]), sizeof(int), 1, arrayFiles[currentSuffix]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:1599:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1599 | fread(&(suffixSequences[currentSuffix]), sizeof(int), 1, arrayFiles[currentSuffix]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneExpression... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneExpression.obj/ gcc BCSeries.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneExpression.obj/BCSeries.m.o gcc BCSample.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneExpression.obj/BCSample.m.o gcc BCPlatform.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneExpression.obj/BCPlatform.m.o gcc BCParseSOFT.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneExpression.obj/BCParseSOFT.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCGeneExpression.obj/BCSeries.m.o obj/BCGeneExpression.obj/BCSample.m.o obj/BCGeneExpression.obj/BCPlatform.m.o obj/BCGeneExpression.obj/BCParseSOFT.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneticCode... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneticCode.obj/ gcc BCCodonDNA.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneticCode.obj/BCCodonDNA.m.o gcc BCCodon.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneticCode.obj/BCCodon.m.o gcc BCCodonRNA.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneticCode.obj/BCCodonRNA.m.o gcc BCGeneticCode.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneticCode.obj/BCGeneticCode.m.o BCGeneticCode.m: In function '+[BCGeneticCode priv:createCodonArraysFromDictionary:]': BCGeneticCode.m:221:23: warning: variable 'RNACodon' set but not used [-Wunused-but-set-variable] 221 | BCCodon *aCodon, *RNACodon; | ^~~~~~~~ gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCGeneticCode.obj/BCCodonDNA.m.o obj/BCGeneticCode.obj/BCCodon.m.o obj/BCGeneticCode.obj/BCCodonRNA.m.o obj/BCGeneticCode.obj/BCGeneticCode.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCProteinStructure... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCProteinStructure.obj/ gcc BCAtom.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCProteinStructure.obj/BCAtom.m.o gcc BCProteinStructure.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCProteinStructure.obj/BCProteinStructure.m.o gcc BCSecondaryStructure.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o gcc BCChain.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCProteinStructure.obj/BCChain.m.o gcc BCResidue.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCProteinStructure.obj/BCResidue.m.o gcc BCSequenceStructure.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCProteinStructure.obj/BCSequenceStructure.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCProteinStructure.obj/BCAtom.m.o obj/BCProteinStructure.obj/BCProteinStructure.m.o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o obj/BCProteinStructure.obj/BCChain.m.o obj/BCProteinStructure.obj/BCResidue.m.o obj/BCProteinStructure.obj/BCSequenceStructure.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequence... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequence.obj/ gcc BCAnnotation.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequence.obj/BCAnnotation.m.o gcc BCSequence.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequence.obj/BCSequence.m.o gcc BCSequenceArray.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequence.obj/BCSequenceArray.m.o gcc BCSequenceCodon.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequence.obj/BCSequenceCodon.m.o BCSequenceCodon.m: In function '-[BCSequenceCodon openReadingFramesLongerThanCutoff:]': BCSequenceCodon.m:301:16: warning: 'inORF' may be used uninitialized in this function [-Wmaybe-uninitialized] 301 | if ( inORF ) | ^ gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCSequence.obj/BCAnnotation.m.o obj/BCSequence.obj/BCSequence.m.o obj/BCSequence.obj/BCSequenceArray.m.o obj/BCSequence.obj/BCSequenceCodon.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequenceIO... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequenceIO.obj/ gcc BCSequenceReader.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequenceIO.obj/BCSequenceReader.m.o BCSequenceReader.m: In function '-[BCSequenceReader readFileUsingText:]': BCSequenceReader.m:167:3: warning: no '-initWithRTF:documentAttributes:' method found 167 | NSAttributedString *rtfstring = [[NSAttributedString alloc] initWithRTF: [entryString dataUsingEncoding: NSUTF8StringEncoding] documentAttributes: nil]; | ^~~~~~~~~~~~~~~~~~ BCSequenceReader.m:167:3: warning: (messages without a matching method signature will be assumed to return 'id' and accept '...' as arguments) BCSequenceReader.m: In function '-[BCSequenceReader readMacVectorFile:]': BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] 651 | NSMutableArray *annotationsArray; | ^~~~~~~~~~~~~~~~ BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:798:3: warning: passing argument 2 of 'scanUpToString:intoString:' from incompatible pointer type [-Wincompatible-pointer-types] 798 | [lineScanner scanUpToString:@" " intoString: nil]; | ^ | | | id BCSequenceReader.m:798:3: note: expected 'struct NSString **' but argument is of type 'id' BCSequenceReader.m: In function '-[BCSequenceReader readPhylipFile:]': BCSequenceReader.m:1113:31: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] 1113 | NSMutableArray *linesArray, *annotationsArray, *namesArray, *sequenceArray; | ^~~~~~~~~~~~~~~~ BCSequenceReader.m: In function '-[BCSequenceReader readSwissProtFile:]': BCSequenceReader.m:426:3: warning: 'sequenceString' may be used uninitialized in this function [-Wmaybe-uninitialized] 426 | newSequence = [BCSequence sequenceWithString: sequenceString]; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:3: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wmaybe-uninitialized] 822 | sequenceString = [line substringFromIndex: sequenceRange.location]; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSequenceReader.m: In function '-[BCSequenceReader readFASTQFile:]': BCSequenceReader.m:1310:6: warning: 'seqData' may be used uninitialized in this function [-Wmaybe-uninitialized] 1310 | BCSequence *newSequence = [[BCSequence alloc] initWithData: seqData symbolSet: nil]; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc BCSequenceWriter.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequenceIO.obj/BCSequenceWriter.m.o gcc BCCachedSequenceFile.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o gcc BCCachedFastaFile.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:58:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 58 | fread(&c, sizeof(char), 1, g1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:73:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | fread(&c, sizeof(char), 1, g1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:76:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fread(&c, sizeof(char), 1, g1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:97:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fread(&c, sizeof(char), 1, g1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m: In function '-[BCCachedFastaFile symbols:ForCurrentSequenceAtPosition:ofLength:]': BCCachedFastaFile.m:149:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | fread(&c, sizeof(char), 1, fileHandle); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:104:3: warning: 'filePos' may be used uninitialized in this function [-Wmaybe-uninitialized] 104 | [d setObject: [NSNumber numberWithUnsignedLongLong: (filePos - 1)] forKey: @"end"]; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCSequenceIO.obj/BCSequenceReader.m.o obj/BCSequenceIO.obj/BCSequenceWriter.m.o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSymbol... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSymbol.obj/ gcc BCAminoAcid.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSymbol.obj/BCAminoAcid.m.o gcc BCNucleotide.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSymbol.obj/BCNucleotide.m.o gcc BCSymbol.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSymbol.obj/BCSymbol.m.o gcc BCNucleotideDNA.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSymbol.obj/BCNucleotideDNA.m.o gcc BCNucleotideRNA.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSymbol.obj/BCNucleotideRNA.m.o gcc BCSymbolSet.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCSymbol.obj/BCSymbolSet.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCSymbol.obj/BCAminoAcid.m.o obj/BCSymbol.obj/BCNucleotide.m.o obj/BCSymbol.obj/BCSymbol.m.o obj/BCSymbol.obj/BCNucleotideDNA.m.o obj/BCSymbol.obj/BCNucleotideRNA.m.o obj/BCSymbol.obj/BCSymbolSet.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCTools... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCTools.obj/ gcc BCSequenceTool.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCSequenceTool.m.o gcc BCToolDigest.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolDigest.m.o gcc BCToolHydropathyCalculator.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolHydropathyCalculator.m.o gcc BCToolMassCalculator.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolMassCalculator.m.o gcc BCToolComplement.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolComplement.m.o gcc BCToolSequenceFinder.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolSequenceFinder.m.o gcc BCToolSymbolCounter.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolSymbolCounter.m.o gcc BCToolTranslator.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolTranslator.m.o gcc BCToolTranslatorDNA.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCTools.obj/BCToolTranslatorDNA.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCTools.obj/BCSequenceTool.m.o obj/BCTools.obj/BCToolDigest.m.o obj/BCTools.obj/BCToolHydropathyCalculator.m.o obj/BCTools.obj/BCToolMassCalculator.m.o obj/BCTools.obj/BCToolComplement.m.o obj/BCTools.obj/BCToolSequenceFinder.m.o obj/BCTools.obj/BCToolSymbolCounter.m.o obj/BCTools.obj/BCToolTranslator.m.o obj/BCTools.obj/BCToolTranslatorDNA.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCUtils... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCUtils.obj/ gcc BCDataMatrix.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCUtils.obj/BCDataMatrix.m.o gcc BCUtilData.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCUtils.obj/BCUtilData.m.o gcc BCUtilStrings.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCUtils.obj/BCUtilStrings.m.o BCUtilStrings.m: In function '-[NSString(StringAdditions) stringBeginsWithTwoNumbers]': BCUtilStrings.m:98:2: warning: passing argument 1 of 'scanInt:' from incompatible pointer type [-Wincompatible-pointer-types] 98 | if ([scanner scanInt:nil]) | ^~ | | | id BCUtilStrings.m:98:2: note: expected 'int *' but argument is of type 'id' BCUtilStrings.m:100:3: warning: passing argument 1 of 'scanInt:' from incompatible pointer type [-Wincompatible-pointer-types] 100 | if ([scanner scanInt:nil]) | ^~ | | | id BCUtilStrings.m:100:3: note: expected 'int *' but argument is of type 'id' gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCUtils.obj/BCDataMatrix.m.o obj/BCUtils.obj/BCUtilData.m.o obj/BCUtils.obj/BCUtilStrings.m.o ; make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ gcc BCStringDefinitions.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I. -I./BCAnalysis -I./BCGeneticCode -I./BCProteinStructure -I./BCSequence -I./BCSequenceIO -I./BCSymbol -I./BCTools -I./BCTools/BCDigest -I./BCTools/BCSequenceProperty -I./BCTools/BCSequenceTools -I./BCTools/BCTranslation -I./BCUtils -I./../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCFoundation.obj/BCStringDefinitions.m.o gcc BCPreferences.m -c \ -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I. -I./BCAnalysis -I./BCGeneticCode -I./BCProteinStructure -I./BCSequence -I./BCSequenceIO -I./BCSymbol -I./BCTools -I./BCTools/BCDigest -I./BCTools/BCSequenceProperty -I./BCTools/BCSequenceTools -I./BCTools/BCTranslation -I./BCUtils -I./../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCFoundation.obj/BCPreferences.m.o gcc -nostdlib -r -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./obj/subproject.o obj/BCFoundation.obj/BCStringDefinitions.m.o obj/BCFoundation.obj/BCPreferences.m.o BCAlignment/obj/subproject.o BCAnalysis/obj/subproject.o BCGeneExpression/obj/subproject.o BCGeneticCode/obj/subproject.o BCProteinStructure/obj/subproject.o BCSequence/obj/subproject.o BCSequenceIO/obj/subproject.o BCSymbol/obj/subproject.o BCTools/obj/subproject.o BCUtils/obj/subproject.o ; make[2]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BioCocoa.obj/ classes=""; \ for object_file in ./BCFoundation/obj/subproject.o __dummy__; do \ if [ "$object_file" != "__dummy__" ]; then \ sym=`nm -Pg $object_file | sed -n -e '/^__objc_class_name_[A-Za-z0-9_.]* [^U]/ {s/^__objc_class_name_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}' -e '/^\._OBJC_CLASS_[A-Za-z0-9_.]* [^U]/ {s/^\._OBJC_CLASS_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}'`; \ classes="$classes $sym"; \ fi; \ done; \ classlist=""; \ classarray=""; \ for f in $classes __dummy__ ; do \ if [ "$f" != "__dummy__" ]; then \ if [ "$classlist" = "" ]; then \ classlist="@\"$f\""; \ classarray="(\"$f\""; \ else \ classlist="$classlist, @\"$f\""; \ classarray="$classarray, \"$f\""; \ fi; \ fi; \ done; \ if [ "$classlist" = "" ]; then \ classlist="NULL"; \ classarray="()"; \ else \ classlist="$classlist, NULL"; \ classarray="$classarray)"; \ fi; \ echo "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa : NSObject" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m gcc derived_src/NSFramework_BioCocoa.m -c -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fconstant-string-class=NSConstantString -I./derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep -o obj/BioCocoa.obj/NSFramework_BioCocoa.o \ gcc -shared -Wl,-soname,libBioCocoa.so.2 -rdynamic -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -pthread -fexceptions -o ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 obj/BioCocoa.obj/NSFramework_BioCocoa.o BCFoundation/obj/subproject.o -L/usr/local/lib -L/usr/lib -lgnustep-base -lobjc && (cd ./BioCocoa.framework/Versions/2/.; rm -f libBioCocoa.so; if [ "libBioCocoa.so.2" != "libBioCocoa.so.2.2.2" ]; then rm -f libBioCocoa.so.2; ln -s libBioCocoa.so.2.2.2 libBioCocoa.so.2; fi; ln -s libBioCocoa.so.2 libBioCocoa.so; ) || rm -f ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 ; \ (cd ./BioCocoa.framework/Versions/2/.; \ rm -f BioCocoa; \ ln -s libBioCocoa.so BioCocoa) \ /usr/bin/ld: BCFoundation/obj/subproject.o: in function `_i_BCSuffixArray__constructFromSequenceArray_strand_': BCSuffixArray.m:(.text+0xc8af): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f .//$f -o -d .//$f ]; then \ cp -fr .//$f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: .//$f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done (echo "{"; echo ' NOTE = "Automatically generated, do not edit!";'; \ echo " NSExecutable = \"BioCocoa\";"; \ echo " NSMainNibFile = \"\";"; \ echo " NSPrincipalClass = \"BioCocoa\";"; \ echo " Classes = "; \ cat ./derived_src/BioCocoa-class-list; \ echo " ;"; \ echo "}") >BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist if [ -r "" ]; then \ plmerge BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist ; \ fi cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so make[1]: Leaving directory '/build/reproducible-path/biococoa-2.2.2' touch debian/stamp-makefile-build CDBS WARNING: DEB_MAKE_CHECK_TARGET unset, not running checks GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/reproducible-path/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 install DESTDIR=/build/reproducible-path/biococoa-2.2.2/debian/tmp/ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM make[1]: Entering directory '/build/reproducible-path/biococoa-2.2.2' This is gnustep-make 2.8.0. Type 'make print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... make[4]: Nothing to be done for 'internal-subproject-build-headers'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... make[3]: Nothing to be done for 'internal-subproject-build-headers'. make[2]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi Making all in subprojects of framework BioCocoa... make[2]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' Making all for subproject BCAlignment... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' Making all for subproject BCSequence... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' Making all for subproject BCSymbol... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' Making all for subproject BCTools... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCUtils... make[5]: Nothing to be done for 'internal-subproject-compile'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... make[4]: Nothing to be done for 'internal-subproject-compile'. make[2]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... make[3]: Nothing to be done for 'internal-framework-compile'. for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f .//$f -o -d .//$f ]; then \ cp -fr .//$f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: .//$f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so Making install in subprojects of framework BioCocoa... make[2]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' Making install for subproject BCAlignment... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' Making install for subproject BCSequence... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' Making install for subproject BCSymbol... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' Making install for subproject BCTools... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCUtils... make[4]: Nothing to be done for 'internal-subproject-install'. make[3]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCFoundation... make[3]: Nothing to be done for 'internal-subproject-install'. make[2]: Leaving directory '/build/reproducible-path/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/include/GNUstep (cd .; \ tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list \ BioCocoa.framework) \ | (cd /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/include/GNUstep /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/.; \ rm -f libBioCocoa.so; \ rm -f libBioCocoa.so.2; \ rm -f libBioCocoa.so.2.2.2; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/. /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2"; then \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/. /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/. /build/reproducible-path/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 make[1]: Leaving directory '/build/reproducible-path/biococoa-2.2.2' touch debian/stamp-makefile-install Adding cdbs dependencies to debian/libbiococoa-dev.substvars dh_installdirs -plibbiococoa-dev \ Adding cdbs dependencies to debian/libbiococoa2.substvars dh_installdirs -plibbiococoa2 \ dh_installdocs -plibbiococoa-dev dh_installexamples -plibbiococoa-dev dh_installman -plibbiococoa-dev dh_installinfo -plibbiococoa-dev dh_installmenu -plibbiococoa-dev dh_installcron -plibbiococoa-dev dh_systemd_enable -plibbiococoa-dev dh_installinit -plibbiococoa-dev dh_installdebconf -plibbiococoa-dev dh_installemacsen -plibbiococoa-dev dh_installcatalogs -plibbiococoa-dev dh_installpam -plibbiococoa-dev dh_installlogrotate -plibbiococoa-dev dh_installlogcheck -plibbiococoa-dev dh_installchangelogs -plibbiococoa-dev ./ChangeLog dh_installudev -plibbiococoa-dev dh_lintian -plibbiococoa-dev dh_bugfiles -plibbiococoa-dev dh_install -plibbiococoa-dev --sourcedir=/build/reproducible-path/biococoa-2.2.2/debian/tmp/ dh_systemd_start -plibbiococoa-dev dh_link -plibbiococoa-dev dh_installmime -plibbiococoa-dev dh_installgsettings -plibbiococoa-dev gsdh_gnustep -plibbiococoa-dev dh_link -plibbiococoa-dev dh_installdocs -plibbiococoa2 dh_installexamples -plibbiococoa2 dh_installman -plibbiococoa2 dh_installinfo -plibbiococoa2 dh_installmenu -plibbiococoa2 dh_installcron -plibbiococoa2 dh_systemd_enable -plibbiococoa2 dh_installinit -plibbiococoa2 dh_installdebconf -plibbiococoa2 dh_installemacsen -plibbiococoa2 dh_installcatalogs -plibbiococoa2 dh_installpam -plibbiococoa2 dh_installlogrotate -plibbiococoa2 dh_installlogcheck -plibbiococoa2 dh_installchangelogs -plibbiococoa2 ./ChangeLog dh_installudev -plibbiococoa2 dh_lintian -plibbiococoa2 dh_bugfiles -plibbiococoa2 dh_install -plibbiococoa2 --sourcedir=/build/reproducible-path/biococoa-2.2.2/debian/tmp/ dh_systemd_start -plibbiococoa2 dh_link -plibbiococoa2 dh_installmime -plibbiococoa2 dh_installgsettings -plibbiococoa2 gsdh_gnustep -plibbiococoa2 dh_link -plibbiococoa2 dh_strip -plibbiococoa-dev dh_strip_nondeterminism -plibbiococoa-dev dh_compress -plibbiococoa-dev dh_fixperms -plibbiococoa-dev dh_makeshlibs -plibbiococoa-dev dh_strip -plibbiococoa2 dh_strip_nondeterminism -plibbiococoa2 dh_compress -plibbiococoa2 dh_fixperms -plibbiococoa2 dh_makeshlibs -plibbiococoa2 --noscripts dh_installdeb -plibbiococoa-dev dh_perl -plibbiococoa-dev dh_shlibdeps -plibbiococoa-dev dh_installdeb -plibbiococoa2 dh_perl -plibbiococoa2 dh_shlibdeps -plibbiococoa2 dh_gencontrol -plibbiococoa-dev dpkg-gencontrol: warning: Depends field of package libbiococoa-dev: substitution variable ${gnustep:Depends} used, but is not defined dh_md5sums -plibbiococoa-dev dh_builddeb -plibbiococoa-dev dpkg-deb: building package 'libbiococoa-dev' in '../libbiococoa-dev_2.2.2-5_amd64.deb'. dh_gencontrol -plibbiococoa2 dpkg-gencontrol: warning: Depends field of package libbiococoa2: substitution variable ${gnustep:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libbiococoa2: substitution variable ${gnustep:Depends} used, but is not defined dh_md5sums -plibbiococoa2 dh_builddeb -plibbiococoa2 dpkg-deb: building package 'libbiococoa2' in '../libbiococoa2_2.2.2-5_amd64.deb'. dpkg-deb: building package 'libbiococoa2-dbgsym' in '../libbiococoa2-dbgsym_2.2.2-5_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biococoa_2.2.2-5_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: not including original 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/4148400 and its subdirectories I: Current time: Thu Sep 4 12:07:44 -12 2025 I: pbuilder-time-stamp: 1757030864