Sun Jul 12 19:36:21 UTC 2020 I: starting to build biococoa/buster/armhf on jenkins on '2020-07-12 19:35' Sun Jul 12 19:36:21 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_9/948/console.log Sun Jul 12 19:36:21 UTC 2020 I: Downloading source for buster/biococoa=2.2.2-4 --2020-07-12 19:36:22-- http://deb.debian.org/debian/pool/main/b/biococoa/biococoa_2.2.2-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2117 (2.1K) Saving to: ‘biococoa_2.2.2-4.dsc’ 0K .. 100% 194M=0s 2020-07-12 19:36:22 (194 MB/s) - ‘biococoa_2.2.2-4.dsc’ saved [2117/2117] Sun Jul 12 19:36:22 UTC 2020 I: biococoa_2.2.2-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: biococoa Binary: libbiococoa-dev, libbiococoa2 Architecture: any Version: 2.2.2-4 Maintainer: Debian Med Packaging Team Uploaders: Scott Christley , Andreas Tille , Charles Plessy Homepage: http://bioinformatics.org/biococoa/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/biococoa Vcs-Git: https://salsa.debian.org/med-team/biococoa.git Build-Depends: cdbs, gnustep-make, debhelper (>= 11~), libgnustep-base-dev Package-List: libbiococoa-dev deb libdevel optional arch=any libbiococoa2 deb libs optional arch=any Checksums-Sha1: 5c3541d5e22d80d3ad85f859f79828422c9d618f 358850 biococoa_2.2.2.orig.tar.gz e0deaefa674b923b65ea918209c629f771f6eb8b 8936 biococoa_2.2.2-4.debian.tar.xz Checksums-Sha256: 383eea4e04ca584ecf5bc06507996acf193d3b1df9afecaca6fb58cbe41df384 358850 biococoa_2.2.2.orig.tar.gz 6ce51ec281a4cc5373441f18a3d5e760535b43488d1a16793318e08289731192 8936 biococoa_2.2.2-4.debian.tar.xz Files: 5d7238f1481385a35679069c8a96e7da 358850 biococoa_2.2.2.orig.tar.gz c5ceda69368ae5aa187e1f63513cff6e 8936 biococoa_2.2.2-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlu8wRMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHdPQ/8Cq4FJ/JGLW10VHW18GGGvsWJAb+5JII1 mlJjj5uydW6AYSJrewBzvaHqzBxcqCMxyJVU4sA2hiKUy1ccw5G0cIXMC5p/7zII 2YJeqaTRt0jw/X7sWgmWMfj5jC4+l1Tabkz96dztbrr0Axs1b2WWgKTVyh7UwFy4 ThayDCXs7ohtj3jDxFdQiEq5snTMylcucvXTyeVPlVTa48eCdRfOIJsxQwnSUsP7 +qtn2lbuq9DGi13CEMhiKXER62lbtrnMFem5DjlX5nfbNSiJixio5wMJVqDLsUdo OM+z751mEbEyLIl6TH7ACgB1LBNI3oCY1MtHfEGxVNjVuquJ/dbadRQBpGPasKCH UXsLR6CJOfj6IlJcbQKQulIFvbbDI10tjfu241DQLv2u0UN06czVM4LVQg02S0zg ptei5ZM5V4gxSLsqUil17M1wO708Z+86y1kzwZN8kZysdwChbCf3dQdZu7lruwgC nmoA+9JH42CpNddjXtyvcUYpcPYi8Hm7ytIDyI+VCuwUlwkPS4s6PebV5PMtENrK 1TXhWqMi+MbllYnAqrWLKmwOfZTWSvhkv3MDJ6u6P2fWx8fm2w4k+52L/mOrhfYK jbr6t69bntben8hNVCSdsJZ6Mo59KENyySHbT9ueTTS9RK5VqxT1qhunv1+EgNvt DrpRM6IX+qo= =9HQv -----END PGP SIGNATURE----- Sun Jul 12 19:36:22 UTC 2020 I: Checking whether the package is not for us Sun Jul 12 19:36:22 UTC 2020 I: Starting 1st build on remote node ff64a-armhf-rb.debian.net. Sun Jul 12 19:36:22 UTC 2020 I: Preparing to do remote build '1' on ff64a-armhf-rb.debian.net. Sun Jul 12 19:38:59 UTC 2020 I: Deleting $TMPDIR on ff64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 12 07:36:28 -12 2020 I: pbuilder-time-stamp: 1594582588 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biococoa_2.2.2-4.dsc] I: copying [./biococoa_2.2.2.orig.tar.gz] I: copying [./biococoa_2.2.2-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Oct 9 02:54:11 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biococoa_2.2.2-4.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_2.2.2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link-libs.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/22982/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='8e2f8fdc19f5400199b6de21c9a8443f' 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='22982' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/pbuilderrc_kdfC --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/b1 --logfile b1/build.log biococoa_2.2.2-4.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux ff64a 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 11 20:25 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/22982/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: armhf 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 ... 18932 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} bsdmainutils{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-8{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbsd0{a} libcroco3{a} libdbus-1-3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgc1c2{a} libglib2.0-0{a} libgnustep-base-dev{a} libgnustep-base1.26{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libobjc-8-dev{a} libobjc4{a} libpipeline1{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} libxslt1.1{a} lsb-base{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 32.5 MB of archives. After unpacking 101 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 19 http://deb.debian.org/debian buster/main armhf openssl armhf 1.1.1d-0+deb10u3 [818 kB] Get: 20 http://deb.debian.org/debian buster/main armhf ca-certificates all 20190110 [157 kB] Get: 21 http://deb.debian.org/debian buster/main armhf cdbs all 0.4.159 [83.7 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 23 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 26 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 28 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 34 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 35 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 36 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 37 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 38 http://deb.debian.org/debian buster/main armhf gnustep-common armhf 2.7.0-4 [116 kB] Get: 39 http://deb.debian.org/debian buster/main armhf gnustep-base-common all 1.26.0-4+deb10u1 [284 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libavahi-common-data armhf 0.7-4+b1 [122 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libavahi-common3 armhf 0.7-4+b1 [51.1 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libdbus-1-3 armhf 1.12.16-1 [190 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libavahi-client3 armhf 0.7-4+b1 [54.5 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libgc1c2 armhf 1:7.6.4-0.4 [212 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libobjc4 armhf 8.3.0-6 [42.2 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libxslt1.1 armhf 1.1.32-2.2~deb10u1 [217 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libgnustep-base1.26 armhf 1.26.0-4+deb10u1 [1297 kB] Get: 48 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 49 http://deb.debian.org/debian buster/main armhf gnustep-base-runtime armhf 1.26.0-4+deb10u1 [402 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libobjc-8-dev armhf 8.3.0-6 [210 kB] Get: 51 http://deb.debian.org/debian buster/main armhf gobjc-8 armhf 8.3.0-6 [6643 kB] Get: 52 http://deb.debian.org/debian buster/main armhf gobjc armhf 4:8.3.0-1 [988 B] Get: 53 http://deb.debian.org/debian buster/main armhf gnustep-make all 2.7.0-4 [211 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libgnustep-base-dev armhf 1.26.0-4+deb10u1 [1832 kB] Fetched 32.5 MB in 3s (9307 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... 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Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up gnustep-base-common (1.26.0-4+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libxslt1.1:armhf (1.1.32-2.2~deb10u1) ... Setting up libavahi-client3:armhf (0.7-4+b1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gobjc (4:8.3.0-1) ... Setting up gettext (0.19.8.1-9) ... Setting up gnustep-make (2.7.0-4) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... 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I: Building the package I: Running cd /build/biococoa-2.2.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package biococoa dpkg-buildpackage: info: source version 2.2.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot 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 -ffile-prefix-map=/build/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/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/biococoa-2.2.2' This is gnustep-make 2.7.0. 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/biococoa-2.2.2/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/biococoa-2.2.2/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory '/build/biococoa-2.2.2/BCFoundation/BCUtils' make[2]: Leaving directory '/build/biococoa-2.2.2/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory '/build/biococoa-2.2.2' dh_clean rm -f debian/libbiococoa2.install rm -f debian/libbiococoa-dev.install debian/rules build test -x debian/rules mkdir -p "." GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -ffile-prefix-map=/build/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/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/biococoa-2.2.2' This is gnustep-make 2.7.0. 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/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/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/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/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/biococoa-2.2.2/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/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 -fgnu-runtime -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] fread(&sa1Offset, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:161:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:163:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:164:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:334:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:335:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:352:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1Offset, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:353:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:358:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:359:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2File, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:366:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa2Offset, sizeof(int), 1, sa2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:367:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] fread(&mcp1Length, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:487:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:489:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp2Length, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:515:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:517:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp1Length, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:736:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:738:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp2Length, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:763:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:765:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp1Length, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:911:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:913:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp2Length, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:937:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:939:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp1Length, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1094:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1096:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp2Length, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1124:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1126:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp1Length, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1168:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1170:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp2Length, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1187:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1189:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp2Length, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1223:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp2NumFiles, sizeof(int), 1, mcp2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1225:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcp1Length, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1240:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcp1NumFiles, sizeof(int), 1, mcp1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1242:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcpLength, sizeof(int), 1, mcp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1273:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpNumFiles, sizeof(int), 1, mcp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1275:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcpLength, sizeof(int), 1, mcp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1482:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpNumFiles, sizeof(int), 1, mcp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1485:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] fread(&mcpLength, sizeof(int), 1, mcp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1604:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&mcpNumFiles, sizeof(int), 1, mcp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCMCP.m:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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 -fgnu-runtime -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] fread(&sa1Offset, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:897:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1File, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:932:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&sa1Offset, sizeof(int), 1, sa1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSuffixArray.m:933:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] 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] 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] 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/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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] 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/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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] 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/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/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 -fgnu-runtime -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 NSAttributedString *rtfstring = [[NSAttributedString alloc] initWithRTF: [entryString dataUsingEncoding: NSUTF8StringEncoding] documentAttributes: nil]; ^~~~~~~~~~~~~~~~~~ BCSequenceReader.m:167:3: warning: (Messages without a matching method signature BCSequenceReader.m:167:3: warning: will be assumed to return 'id' and accept BCSequenceReader.m:167:3: warning: '...' as arguments.) BCSequenceReader.m: In function '-[BCSequenceReader readMacVectorFile:]': BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] 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] [lineScanner scanUpToString:@" " intoString: nil]; ^ 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] NSMutableArray *linesArray, *annotationsArray, *namesArray, *sequenceArray; ^~~~~~~~~~~~~~~~ BCSequenceReader.m: In function '-[BCSequenceReader readSwissProtFile:]': BCSequenceReader.m:421:2: warning: 'sequenceString' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( [sequenceString length]) ~~~~~~~~~~~~~~~~~~~~~~~ BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:3: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wmaybe-uninitialized] 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] 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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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] fread(&c, sizeof(char), 1, g1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:73:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, g1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:76:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&c, sizeof(char), 1, g1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:97:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] 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] [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/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/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 -fgnu-runtime -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 -fgnu-runtime -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 -fgnu-runtime -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] if ([scanner scanInt:nil]) ^~ 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] if ([scanner scanInt:nil]) ^~ 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/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 -fgnu-runtime -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 -fgnu-runtime -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/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;}'`; \ 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 -fgnu-runtime -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_': BCUtilStrings.m:(.text+0x8850): 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/biococoa-2.2.2' touch debian/stamp-makefile-build CDBS WARNING: DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot 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 "." CDBS WARNING: DEB_MAKE_CHECK_TARGET unset, not running checks GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -ffile-prefix-map=/build/biococoa-2.2.2=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/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/biococoa-2.2.2/debian/tmp/ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM make[1]: Entering directory '/build/biococoa-2.2.2' This is gnustep-make 2.7.0. 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/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/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/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/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/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/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/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/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/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory '/build/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/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory '/build/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/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/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /build/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /build/biococoa-2.2.2/debian/tmp///usr/include/GNUstep (cd .; \ tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list \ BioCocoa.framework) \ | (cd /build/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /build/biococoa-2.2.2/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /build/biococoa-2.2.2/debian/tmp///usr/include/GNUstep /build/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /build/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/biococoa-2.2.2/debian/tmp///usr/lib/. /build/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/build/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/biococoa-2.2.2/debian/tmp///usr/lib/. /build/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/biococoa-2.2.2/debian/tmp///usr/lib/. /build/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/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/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/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 dh_md5sums -plibbiococoa-dev dh_builddeb -plibbiococoa-dev dpkg-deb: building package 'libbiococoa-dev' in '../libbiococoa-dev_2.2.2-4_armhf.deb'. dh_gencontrol -plibbiococoa2 dh_md5sums -plibbiococoa2 dh_builddeb -plibbiococoa2 dpkg-deb: building package 'libbiococoa2-dbgsym' in '../libbiococoa2-dbgsym_2.2.2-4_armhf.deb'. dpkg-deb: building package 'libbiococoa2' in '../libbiococoa2_2.2.2-4_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biococoa_2.2.2-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/22982 and its subdirectories I: Current time: Sun Jul 12 07:38:54 -12 2020 I: pbuilder-time-stamp: 1594582734 Sun Jul 12 19:39:01 UTC 2020 I: 1st build successful. Starting 2nd build on remote node cbxi4pro0-armhf-rb.debian.net. Sun Jul 12 19:39:01 UTC 2020 I: Preparing to do remote build '2' on cbxi4pro0-armhf-rb.debian.net. Sun Jul 12 19:47:58 UTC 2020 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net. Sun Jul 12 19:48:01 UTC 2020 I: biococoa_2.2.2-4_armhf.changes: Format: 1.8 Date: Tue, 09 Oct 2018 16:25:32 +0200 Source: biococoa Binary: libbiococoa-dev libbiococoa2 libbiococoa2-dbgsym Architecture: armhf Version: 2.2.2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbiococoa-dev - Bioinformatics framework for GNUstep and Cocoa (development files libbiococoa2 - Bioinformatics framework for GNUstep and Cocoa (library files) Changes: biococoa (2.2.2-4) unstable; urgency=medium . * Drop unneeded get-orig-source target * DEP5 * debhelper 10 (dh_systemd_enable is no longer used in compat >= 11, please use dh_installsystemd instead -> that's a cdbs issue) * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 58fcc4b456a83d58b540c04d73323268e7281207 5645 biococoa_2.2.2-4_armhf.buildinfo 5ea160685c77d7ad09d2a96e17d23425d5094e59 117488 libbiococoa-dev_2.2.2-4_armhf.deb 62336c8dc0886ee88299f9e7b5fdfd73bc4d4b66 26844 libbiococoa2-dbgsym_2.2.2-4_armhf.deb 5ab1ed7651b5f0c96191df83577d09e07e7d56ab 95524 libbiococoa2_2.2.2-4_armhf.deb Checksums-Sha256: 88816cf629e9fa2f04dd1910cf8e23eed746c9b17e7758d9b1d6024777a677ab 5645 biococoa_2.2.2-4_armhf.buildinfo 9242cc872ae84f1e90a07622496214666b1940cd7ed52dc990041fd97f35403f 117488 libbiococoa-dev_2.2.2-4_armhf.deb 830b145f890840cdb3828b838678061f4ec9bf2604ac0e6dc12a19bbc4764c5d 26844 libbiococoa2-dbgsym_2.2.2-4_armhf.deb b469d91874acaf673775186134f38930005646498e27ed8229613e11043f1034 95524 libbiococoa2_2.2.2-4_armhf.deb Files: 1564a46cef0bdd53fa0b8d885da4b408 5645 science optional biococoa_2.2.2-4_armhf.buildinfo 020f66d27a85d2531f27d0ca9c85ae01 117488 libdevel optional libbiococoa-dev_2.2.2-4_armhf.deb a2a3e7d685b58b3b9bc7bc6654c7f872 26844 debug optional libbiococoa2-dbgsym_2.2.2-4_armhf.deb f6590e4614450a8369948ed9b2ed1bcb 95524 libs optional libbiococoa2_2.2.2-4_armhf.deb Sun Jul 12 19:48:11 UTC 2020 I: diffoscope 151 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/biococoa_2.2.2-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/biococoa_2.2.2-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/biococoa_2.2.2-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/b1/biococoa_2.2.2-4_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.0LjMP8CNdQ/b2/biococoa_2.2.2-4_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.300s) 0.300s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jul 12 19:48:31 UTC 2020 I: diffoscope 151 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 12 19:48:31 UTC 2020 I: biococoa from buster built successfully and reproducibly on armhf. Sun Jul 12 19:48:32 UTC 2020 I: Submitting .buildinfo files to external archives: Sun Jul 12 19:48:32 UTC 2020 I: Submitting 8.0K b1/biococoa_2.2.2-4_armhf.buildinfo.asc Sun Jul 12 19:48:33 UTC 2020 I: Submitting 8.0K b2/biococoa_2.2.2-4_armhf.buildinfo.asc Sun Jul 12 19:48:34 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 12 19:48:34 UTC 2020 I: Done submitting .buildinfo files. Sun Jul 12 19:48:34 UTC 2020 I: Removing signed biococoa_2.2.2-4_armhf.buildinfo.asc files: removed './b1/biococoa_2.2.2-4_armhf.buildinfo.asc' removed './b2/biococoa_2.2.2-4_armhf.buildinfo.asc'