sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ biococoa 2.2.2-1 (armhf) 31 May 2012 10:11 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: biococoa Version: 2.2.2-1 Source Version: 2.2.2-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/biococoa-v_EcOf/biococoa-2.2.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/biococoa-v_EcOf' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-ea561e20-7d8c-457b-b8ac-0d604f08a19f' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'biococoa' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/biococoa/trunk/ Need to get 370 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main biococoa 2.2.2-1 (dsc) [1423 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main biococoa 2.2.2-1 (tar) [359 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main biococoa 2.2.2-1 (diff) [9638 B] Fetched 370 kB in 0s (2733 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-jT5cAp/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded. Need to get 0 B/706 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10652 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper, libgnustep-base-dev (>= 1.16.1), quilt Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper, libgnustep-base-dev (>= 1.16.1), quilt dpkg-deb: building package `sbuild-build-depends-biococoa-dummy' in `/«BUILDDIR»/resolver-5NTjQx/apt_archive/sbuild-build-depends-biococoa-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install biococoa build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils cdbs debhelper diffstat file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-4.6 groff-base html2text intltool-debian libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libdbus-1-3 libffi5 libgcrypt11 libglib2.0-0 libgnustep-base-dev libgnustep-base1.22 libgnutls26 libgpg-error0 libicu48 libmagic1 libobjc3 libp11-kit0 libpcre3 libpipeline1 libtasn1-3 libunistring0 libxml2 libxslt1.1 man-db po-debconf quilt sgml-base xml-core Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc gnustep-base-doc gnustep-make-doc gcc-4.6-doc libobjc3-dbg groff rng-tools less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent sgml-base-doc Recommended packages: curl wget lynx-cur autopoint dbus libglib2.0-data shared-mime-info libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils cdbs debhelper diffstat file gettext gettext-base gnustep-base-common gnustep-base-runtime gnustep-common gnustep-make gobjc gobjc-4.6 groff-base html2text intltool-debian libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libdbus-1-3 libffi5 libgcrypt11 libglib2.0-0 libgnustep-base-dev libgnustep-base1.22 libgnutls26 libgpg-error0 libicu48 libmagic1 libobjc3 libp11-kit0 libpcre3 libpipeline1 libtasn1-3 libunistring0 libxml2 libxslt1.1 man-db po-debconf quilt sbuild-build-depends-biococoa-dummy sgml-base xml-core debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 45 newly installed, 0 to remove and 3 not upgraded. Need to get 0 B/28.4 MB of archives. After this operation, 77.2 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10652 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libgpg-error0:armhf. Unpacking libgpg-error0:armhf (from .../libgpg-error0_1.10-3_armhf.deb) ... Selecting previously unselected package libgcrypt11:armhf. Unpacking libgcrypt11:armhf (from .../libgcrypt11_1.5.0-3_armhf.deb) ... Selecting previously unselected package libp11-kit0:armhf. Unpacking libp11-kit0:armhf (from .../libp11-kit0_0.12-3_armhf.deb) ... Selecting previously unselected package libtasn1-3:armhf. Unpacking libtasn1-3:armhf (from .../libtasn1-3_2.12-1_armhf.deb) ... Selecting previously unselected package libgnutls26:armhf. Unpacking libgnutls26:armhf (from .../libgnutls26_2.12.19-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9.1_armhf.deb) ... Selecting previously unselected package libavahi-common-data:armhf. Unpacking libavahi-common-data:armhf (from .../libavahi-common-data_0.6.31-1_armhf.deb) ... Selecting previously unselected package libavahi-common3:armhf. Unpacking libavahi-common3:armhf (from .../libavahi-common3_0.6.31-1_armhf.deb) ... Selecting previously unselected package libdbus-1-3:armhf. Unpacking libdbus-1-3:armhf (from .../libdbus-1-3_1.5.12-1_armhf.deb) ... Selecting previously unselected package libavahi-client3:armhf. Unpacking libavahi-client3:armhf (from .../libavahi-client3_0.6.31-1_armhf.deb) ... 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Selecting previously unselected package sbuild-build-depends-biococoa-dummy. Unpacking sbuild-build-depends-biococoa-dummy (from .../sbuild-build-depends-biococoa-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libgpg-error0:armhf (1.10-3) ... Setting up libgcrypt11:armhf (1.5.0-3) ... Setting up libp11-kit0:armhf (0.12-3) ... Setting up libtasn1-3:armhf (2.12-1) ... Setting up libgnutls26:armhf (2.12.19-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9.1) ... Setting up libavahi-common-data:armhf (0.6.31-1) ... Setting up libavahi-common3:armhf (0.6.31-1) ... Setting up libdbus-1-3:armhf (1.5.12-1) ... Setting up libavahi-client3:armhf (0.6.31-1) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libicu48:armhf (4.8.1.1-6) ... Setting up libobjc3:armhf (4.6.3-1.1+rpi2) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.2) ... 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 groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up autotools-dev (20120210.1) ... Setting up cdbs (0.4.111) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up diffstat (1.55-2) ... Setting up gnustep-common (2.6.2-2) ... Setting up sgml-base (1.26+nmu1) ... Setting up xml-core (0.13) ... Setting up gnustep-base-common (1.22.1-2) ... Setting up libxslt1.1 (1.1.26-8.1+rpi1) ... Setting up libgnustep-base1.22 (1.22.1-2) ... Setting up gnustep-base-runtime (1.22.1-2) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up gobjc-4.6 (4.6.3-1.1+rpi2) ... Setting up gobjc (4:4.6.2-4) ... Setting up gnustep-make (2.6.2-2) ... Setting up libgnustep-base-dev (1.22.1-2) ... Setting up quilt (0.60-2) ... Setting up sbuild-build-depends-biococoa-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.3 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-32 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.9.3 autotools-dev_20120210.1 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.2 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.111 coreutils_8.13-3.2 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2012.3 debianutils_4.3 diffstat_1.55-2 diffutils_1:3.2-6 dpkg_1.16.3 dpkg-dev_1.16.3 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gnustep-base-common_1.22.1-2 gnustep-base-runtime_1.22.1-2 gnustep-common_2.6.2-2 gnustep-make_2.6.2-2 gobjc_4:4.6.2-4 gobjc-4.6_4.6.3-1.1+rpi2 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-7 libapt-pkg4.12_0.9.3 libattr1_1:2.4.46-7 libavahi-client3_0.6.31-1 libavahi-common-data_0.6.31-1 libavahi-common3_0.6.31-1 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdbus-1-3_1.5.12-1 libdpkg-perl_1.16.3 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-1.1 libgnustep-base-dev_1.22.1-2 libgnustep-base1.22_1.22.1-2 libgnutls26_2.12.19-1 libgomp1_4.7.0-1.1+rpi libgpg-error0_1.10-3 libicu48_4.8.1.1-6 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-7 libncursesw5_5.9-7 libobjc3_4.6.3-1.1+rpi2 libp11-kit0_0.12-3 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 libslang2_2.2.4-10 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtasn1-3_2.12-1 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9.1 libxslt1.1_1.1.26-8.1+rpi1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian4 make_3.81-8.2 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-32 ncurses-base_5.9-7 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sbuild-build-depends-biococoa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.7 sgml-base_1.26+nmu1 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xml-core_0.13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Nov 25 14:59:38 2010 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./biococoa_2.2.2-1.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_2.2.2-1.debian.tar.gz dpkg-source: info: applying link-libs.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-ea561e20-7d8c-457b-b8ac-0d604f08a19f SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-1 dpkg-source --before-build biococoa-2.2.2 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 -k clean This is gnustep-make 2.6.2. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/«PKGBUILDDIR»' rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory `/«PKGBUILDDIR»/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' make[2]: Leaving directory `/«PKGBUILDDIR»/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean rm -f debian/libbiococoa2.install rm -f debian/libbiococoa-dev.install /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Removing patch link-libs.patch Restoring GNUmakefile No patches applied rm -rf ./.pc rm -f debian/stamp-patch* debian/rules build-arch test -x debian/rules mkdir -p "." /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch link-libs.patch patching file GNUmakefile Hunk #1 succeeded at 39 (offset 6 lines). Now at patch link-libs.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/«PKGBUILDDIR»' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 This is gnustep-make 2.6.2. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/«PKGBUILDDIR»' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/«PKGBUILDDIR»/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 -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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 intersectToFile:withMCP:]': BCMCP.m:486:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:487:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:489:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:490:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:514:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:515:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:517:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:518:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:735:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:736:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:738:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:739:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:762:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:763:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:765:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:766:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP unionToFile:withMCP:]': BCMCP.m:910:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:911:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:913:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:914:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:936:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:937:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:939:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:940:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1093:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1094:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1096:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1097:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1123:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1124:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1126:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1127:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1167:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1168:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1170:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1171:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1186:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1187:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1189:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1190:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1222:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1223:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1225:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1226:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1239:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1240:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1242:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1243:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP trimToFile:]': BCMCP.m:1272:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1273:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1275:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1276:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP outputFormat:withMinimumLength:]': BCMCP.m:1481:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1482:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1485:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1486:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1603:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1604:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1606:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1607:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '+[BCMCP mcpToFile:suffixArray:withSuffixArray:lowerBound:]': BCMCP.m:160:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:161:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:163:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:164:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:334:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:335:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:352:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:353:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:358:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:359:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:366:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:367:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc BCSuffixArray.m -c \ -MMD -MP -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 constructFromSequenceArray:strand:]': BCSuffixArray.m:487:13: warning: ignoring return value of 'mktemp', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:513:13: warning: ignoring return value of 'mktemp', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m: In function '-[BCSuffixArray dumpSuffixArray]': BCSuffixArray.m:896:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:897:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:932:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:933:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m: In function '-[BCSuffixArrayUnionEnumerator nextSuffixPosition:sequence:suffixArray:]': BCSuffixArray.m:1464:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1465:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1598:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1599:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 BCSeries.m: In function '+[BCSeries keysForSeries:withInternalKeys:]': BCSeries.m:113:7: warning: 'iKeys' may be used uninitialized in this function [-Wuninitialized] gcc BCSample.m -c \ -MMD -MP -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 -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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 -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 -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 -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] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 -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 -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 -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 -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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 BCAnnotation.m: In function '-[BCAnnotation isEqualToAnnotation:]': BCAnnotation.m:214:2: warning: 'NSObject' may not respond to '-isEqualTo:' [enabled by default] BCAnnotation.m:214:2: warning: (Messages without a matching method signature [enabled by default] BCAnnotation.m:214:2: warning: will be assumed to return 'id' and accept [enabled by default] BCAnnotation.m:214:2: warning: '...' as arguments.) [enabled by default] BCAnnotation.m:214:2: warning: return makes integer from pointer without a cast [enabled by default] gcc BCSequence.m -c \ -MMD -MP -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 -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 -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 [-Wuninitialized] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 [enabled by default] BCSequenceReader.m:167:3: warning: (Messages without a matching method signature [enabled by default] BCSequenceReader.m:167:3: warning: will be assumed to return 'id' and accept [enabled by default] BCSequenceReader.m:167:3: warning: '...' as arguments.) [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readMacVectorFile:]': BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:782:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m:798:3: warning: passing argument 2 of 'scanUpToString:intoString:' from incompatible pointer type [enabled by default] BCSequenceReader.m:798:3: note: expected 'struct NSString **' but argument is of type 'id' BCSequenceReader.m: In function '-[BCSequenceReader readGDEFile:]': BCSequenceReader.m:891:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readPirFile:]': BCSequenceReader.m:976:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readPhylipFile:]': BCSequenceReader.m:1130:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m:1113:31: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] BCSequenceReader.m: In function '-[BCSequenceReader readRawFile:]': BCSequenceReader.m:1195:3: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readSwissProtFile:]': BCSequenceReader.m:426:15: warning: 'sequenceString' may be used uninitialized in this function [-Wuninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:18: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wuninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readFASTQFile:]': BCSequenceReader.m:1310:18: warning: 'seqData' may be used uninitialized in this function [-Wuninitialized] gcc BCSequenceWriter.m -c \ -MMD -MP -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 -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 -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:58:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:73:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:76:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:97:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m: In function '-[BCCachedFastaFile symbols:ForCurrentSequenceAtPosition:ofLength:]': BCCachedFastaFile.m:149:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:104:3: warning: 'filePos' may be used uninitialized in this function [-Wuninitialized] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 -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 -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 -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 -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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 -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 -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 -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 -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 -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 -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 -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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory `/«PKGBUILDDIR»/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 -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 -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 -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 [enabled by default] 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 [enabled by default] BCUtilStrings.m:100:3: note: expected 'int *' but argument is of type 'id' gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ gcc BCStringDefinitions.m -c \ -MMD -MP -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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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 `/«PKGBUILDDIR»/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 "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv { return nil; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath { return @\"/usr/local/lib/GNUstep/Frameworks\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$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 -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,defs -Wl,--as-needed -pthread -shared-libgcc -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) \ 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 "BioCocoaInfo.plist" ]; then \ plmerge BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist BioCocoaInfo.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 `/«PKGBUILDDIR»' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_clean -k dh_clean: dh_clean -k is deprecated; use dh_prep instead 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 "." DEB_MAKE_CHECK_TARGET unset, not running checks GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp/ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM This is gnustep-make 2.6.2. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/«PKGBUILDDIR»' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/«PKGBUILDDIR»/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCTools' Making build-headers for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-build-headers'. make[2]: Leaving directory `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' Making all for subproject BCAlignment... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' Making all for subproject BCSequence... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' Making all for subproject BCSymbol... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCTools' Making all for subproject BCTools... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making all for subproject BCUtils... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making all for subproject BCFoundation... make[4]: Nothing to be done for `internal-subproject-compile'. make[2]: Leaving directory `/«PKGBUILDDIR»/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 Making install in subprojects of framework BioCocoa... make[2]: Entering directory `/«PKGBUILDDIR»/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' Making install for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAlignment' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCAnalysis' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneExpression' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCGeneticCode' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCProteinStructure' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' Making install for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequence' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSequenceIO' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' Making install for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCSymbol' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCTools' Making install for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCTools' make[3]: Entering directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making install for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/«PKGBUILDDIR»/BCFoundation/BCUtils' Making install for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-install'. make[2]: Leaving directory `/«PKGBUILDDIR»/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /«PKGBUILDDIR»/debian/tmp///usr/include/GNUstep rm -rf /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework; \ (cd .; tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list BioCocoa.framework) | (cd /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /«PKGBUILDDIR»/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /«PKGBUILDDIR»/debian/tmp///usr/include/GNUstep /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /«PKGBUILDDIR»/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 /«PKGBUILDDIR»/debian/tmp///usr/lib/. /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2"; then \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /«PKGBUILDDIR»/debian/tmp///usr/lib/. /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /«PKGBUILDDIR»/debian/tmp///usr/lib/. /«PKGBUILDDIR»/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 make[1]: Leaving directory `/«PKGBUILDDIR»' 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_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=/«PKGBUILDDIR»/debian/tmp/ dh_link -plibbiococoa-dev dh_installmime -plibbiococoa-dev dh_installgsettings -plibbiococoa-dev gsdh_gnustep -plibbiococoa-dev dh_link -plibbiococoa-dev rm -f debian/libbiococoa-dev//usr/lib/GNUstep/Frameworks/*.framework/Versions/Current dh_installdocs -plibbiococoa2 dh_installexamples -plibbiococoa2 dh_installman -plibbiococoa2 dh_installinfo -plibbiococoa2 dh_installmenu -plibbiococoa2 dh_installcron -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=/«PKGBUILDDIR»/debian/tmp/ dh_link -plibbiococoa2 dh_installmime -plibbiococoa2 dh_installgsettings -plibbiococoa2 gsdh_gnustep -plibbiococoa2 dh_link -plibbiococoa2 dh_strip -plibbiococoa-dev dh_compress -plibbiococoa-dev dh_fixperms -plibbiococoa-dev dh_makeshlibs -plibbiococoa-dev dh_strip -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 dpkg-shlibdeps: warning: debian/libbiococoa2/usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_gencontrol -plibbiococoa-dev dh_md5sums -plibbiococoa-dev dh_builddeb -plibbiococoa-dev dpkg-deb: building package `libbiococoa-dev' in `../libbiococoa-dev_2.2.2-1_armhf.deb'. dh_gencontrol -plibbiococoa2 dh_md5sums -plibbiococoa2 dh_builddeb -plibbiococoa2 dpkg-deb: building package `libbiococoa2' in `../libbiococoa2_2.2.2-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../biococoa_2.2.2-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build biococoa-2.2.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120531-1017 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ biococoa_2.2.2-1_armhf.changes: ─────────────────────────────── Format: 1.8 Date: Thu, 25 Nov 2010 15:46:38 +0100 Source: biococoa Binary: libbiococoa-dev libbiococoa2 Architecture: armhf Version: 2.2.2-1 Distribution: testing Urgency: low Maintainer: buildd 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 (2.2.2-1) unstable; urgency=low . * New upstream version Checksums-Sha1: 7a61c15da0d2081eeb6822cf4b2fc967b2e55a18 130200 libbiococoa-dev_2.2.2-1_armhf.deb 69776dd4c3f09af7570214ef0f1d48dca2daace9 130424 libbiococoa2_2.2.2-1_armhf.deb Checksums-Sha256: 15b4c5c5181adedfbb6209a019c28b30590891f8df64296ee82e8705a6dc54db 130200 libbiococoa-dev_2.2.2-1_armhf.deb a413a8269bcc69534a110f168712645c6d2eb7b84ab45bf25e97ed3e9bd7a9af 130424 libbiococoa2_2.2.2-1_armhf.deb Files: 33b4ee574b3e1735b859f14d82ffe1e3 130200 libdevel optional libbiococoa-dev_2.2.2-1_armhf.deb 1abb74df397c848a023dd021cb66544c 130424 libs optional libbiococoa2_2.2.2-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ libbiococoa-dev_2.2.2-1_armhf.deb ───────────────────────────────── new debian package, version 2.0. size 130200 bytes: control archive= 3692 bytes. 1289 bytes, 24 lines control 10151 bytes, 94 lines md5sums Package: libbiococoa-dev Source: biococoa Version: 2.2.2-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 436 Depends: libbiococoa2 (= 2.2.2-1), libgnustep-base-dev, gnustep-fslayout-fhs Section: libdevel Priority: optional Homepage: http://bioinformatics.org/biococoa/ Description: Bioinformatics framework for GNUstep and Cocoa (development files) BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications. . This package contains the development files, documentation and examples for developing GNUstep applications using the BioCocoa framework. drwxr-xr-x root/root 0 2012-05-31 10:16 ./ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/doc/libbiococoa-dev/ -rw-r--r-- root/root 542 2010-10-14 12:55 ./usr/share/doc/libbiococoa-dev/changelog.gz drwxr-xr-x root/root 0 2012-05-31 10:13 ./usr/share/doc/libbiococoa-dev/Tests/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/ -rw-r--r-- root/root 1671 2009-07-02 16:13 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/TestBCSuffixArray.h -rw-r--r-- root/root 1743 2009-07-02 16:13 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/TestBCCachedSequenceFile.m.gz drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/ -rw-r--r-- root/root 15650 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/transposon.fasta.gz -rw-r--r-- root/root 1814 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/pCDNA3.xdna.gz -rw-r--r-- root/root 640 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/test.fa -rw-r--r-- root/root 1354 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/hB2AR-CDS.xdna -rw-r--r-- root/root 2570 2008-10-15 16:11 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/test.fastq -rw-r--r-- root/root 2957 2007-09-20 12:49 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/UBBYB -rw-r--r-- root/root 526 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/hB2AR-protein.xprt -rw-r--r-- root/root 8650 2007-09-20 12:49 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/pBR322.gz -rw-r--r-- root/root 18381 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/transposon.clustalw.gz -rw-r--r-- root/root 3618 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/hB26H-N,S oligos.gz -rw-r--r-- root/root 5021 2007-09-21 13:47 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/DataFiles/pvL1392-SFhB26H.gz -rw-r--r-- root/root 2935 2009-07-02 16:13 ./usr/share/doc/libbiococoa-dev/Tests/Test-BCFoundation/TestBCSequenceInit.m.gz 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./usr/include/GNUstep/Frameworks/BioCocoa.framework/Headers -> Versions/2 lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/include/GNUstep/BioCocoa -> ../../lib/GNUstep/Frameworks/BioCocoa.framework/Headers libbiococoa2_2.2.2-1_armhf.deb ────────────────────────────── new debian package, version 2.0. size 130424 bytes: control archive= 1159 bytes. 1267 bytes, 23 lines control 671 bytes, 7 lines md5sums 27 bytes, 1 lines shlibs Package: libbiococoa2 Source: biococoa Version: 2.2.2-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 444 Depends: gnustep-base-runtime (>= 1.22.1), libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libgnustep-base1.22 (>= 1.22.1), libobjc3 (>= 4.2.1), gnustep-fslayout-fhs Section: libs Priority: optional Homepage: http://bioinformatics.org/biococoa/ Description: Bioinformatics framework for GNUstep and Cocoa (library files) BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications. . This package contains the runtime libraries. drwxr-xr-x root/root 0 2012-05-31 10:16 ./ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ -rw-r--r-- root/root 338932 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2 drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/doc/libbiococoa2/ -rw-r--r-- root/root 542 2010-10-14 12:55 ./usr/share/doc/libbiococoa2/changelog.gz -rw-r--r-- root/root 1720 2010-11-25 06:46 ./usr/share/doc/libbiococoa2/changelog.Debian.gz -rw-r--r-- root/root 13904 2010-09-14 13:17 ./usr/share/doc/libbiococoa2/copyright drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/GNUstep/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/ drwxr-xr-x root/root 0 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/ -rw-r--r-- root/root 15033 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/nucleotides.plist -rw-r--r-- root/root 13143 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/aminoacids.plist -rw-r--r-- root/root 957 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Versions/2/Info-gnustep.plist lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/lib/libBioCocoa.so.2 -> GNUstep/Frameworks/BioCocoa.framework/Versions/Current/libBioCocoa.so.2 lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Resources -> Versions/Current/Resources lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current -> 2 lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/Resources -> ../../../../../../share/GNUstep/Frameworks/BioCocoa.framework/Versions/2 lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2 -> libBioCocoa.so.2.2.2 lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/lib/libBioCocoa.so.2.2.2 -> GNUstep/Frameworks/BioCocoa.framework/Versions/Current/libBioCocoa.so.2.2.2 lrwxrwxrwx root/root 0 2012-05-31 10:16 ./usr/share/GNUstep/Frameworks/BioCocoa.framework/Resources -> Versions/2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: autotools-dev* bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base* gnustep-base-common* gnustep-base-runtime* gnustep-common* gnustep-make* gobjc* gobjc-4.6* groff-base* html2text* intltool-debian* libavahi-client3* libavahi-common-data* libavahi-common3* libcroco3* libdbus-1-3* libffi5* libgcrypt11* libglib2.0-0* libgnustep-base-dev* libgnustep-base1.22* libgnutls26* libgpg-error0* libicu48* libmagic1* libobjc3* libp11-kit0* libpcre3* libpipeline1* libtasn1-3* libunistring0* libxml2* libxslt1.1* man-db* po-debconf* quilt* sbuild-build-depends-biococoa-dummy* sbuild-build-depends-core-dummy* sgml-base* xml-core* 0 upgraded, 0 newly installed, 46 to remove and 3 not upgraded. After this operation, 77.2 MB disk space will be freed. 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Purging configuration files for xml-core ... dpkg: warning: while removing xml-core, directory '/etc/sgml' not empty so not removed. Removing sgml-base ... Purging configuration files for sgml-base ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 8124 Build-Time: 214 Distribution: testing Install-Time: 99 Job: biococoa_2.2.2-1 Package: biococoa Package-Time: 331 Source-Version: 2.2.2-1 Space: 8124 Status: successful Version: 2.2.2-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120531-1017 Build needed 00:05:31, 8124k disc space