origdir = ../tarballs /home/sw/bin/buildPackage: line 17: .svn/deb-layout: No such file or directory Complete layout information: buildArea=/sw/debian-med/trunk/packages/biococoa/build-area origDir=/sw/debian-med/trunk/packages/biococoa/tarballs tagsDir=/sw/debian-med/trunk/packages/biococoa/tags tagsUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/biococoa/tags trunkDir=/sw/debian-med/trunk/packages/biococoa/trunk trunkUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/biococoa/trunk UNRELEASED tag found - you don't want to release with it, do you? mergeWithUpstream mode detected, looking for /sw/debian-med/trunk/packages/biococoa/tarballs/biococoa_2.2.2.orig.tar.gz I: mergeWithUpstream property set, looking for upstream source tarball... tar --no-same-owner --no-same-permissions --extract --gzip --file /sw/debian-med/trunk/packages/biococoa/tarballs/biococoa-2.2.2-src.tgz --directory /sw/debian-med/trunk/packages/biococoa/build-area/tmp-0.123726332633854 mv /sw/debian-med/trunk/packages/biococoa/build-area/tmp-0.123726332633854/biococoa-2.2.2 /sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2 mkdir -p /sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/debian/patches /sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/debian <1 more argument> cp --parents -laf debian/patches/link-libs.patch debian/manpages debian/copyright debian/BioCocoa.3 debian/rules debian/compat debian/patches/series debian/control <6 more arguments> rm -rf /sw/debian-med/trunk/packages/biococoa/build-area/tmp-0.123726332633854 chmod -R u+r+w+X,g+r-w+X,o+r-w+X -- /sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2 /bin/sh -c pdebuild --buildresult /sw/packages/build-area -- --basetgz /var/cache/pbuilder/base-sid-amd64.tgz --architecture amd64 --distribution sid W: /home/sw/.pbuilderrc does not exist dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-2 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build biococoa-2.2.2 dpkg-source: info: applying link-libs.patch 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 `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2' rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation/BCUtils' make[2]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2' 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 `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2/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* dpkg-source -b biococoa-2.2.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: applying link-libs.patch dpkg-source: info: building biococoa using existing ./biococoa_2.2.2.orig.tar.gz dpkg-source: info: building biococoa in biococoa_2.2.2-2.debian.tar.gz dpkg-source: info: building biococoa in biococoa_2.2.2-2.dsc dpkg-genchanges -S >../biococoa_2.2.2-2_source.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build biococoa-2.2.2 dpkg-source: info: unapplying link-libs.patch dpkg-buildpackage: binary and diff upload (original source NOT included) W: /home/sw/.pbuilderrc does not exist I: using fakeroot in build. I: Current time: Tue Mar 26 11:44:26 CET 2013 I: pbuilder-time-stamp: 1364294666 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/base-sid-amd64.tgz] I: creating local configuration I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /run/shm filesystem I: mounting /dev/pts filesystem I: policy-rc.d already exists I: Obtaining the cached apt archive contents I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cdbs, debhelper (>= 8), libgnustep-base-dev (>= 1.16.1), quilt dpkg-deb: building package `pbuilder-satisfydepends-dummy' in `/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 12010 files and directories currently installed.) Unpacking pbuilder-satisfydepends-dummy (from .../pbuilder-satisfydepends-dummy.deb) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cdbs; however: Package cdbs is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 8); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libgnustep-base-dev (>= 1.16.1); however: Package libgnustep-base-dev is not installed. pbuilder-satisfydepends-dummy depends on quilt; however: Package quilt is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... The following NEW packages will be installed: autotools-dev{a} bsdmainutils{a} cdbs{a} debhelper{a} diffstat{a} file{a} gettext{a} gettext-base{a} gnustep-base-common{a} gnustep-base-runtime{a} gnustep-common{a} gnustep-make{a} gobjc{a} gobjc-4.7{a} groff-base{a} html2text{a} intltool-debian{a} libasprintf-dev{a} libasprintf0c2{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libcroco3{a} libdbus-1-3{a} libffi5{a} libgcrypt11{a} libgettextpo-dev{a} libgettextpo0{a} libglib2.0-0{a} libgnustep-base-dev{a} libgnustep-base1.22{a} libgnutls26{a} libgpg-error0{a} libicu48{a} libmagic1{a} libobjc4{a} libp11-kit0{a} libpcre3{a} libpipeline1{a} libtasn1-3{a} libunistring0{a} libxml2{a} libxslt1.1{a} man-db{a} po-debconf{a} quilt{a} sgml-base{a} xml-core{a} 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/26.6 MB of archives. After unpacking 88.3 MB will be used. Writing extended state information... debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (Reading database ... 12010 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-2_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-1_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgpg-error0:amd64. Unpacking libgpg-error0:amd64 (from .../libgpg-error0_1.10-3.1_amd64.deb) ... Selecting previously unselected package libgcrypt11:amd64. Unpacking libgcrypt11:amd64 (from .../libgcrypt11_1.5.0-5_amd64.deb) ... Selecting previously unselected package libp11-kit0:amd64. Unpacking libp11-kit0:amd64 (from .../libp11-kit0_0.12-3_amd64.deb) ... Selecting previously unselected package libtasn1-3:amd64. Unpacking libtasn1-3:amd64 (from .../libtasn1-3_2.13-2_amd64.deb) ... Selecting previously unselected package libgnutls26:amd64. Unpacking libgnutls26:amd64 (from .../libgnutls26_2.12.20-5_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.11-2.1_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_amd64.deb) ... Selecting previously unselected package libavahi-common-data:amd64. Unpacking libavahi-common-data:amd64 (from .../libavahi-common-data_0.6.31-2_amd64.deb) ... Selecting previously unselected package libavahi-common3:amd64. Unpacking libavahi-common3:amd64 (from .../libavahi-common3_0.6.31-2_amd64.deb) ... Selecting previously unselected package libdbus-1-3:amd64. Unpacking libdbus-1-3:amd64 (from .../libdbus-1-3_1.6.8-1_amd64.deb) ... Selecting previously unselected package libavahi-client3:amd64. Unpacking libavahi-client3:amd64 (from .../libavahi-client3_0.6.31-2_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.6-2_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libicu48:amd64. Unpacking libicu48:amd64 (from .../libicu48_4.8.1.1-12_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.7.2-5_amd64.deb) ... Selecting previously unselected package libxslt1.1:amd64. Unpacking libxslt1.1:amd64 (from .../libxslt1.1_1.1.26-14_amd64.deb) ... Selecting previously unselected package sgml-base. Unpacking sgml-base (from .../sgml-base_1.26+nmu4_all.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_1%3a5.11-2.1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20120608.1_all.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package libasprintf-dev:amd64. Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgettextpo-dev:amd64. Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-3_amd64.deb) ... Selecting previously unselected package gnustep-common. Unpacking gnustep-common (from .../gnustep-common_2.6.2-2_amd64.deb) ... Selecting previously unselected package xml-core. Unpacking xml-core (from .../xml-core_0.13+nmu2_all.deb) ... Selecting previously unselected package gnustep-base-common. Unpacking gnustep-base-common (from .../gnustep-base-common_1.22.1-4_all.deb) ... Selecting previously unselected package libgnustep-base1.22. Unpacking libgnustep-base1.22 (from .../libgnustep-base1.22_1.22.1-4_amd64.deb) ... Selecting previously unselected package gnustep-base-runtime. Unpacking gnustep-base-runtime (from .../gnustep-base-runtime_1.22.1-4_amd64.deb) ... Selecting previously unselected package gobjc-4.7. Unpacking gobjc-4.7 (from .../gobjc-4.7_4.7.2-5_amd64.deb) ... Selecting previously unselected package gobjc. Unpacking gobjc (from .../gobjc_4%3a4.7.2-1_amd64.deb) ... Selecting previously unselected package gnustep-make. Unpacking gnustep-make (from .../gnustep-make_2.6.2-2_all.deb) ... Selecting previously unselected package libgnustep-base-dev. Unpacking libgnustep-base-dev (from .../libgnustep-base-dev_1.22.1-4_amd64.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ... Setting up libpipeline1:amd64 (1.2.2-2) ... Setting up groff-base (1.22.2-1) ... Setting up bsdmainutils (9.0.4) ... 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 man-db (2.6.3-3) ... Building database of manual pages ... Setting up libasprintf0c2:amd64 (0.18.1.1-10) ... Setting up libgpg-error0:amd64 (1.10-3.1) ... Setting up libgcrypt11:amd64 (1.5.0-5) ... Setting up libp11-kit0:amd64 (0.12-3) ... Setting up libtasn1-3:amd64 (2.13-2) ... Setting up libgnutls26:amd64 (2.12.20-5) ... Setting up libmagic1:amd64 (1:5.11-2.1) ... Setting up libpcre3:amd64 (1:8.31-2) ... Setting up libxml2:amd64 (2.8.0+dfsg1-7+nmu1) ... Setting up libavahi-common-data:amd64 (0.6.31-2) ... Setting up libavahi-common3:amd64 (0.6.31-2) ... Setting up libdbus-1-3:amd64 (1.6.8-1) ... Setting up libavahi-client3:amd64 (0.6.31-2) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.6-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-10) ... Setting up libicu48:amd64 (4.8.1.1-12) ... Setting up libobjc4:amd64 (4.7.2-5) ... Setting up libxslt1.1:amd64 (1.1.26-14) ... Setting up sgml-base (1.26+nmu4) ... Setting up file (1:5.11-2.1) ... Setting up gettext-base (0.18.1.1-10) ... Setting up autotools-dev (20120608.1) ... Setting up cdbs (0.4.120) ... Setting up html2text (1.3.2a-15) ... Setting up libasprintf-dev:amd64 (0.18.1.1-10) ... Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ... Setting up gettext (0.18.1.1-10) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120909) ... Setting up diffstat (1.55-3) ... Setting up gnustep-common (2.6.2-2) ... Setting up xml-core (0.13+nmu2) ... Setting up gobjc-4.7 (4.7.2-5) ... Setting up gobjc (4:4.7.2-1) ... Setting up gnustep-make (2.6.2-2) ... Setting up quilt (0.60-8) ... Processing triggers for sgml-base ... Setting up gnustep-base-common (1.22.1-4) ... Setting up libgnustep-base1.22 (1.22.1-4) ... Setting up gnustep-base-runtime (1.22.1-4) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libgnustep-base-dev (1.22.1-4) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: fakeroot debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/109 kB of archives. After this operation, 325 kB of additional disk space will be used. Selecting previously unselected package fakeroot. (Reading database ... 14337 files and directories currently installed.) Unpacking fakeroot (from .../fakeroot_1.18.4-2_amd64.deb) ... Processing triggers for man-db ... Setting up fakeroot (1.18.4-2) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode I: Copying back the cached apt archive contents I: Copying source file I: copying [../biococoa_2.2.2-2.dsc] I: copying [../biococoa_2.2.2.orig.tar.gz] I: copying [../biococoa_2.2.2-2.debian.tar.gz] I: Extracting source dpkg-source: warning: extracting unsigned source package (biococoa_2.2.2-2.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_2.2.2-2.debian.tar.gz dpkg-source: info: applying link-libs.patch I: Building the package I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" dpkg-buildpackage -us -uc -rfakeroot dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-2 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build biococoa-2.2.2 dpkg-buildpackage: host architecture amd64 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 `/tmp/buildd/biococoa-2.2.2' rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' make[2]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory `/tmp/buildd/biococoa-2.2.2' 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 `/tmp/buildd/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/tmp/buildd/biococoa-2.2.2' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/tmp/buildd/biococoa-2.2.2/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* dpkg-source -b biococoa-2.2.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: applying link-libs.patch dpkg-source: info: building biococoa using existing ./biococoa_2.2.2.orig.tar.gz dpkg-source: info: building biococoa in biococoa_2.2.2-2.debian.tar.gz dpkg-source: info: building biococoa in biococoa_2.2.2-2.dsc debian/rules build test -x debian/rules mkdir -p "." /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/tmp/buildd/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/tmp/buildd/biococoa-2.2.2' cd . && QUILT_PATCHES=/tmp/buildd/biococoa-2.2.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 File series fully applied, ends at patch link-libs.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/tmp/buildd/biococoa-2.2.2' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/tmp/buildd/biococoa-2.2.2' 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 `/tmp/buildd/biococoa-2.2.2' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... /usr/share/GNUstep/Makefiles/mkinstalldirs ../../BioCocoa.framework/Versions/2/Headers /usr/bin/install -c -p -m 644 BCPairwiseAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h /usr/bin/install -c -p -m 644 BCScoreMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h /usr/bin/install -c -p -m 644 BCSequenceAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... /usr/bin/install -c -p -m 644 BCMCP.h ../../BioCocoa.framework/Versions/2/Headers/BCMCP.h /usr/bin/install -c -p -m 644 BCSuffixArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... /usr/bin/install -c -p -m 644 BCSeries.h ../../BioCocoa.framework/Versions/2/Headers/BCSeries.h /usr/bin/install -c -p -m 644 BCSample.h ../../BioCocoa.framework/Versions/2/Headers/BCSample.h /usr/bin/install -c -p -m 644 BCPlatform.h ../../BioCocoa.framework/Versions/2/Headers/BCPlatform.h /usr/bin/install -c -p -m 644 BCParseSOFT.h ../../BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... /usr/bin/install -c -p -m 644 BCCodonDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h /usr/bin/install -c -p -m 644 BCCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCCodon.h /usr/bin/install -c -p -m 644 BCCodonRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h /usr/bin/install -c -p -m 644 BCGeneticCode.h ../../BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... /usr/bin/install -c -p -m 644 BCAtom.h ../../BioCocoa.framework/Versions/2/Headers/BCAtom.h /usr/bin/install -c -p -m 644 BCProteinStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h /usr/bin/install -c -p -m 644 BCSecondaryStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h /usr/bin/install -c -p -m 644 BCChain.h ../../BioCocoa.framework/Versions/2/Headers/BCChain.h /usr/bin/install -c -p -m 644 BCResidue.h ../../BioCocoa.framework/Versions/2/Headers/BCResidue.h /usr/bin/install -c -p -m 644 BCSequenceStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... /usr/bin/install -c -p -m 644 BCAnnotation.h ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h /usr/bin/install -c -p -m 644 BCSequence.h ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h /usr/bin/install -c -p -m 644 BCSequenceArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h /usr/bin/install -c -p -m 644 BCSequenceCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... /usr/bin/install -c -p -m 644 BCSequenceReader.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h /usr/bin/install -c -p -m 644 BCSequenceWriter.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h /usr/bin/install -c -p -m 644 BCCachedSequenceFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h /usr/bin/install -c -p -m 644 BCCachedFastaFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... /usr/bin/install -c -p -m 644 BCAminoAcid.h ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h /usr/bin/install -c -p -m 644 BCNucleotide.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h /usr/bin/install -c -p -m 644 BCSymbol.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h /usr/bin/install -c -p -m 644 BCNucleotideDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h /usr/bin/install -c -p -m 644 BCNucleotideRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h /usr/bin/install -c -p -m 644 BCSymbolSet.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... /usr/bin/install -c -p -m 644 BCSequenceTool.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h /usr/bin/install -c -p -m 644 BCToolDigest.h ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h /usr/bin/install -c -p -m 644 BCToolHydropathyCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h /usr/bin/install -c -p -m 644 BCToolMassCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h /usr/bin/install -c -p -m 644 BCToolComplement.h ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h /usr/bin/install -c -p -m 644 BCToolSequenceFinder.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h /usr/bin/install -c -p -m 644 BCToolSymbolCounter.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h /usr/bin/install -c -p -m 644 BCToolTranslator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h /usr/bin/install -c -p -m 644 BCToolTranslatorDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... /usr/bin/install -c -p -m 644 BCDataMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h /usr/bin/install -c -p -m 644 BCUtilData.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h /usr/bin/install -c -p -m 644 BCUtilStrings.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... /usr/bin/install -c -p -m 644 BCFoundation.h ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h /usr/bin/install -c -p -m 644 BCFoundationDefines.h ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h /usr/bin/install -c -p -m 644 BCStringDefinitions.h ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h /usr/bin/install -c -p -m 644 BCPreferences.h ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h make[2]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs ./derived_src; \ touch derived_src/.stamp /usr/share/GNUstep/Makefiles/mkinstalldirs BioCocoa.framework/Versions/2/Resources cd ./BioCocoa.framework/Versions; \ rm -f Current; \ ln -s 2 Current cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of framework BioCocoa... make[2]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAlignment... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAlignment.obj/ gcc BCPairwiseAlignment.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAnalysis... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAnalysis.obj/ gcc BCMCP.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneExpression... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneExpression.obj/ gcc BCSeries.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -fgnu-runtime -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ -o obj/BCGeneExpression.obj/BCSeries.m.o gcc BCSample.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneticCode... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneticCode.obj/ gcc BCCodonDNA.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCProteinStructure... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCProteinStructure.obj/ gcc BCAtom.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequence... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequence.obj/ gcc BCAnnotation.m -c \ -MMD -MP -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 [-Wmaybe-uninitialized] 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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequenceIO... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequenceIO.obj/ gcc BCSequenceReader.m -c \ -MMD -MP -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 [-Wmaybe-uninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:18: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wmaybe-uninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readFASTQFile:]': BCSequenceReader.m:1310:18: warning: 'seqData' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSymbol... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSymbol.obj/ gcc BCAminoAcid.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCTools... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCTools.obj/ gcc BCSequenceTool.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCUtils... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCUtils.obj/ gcc BCDataMatrix.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ gcc BCStringDefinitions.m -c \ -MMD -MP -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 `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BioCocoa.obj/ classes=""; \ for object_file in ./BCFoundation/obj/subproject.o __dummy__; do \ if [ "$object_file" != "__dummy__" ]; then \ sym=`nm -Pg $object_file | sed -n -e '/^__objc_class_name_[A-Za-z0-9_.]* [^U]/ {s/^__objc_class_name_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}'`; \ classes="$classes $sym"; \ fi; \ done; \ classlist=""; \ classarray=""; \ for f in $classes __dummy__ ; do \ if [ "$f" != "__dummy__" ]; then \ if [ "$classlist" = "" ]; then \ classlist="@\"$f\""; \ classarray="(\"$f\""; \ else \ classlist="$classlist, @\"$f\""; \ classarray="$classarray, \"$f\""; \ fi; \ fi; \ done; \ if [ "$classlist" = "" ]; then \ classlist="NULL"; \ classarray="()"; \ else \ classlist="$classlist, NULL"; \ classarray="$classarray)"; \ fi; \ echo "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv { return nil; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath { return @\"/usr/local/lib/GNUstep/Frameworks\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$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 `/tmp/buildd/biococoa-2.2.2' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot debian/rules binary test -x debian/rules dh_testroot dh_prep dh_installdirs -A sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworklib.install.in > debian/libbiococoa2.install sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworkdev.install.in > debian/libbiococoa-dev.install mkdir -p "." 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=/tmp/buildd/biococoa-2.2.2/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 `/tmp/buildd/biococoa-2.2.2' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-build-headers'. make[2]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi Making all in subprojects of framework BioCocoa... make[2]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making all for subproject BCAlignment... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making all for subproject BCSequence... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making all for subproject BCSymbol... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making all for subproject BCTools... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCUtils... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... make[4]: Nothing to be done for `internal-subproject-compile'. make[2]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... make[3]: Nothing to be done for `internal-framework-compile'. for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f $f -o -d $f ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: $f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done Making install in subprojects of framework BioCocoa... make[2]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' Making install for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' Making install for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' Making install for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' Making install for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-install'. make[2]: Leaving directory `/tmp/buildd/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/include/GNUstep rm -rf /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework; \ (cd .; tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list BioCocoa.framework) | (cd /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/include/GNUstep /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/.; \ rm -f libBioCocoa.so; \ rm -f libBioCocoa.so.2; \ rm -f libBioCocoa.so.2.2.2; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/. /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2"; then \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/. /tmp/buildd/biococoa-2.2.2/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 /tmp/buildd/biococoa-2.2.2/debian/tmp///usr/lib/. /tmp/buildd/biococoa-2.2.2/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 `/tmp/buildd/biococoa-2.2.2' touch debian/stamp-makefile-install Adding cdbs dependencies to debian/libbiococoa-dev.substvars dh_installdirs -plibbiococoa-dev Adding cdbs dependencies to debian/libbiococoa2.substvars dh_installdirs -plibbiococoa2 dh_installdocs -plibbiococoa-dev dh_installexamples -plibbiococoa-dev dh_installman -plibbiococoa-dev dh_installinfo -plibbiococoa-dev dh_installmenu -plibbiococoa-dev dh_installcron -plibbiococoa-dev dh_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=/tmp/buildd/biococoa-2.2.2/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=/tmp/buildd/biococoa-2.2.2/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 dh_gencontrol -plibbiococoa-dev dh_md5sums -plibbiococoa-dev dh_builddeb -plibbiococoa-dev dpkg-deb: building package `libbiococoa-dev' in `../libbiococoa-dev_2.2.2-2_amd64.deb'. dh_gencontrol -plibbiococoa2 dh_md5sums -plibbiococoa2 dh_builddeb -plibbiococoa2 dpkg-deb: building package `libbiococoa2' in `../libbiococoa2_2.2.2-2_amd64.deb'. dpkg-genchanges >../biococoa_2.2.2-2_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build biococoa-2.2.2 dpkg-source: info: unapplying link-libs.patch dpkg-buildpackage: binary and diff upload (original source NOT included) I: Copying back the cached apt archive contents I: unmounting dev/pts filesystem I: unmounting run/shm filesystem I: unmounting proc filesystem I: cleaning the build env I: removing directory /var/cache/pbuilder/build//31373 and its subdirectories I: Current time: Tue Mar 26 11:46:54 CET 2013 I: pbuilder-time-stamp: 1364294814 Could not read the .changes file: /sw/debian-med/trunk/packages/biococoa/build-area/. rm -rf /sw/debian-med/trunk/packages/biococoa/build-area/biococoa-2.2.2