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/transtermhp/build-area origDir=/sw/debian-med/trunk/packages/transtermhp/tarballs tagsDir=/sw/debian-med/trunk/packages/transtermhp/tags tagsUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/transtermhp/tags trunkDir=/sw/debian-med/trunk/packages/transtermhp/trunk trunkUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/transtermhp/trunk UNRELEASED tag found - you don't want to release with it, do you? mergeWithUpstream mode detected, looking for /sw/debian-med/trunk/packages/transtermhp/tarballs/transtermhp_2.09.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/transtermhp/tarballs/transtermhp_2.09.orig.tar.gz --directory <1 more argument> mv /sw/debian-med/trunk/packages/transtermhp/build-area/tmp-0.27183519334449/transterm_hp_v2.09 /sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09 mkdir -p /sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09/debian /sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09/debian/source cp --parents -laf debian/transtermhp.dirs debian/transtermhp.install debian/transtermhp.manpages debian/copyright debian/README.Debian debian/transterm.1 <12 more arguments> rm -rf /sw/debian-med/trunk/packages/transtermhp/build-area/tmp-0.27183519334449 chmod -R u+r+w+X,g+r-w+X,o+r-w+X -- /sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09 /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 transtermhp dpkg-buildpackage: source version 2.09-2 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build transtermhp-2.09 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09' rm -f *.o rm -f transterm 2ndscore core.* make[1]: Leaving directory `/sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09' dh_clean dpkg-source -b transtermhp-2.09 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building transtermhp using existing ./transtermhp_2.09.orig.tar.gz dpkg-source: info: building transtermhp in transtermhp_2.09-2.debian.tar.gz dpkg-source: info: building transtermhp in transtermhp_2.09-2.dsc dpkg-genchanges -S >../transtermhp_2.09-2_source.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build transtermhp-2.09 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: Wed Mar 27 09:51:48 CET 2013 I: pbuilder-time-stamp: 1364374308 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: debhelper (>= 8), quilt (>= 0.47) 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 debhelper (>= 8); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on quilt (>= 0.47); 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: bsdmainutils{a} debhelper{a} diffstat{a} file{a} gettext{a} gettext-base{a} groff-base{a} html2text{a} intltool-debian{a} libasprintf-dev{a} libasprintf0c2{a} libcroco3{a} libffi5{a} libgettextpo-dev{a} libgettextpo0{a} libglib2.0-0{a} libmagic1{a} libpcre3{a} libpipeline1{a} libunistring0{a} libxml2{a} man-db{a} po-debconf{a} quilt{a} 0 packages upgraded, 24 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/9554 kB of archives. After unpacking 26.9 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 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 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 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 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 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 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 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 file (1:5.11-2.1) ... Setting up gettext-base (0.18.1.1-10) ... 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 quilt (0.60-8) ... 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 ... 13506 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 [../transtermhp_2.09-2.dsc] I: copying [../transtermhp_2.09.orig.tar.gz] I: copying [../transtermhp_2.09-2.debian.tar.gz] I: Extracting source dpkg-source: warning: extracting unsigned source package (transtermhp_2.09-2.dsc) dpkg-source: info: extracting transtermhp in transtermhp-2.09 dpkg-source: info: unpacking transtermhp_2.09.orig.tar.gz dpkg-source: info: unpacking transtermhp_2.09-2.debian.tar.gz 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 transtermhp dpkg-buildpackage: source version 2.09-2 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build transtermhp-2.09 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/tmp/buildd/transtermhp-2.09' rm -f *.o rm -f transterm 2ndscore core.* make[1]: Leaving directory `/tmp/buildd/transtermhp-2.09' dh_clean dpkg-source -b transtermhp-2.09 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building transtermhp using existing ./transtermhp_2.09.orig.tar.gz dpkg-source: info: building transtermhp in transtermhp_2.09-2.debian.tar.gz dpkg-source: info: building transtermhp in transtermhp_2.09-2.dsc debian/rules build dh build dh_testdir dh_auto_configure dh_auto_build make[1]: Entering directory `/tmp/buildd/transtermhp-2.09' g++ -g -O3 -Wall -pedantic -c -o seq.o seq.cc seq.cc: In function 'Seq* read_seq(std::istream&)': seq.cc:86:25: warning: converting 'false' to pointer type 'Seq*' [-Wconversion-null] seq.cc:93:25: warning: converting 'false' to pointer type 'Seq*' [-Wconversion-null] seq.cc:112:25: warning: converting 'false' to pointer type 'Seq*' [-Wconversion-null] g++ -g -O3 -Wall -pedantic -c -o distr.o distr.cc g++ -g -O3 -Wall -pedantic -c -o util.o util.cc g++ -g -O3 -Wall -pedantic -c -o map-output.o map-output.cc g++ -g -O3 -Wall -pedantic -c -o gene-reader.o gene-reader.cc g++ -g -O3 -Wall -pedantic -c -o search.o search.cc search.cc: In function 'void find_terms_dp(Seq&, Direction)': search.cc:704:9: warning: variable 'tailoffset' set but not used [-Wunused-but-set-variable] g++ -g -O3 -Wall -pedantic -c -o conf.o conf.cc g++ -g -O3 -Wall -pedantic -c -o ermolaeva-score.o ermolaeva-score.cc g++ -g -O3 -Wall -pedantic -c -o ermolaeva-oldconf.o ermolaeva-oldconf.cc g++ -g -O3 -Wall -pedantic -c -o analysis.o analysis.cc g++ -g -O3 -Wall -pedantic -c -o anti.o anti.cc g++ -g -O3 -Wall -pedantic -c -o transterm.o transterm.cc g++ -g -O3 -Wall -pedantic -o transterm seq.o distr.o util.o map-output.o gene-reader.o search.o conf.o ermolaeva-score.o ermolaeva-oldconf.o analysis.o anti.o transterm.o g++ -g -O3 -Wall -pedantic -c -o 2ndscore.o 2ndscore.cc g++ -g -O3 -Wall -pedantic -o 2ndscore seq.o search.o ermolaeva-score.o util.o 2ndscore.o make[1]: Leaving directory `/tmp/buildd/transtermhp-2.09' fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory `/tmp/buildd/transtermhp-2.09' dh_installchangelogs RELEASE-NOTES.txt make[1]: Leaving directory `/tmp/buildd/transtermhp-2.09' dh_installexamples dh_installman dh_installcatalogs dh_installcron dh_installdebconf dh_installemacsen dh_installifupdown dh_installinfo dh_installinit dh_installmenu dh_installmime dh_installmodules dh_installlogcheck dh_installlogrotate dh_installpam dh_installppp dh_installudev dh_installwm dh_installxfonts dh_installgsettings dh_bugfiles dh_ucf dh_lintian dh_gconf dh_icons dh_perl dh_usrlocal dh_link dh_compress dh_fixperms dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package `transtermhp' in `../transtermhp_2.09-2_amd64.deb'. dpkg-genchanges >../transtermhp_2.09-2_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build transtermhp-2.09 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//32687 and its subdirectories I: Current time: Wed Mar 27 09:53:43 CET 2013 I: pbuilder-time-stamp: 1364374423 Could not read the .changes file: /sw/debian-med/trunk/packages/transtermhp/build-area/. rm -rf /sw/debian-med/trunk/packages/transtermhp/build-area/transtermhp-2.09