DC-Build-Header: dialign-t 1.0.2-2 / Fri Jan 13 02:33:18 +0100 2012 Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-32.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ dialign-t 1.0.2-2 (amd64) 13 Jan 2012 02:34 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: dialign-t Version: 1.0.2-2 Source Version: 1.0.2-2 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 4s (4195 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'dialign-t' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/dialign-t/trunk/ Need to get 1775 kB of source archives. Get:1 http://localhost/debian/ sid/main dialign-t 1.0.2-2 (dsc) [1355 B] Get:2 http://localhost/debian/ sid/main dialign-t 1.0.2-2 (tar) [1765 kB] Get:3 http://localhost/debian/ sid/main dialign-t 1.0.2-2 (diff) [8133 B] Fetched 1775 kB in 0s (17.1 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/dialign-t-S1yCHj/resolver-39peHQ/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64b-44f28b52-a9ad-47c2-b451-d2eb819ea688/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), cdbs Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), cdbs dpkg-deb: building package `sbuild-build-depends-dialign-t-dummy' in `/build/dialign-t-S1yCHj/resolver-eWZdb7/apt_archive/sbuild-build-depends-dialign-t-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install dialign-t build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc groff www-browser libmail-box-perl Recommended packages: autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-dialign-t-dummy 0 upgraded, 19 newly installed, 0 to remove and 10 not upgraded. Need to get 9588 kB/9589 kB of archives. After this operation, 26.3 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 libglib2.0-0 libxml2 libcroco3 libunistring0 bsdmainutils groff-base man-db libmagic1 file gettext-base cdbs html2text gettext intltool-debian po-debconf debhelper sbuild-build-depends-dialign-t-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:4 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:5 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:6 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:7 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:8 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:9 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:10 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:11 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:12 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:13 http://localhost/debian/ sid/main cdbs all 0.4.100 [77.1 kB] Get:14 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:15 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:16 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:17 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:18 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Preconfiguring packages ... Fetched 9588 kB in 0s (41.2 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5_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_8.9.14_all.deb) ... Selecting previously unselected package sbuild-build-depends-dialign-t-dummy. Unpacking sbuild-build-depends-dialign-t-dummy (from .../sbuild-build-depends-dialign-t-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libpcre3 (8.12-4) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up cdbs (0.4.100) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up sbuild-build-depends-dialign-t-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 clang_3.0-5 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 libllvm3.0_3.0-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-dialign-t-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jan 14 16:09:14 2011 CET using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./dialign-t_1.0.2-2.dsc dpkg-source: info: extracting dialign-t in dialign-t-1.0.2 dpkg-source: info: unpacking dialign-t_1.0.2.orig.tar.gz dpkg-source: info: unpacking dialign-t_1.0.2-2.debian.tar.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package dialign-t dpkg-buildpackage: source version 1.0.2-2 dpkg-source --before-build dialign-t-1.0.2 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 /usr/bin/make -C /build/dialign-t-S1yCHj/dialign-t-1.0.2/source CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean make[1]: Entering directory `/build/dialign-t-S1yCHj/dialign-t-1.0.2/source' rm -rf *.o *rtl *jump *addre* *cfg *life *reg *reload *flow* *stack museq dialign-tx make[1]: Leaving directory `/build/dialign-t-S1yCHj/dialign-t-1.0.2/source' dh_clean dpkg-source -b dialign-t-1.0.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building dialign-t using existing ./dialign-t_1.0.2.orig.tar.gz dpkg-source: warning: ignoring deletion of file source/Makefile.orig dpkg-source: info: building dialign-t in dialign-t_1.0.2-2.debian.tar.gz dpkg-source: info: building dialign-t in dialign-t_1.0.2-2.dsc debian/rules build test -x debian/rules mkdir -p "/build/dialign-t-S1yCHj/dialign-t-1.0.2/source" /usr/bin/make -C /build/dialign-t-S1yCHj/dialign-t-1.0.2/source CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" make[1]: Entering directory `/build/dialign-t-S1yCHj/dialign-t-1.0.2/source' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o museq.o museq.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' museq.c:168:2: warning: implicit declaration of function 'free_diag' is invalid in C99 [-Wimplicit-function-declaration] free_diag(adcol.diags[i]); ^ museq.c:278:27: warning: implicit declaration of function 'free_alignment' is invalid in C99 [-Wimplicit-function-declaration] if(! para->FAST_MODE) free_alignment(algn); ^ 2 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o parameters.o parameters.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o io.o io.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o diag.o diag.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' diag.c:739:9: warning: equality comparison result unused [-Wunused-comparison] sdg == NULL; ~~~~^~~~~~~ diag.c:739:9: note: use '=' to turn this equality comparison into an assignment sdg == NULL; ^~ = diag.c:513:8: warning: unused variable 'hasAli' [-Wunused-variable] char hasAli = (algn!=NULL); ^ diag.c:535:8: warning: unused variable 'mstatus' [-Wunused-variable] char mstatus; ^ diag.c:517:18: warning: unused variable 'cons_maxd' [-Wunused-variable] int maxd,maxd2,cons_maxd; ^ diag.c:518:7: warning: unused variable 'score1' [-Wunused-variable] int score1=0,score2 = 0; ^ 5 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o alig.o alig.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' alig.c:144:20: warning: unused variable 'o_apos' [-Wunused-variable] struct algn_pos *o_apos; ^ alig.c:145:20: warning: unused variable 'tpos' [-Wunused-variable] struct algn_pos *tpos; ^ alig.c:593:21: warning: unused variable 'dgc' [-Wunused-variable] struct diag_cont *dgc, *dgc_next; ^ alig.c:579:8: warning: unused variable 'c2n' [-Wunused-variable] int *c2n = smatrix->char2num; ^ alig.c:582:9: warning: unused variable 'data2' [-Wunused-variable] char *data2 = dg->seq_p2.sq->data; ^ alig.c:593:27: warning: unused variable 'dgc_next' [-Wunused-variable] struct diag_cont *dgc, *dgc_next; ^ alig.c:594:10: warning: unused variable 'ttim' [-Wunused-variable] double ttim; ^ alig.c:580:8: warning: unused variable 'sdata' [-Wunused-variable] int *sdata = smatrix ->data; ^ alig.c:583:7: warning: unused variable 'smatrixlen' [-Wunused-variable] int smatrixlen = smatrix->length; ^ alig.c:581:9: warning: unused variable 'data1' [-Wunused-variable] char *data1 = dg->seq_p1.sq->data; ^ alig.c:584:7: warning: unused variable 'a1' [-Wunused-variable] int a1,a2; ^ alig.c:584:10: warning: unused variable 'a2' [-Wunused-variable] int a1,a2; ^ alig.c:585:7: warning: unused variable 'score1' [-Wunused-variable] int score1; ^ 13 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o assemble.o assemble.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' assemble.c:106:7: warning: unused variable 'ep1' [-Wunused-variable] int ep1 = sp1+dg->length-1; ^ assemble.c:854:19: warning: unused variable 'l' [-Wunused-variable] int i,j,si,sj,k,l, l1,l2; ^ assemble.c:854:22: warning: unused variable 'l1' [-Wunused-variable] int i,j,si,sj,k,l, l1,l2; ^ assemble.c:854:25: warning: unused variable 'l2' [-Wunused-variable] int i,j,si,sj,k,l, l1,l2; ^ assemble.c:912:7: warning: unused variable 'survive' [-Wunused-variable] int survive; ^ assemble.c:866:8: warning: unused variable 'changed' [-Wunused-variable] char changed; ^ assemble.c:1327:16: warning: unused variable 'dg' [-Wunused-variable] struct diag *dg, *tdg; ^ assemble.c:1327:21: warning: unused variable 'tdg' [-Wunused-variable] struct diag *dg, *tdg; ^ 8 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o prob.o prob.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' prob.c:158:18: warning: variable 'sq2' is uninitialized when used here [-Wuninitialized] dg.seq_p2.sq = sq2; ^~~ prob.c:126:24: note: initialize the variable 'sq2' to silence this warning struct seq *sq1, *sq2; ^ = NULL prob.c:157:18: warning: variable 'sq1' is uninitialized when used here [-Wuninitialized] dg.seq_p1.sq = sq1; ^~~ prob.c:126:18: note: initialize the variable 'sq1' to silence this warning struct seq *sq1, *sq2; ^ = NULL 2 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o orf.o orf.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o translate.o translate.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' translate.c:453:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ translate.c:464:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ translate.c:599:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 3 warnings generated. rm -f ./museq gcc -o ./museq \ ./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o \ -pipe -Wall -lm ./diag.o: In function `find_all_diags': /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/diag.c:1845: undefined reference to `find_diags_dialign' /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/diag.c:1913: undefined reference to `calc_ov_weight' ./diag.o: In function `old_find_all_diags': /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/diag.c:1997: undefined reference to `find_diags_dialign' /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/diag.c:2100: undefined reference to `calc_ov_weight' ./assemble.o: In function `simple_aligner': /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/assemble.c:459: undefined reference to `calc_weight' /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/assemble.c:476: undefined reference to `calc_weight' /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/assemble.c:532: undefined reference to `align_diag' ./assemble.o: In function `guided_aligner_rec': /build/dialign-t-S1yCHj/dialign-t-1.0.2/source/assemble.c:1128: undefined reference to `confl_diag' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [museq] Error 1 make[1]: Leaving directory `/build/dialign-t-S1yCHj/dialign-t-1.0.2/source' make: *** [debian/stamp-makefile-build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0235 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-44f28b52-a9ad-47c2-b451-d2eb819ea688/build/dialign-t-S1yCHj Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 6276 Build-Time: 5 Distribution: lsid64b Fail-Stage: build Install-Time: 6 Job: dialign-t_1.0.2-2 Package: dialign-t Package-Time: 25 Source-Version: 1.0.2-2 Space: 6276 Status: attempted Version: 1.0.2-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0235 Build needed 00:00:25, 6276k disc space DC-Message: Failed, but took only 117.214172. Retrying, you never know. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-32.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ dialign-t 1.0.2-2 (amd64) 13 Jan 2012 02:36 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: dialign-t Version: 1.0.2-2 Source Version: 1.0.2-2 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 10s (1740 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'dialign-t' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/dialign-t/trunk/ Need to get 1775 kB of source archives. Get:1 http://localhost/debian/ sid/main dialign-t 1.0.2-2 (dsc) [1355 B] Get:2 http://localhost/debian/ sid/main dialign-t 1.0.2-2 (tar) [1765 kB] Get:3 http://localhost/debian/ sid/main dialign-t 1.0.2-2 (diff) [8133 B] Fetched 1775 kB in 0s (35.3 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/dialign-t-g9kNVX/resolver-v0vAWs/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64b-e14b3b7a-236d-44ce-8fbf-64a0311eaccb/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), cdbs Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7), cdbs dpkg-deb: building package `sbuild-build-depends-dialign-t-dummy' in `/build/dialign-t-g9kNVX/resolver-vL0sPT/apt_archive/sbuild-build-depends-dialign-t-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install dialign-t build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc groff www-browser libmail-box-perl Recommended packages: autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-dialign-t-dummy 0 upgraded, 19 newly installed, 0 to remove and 10 not upgraded. Need to get 9588 kB/9589 kB of archives. After this operation, 26.3 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libpcre3 libglib2.0-0 libxml2 libcroco3 libunistring0 bsdmainutils groff-base man-db libmagic1 file gettext-base cdbs html2text gettext intltool-debian po-debconf debhelper sbuild-build-depends-dialign-t-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:3 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:4 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:5 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:6 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:7 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:8 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:9 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:10 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:11 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:12 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:13 http://localhost/debian/ sid/main cdbs all 0.4.100 [77.1 kB] Get:14 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:15 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:16 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:17 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:18 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Preconfiguring packages ... Fetched 9588 kB in 0s (41.7 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5_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_8.9.14_all.deb) ... Selecting previously unselected package sbuild-build-depends-dialign-t-dummy. Unpacking sbuild-build-depends-dialign-t-dummy (from .../sbuild-build-depends-dialign-t-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libpcre3 (8.12-4) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libcroco3 (0.6.2-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up cdbs (0.4.100) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up sbuild-build-depends-dialign-t-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 clang_3.0-5 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 libllvm3.0_3.0-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-dialign-t-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jan 14 16:09:14 2011 CET using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./dialign-t_1.0.2-2.dsc dpkg-source: info: extracting dialign-t in dialign-t-1.0.2 dpkg-source: info: unpacking dialign-t_1.0.2.orig.tar.gz dpkg-source: info: unpacking dialign-t_1.0.2-2.debian.tar.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package dialign-t dpkg-buildpackage: source version 1.0.2-2 dpkg-source --before-build dialign-t-1.0.2 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 /usr/bin/make -C /build/dialign-t-g9kNVX/dialign-t-1.0.2/source CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean make[1]: Entering directory `/build/dialign-t-g9kNVX/dialign-t-1.0.2/source' rm -rf *.o *rtl *jump *addre* *cfg *life *reg *reload *flow* *stack museq dialign-tx make[1]: Leaving directory `/build/dialign-t-g9kNVX/dialign-t-1.0.2/source' dh_clean dpkg-source -b dialign-t-1.0.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building dialign-t using existing ./dialign-t_1.0.2.orig.tar.gz dpkg-source: warning: ignoring deletion of file source/Makefile.orig dpkg-source: info: building dialign-t in dialign-t_1.0.2-2.debian.tar.gz dpkg-source: info: building dialign-t in dialign-t_1.0.2-2.dsc debian/rules build test -x debian/rules mkdir -p "/build/dialign-t-g9kNVX/dialign-t-1.0.2/source" /usr/bin/make -C /build/dialign-t-g9kNVX/dialign-t-1.0.2/source CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" make[1]: Entering directory `/build/dialign-t-g9kNVX/dialign-t-1.0.2/source' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o museq.o museq.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' museq.c:168:2: warning: implicit declaration of function 'free_diag' is invalid in C99 [-Wimplicit-function-declaration] free_diag(adcol.diags[i]); ^ museq.c:278:27: warning: implicit declaration of function 'free_alignment' is invalid in C99 [-Wimplicit-function-declaration] if(! para->FAST_MODE) free_alignment(algn); ^ 2 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o parameters.o parameters.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o io.o io.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o diag.o diag.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' diag.c:739:9: warning: equality comparison result unused [-Wunused-comparison] sdg == NULL; ~~~~^~~~~~~ diag.c:739:9: note: use '=' to turn this equality comparison into an assignment sdg == NULL; ^~ = diag.c:513:8: warning: unused variable 'hasAli' [-Wunused-variable] char hasAli = (algn!=NULL); ^ diag.c:535:8: warning: unused variable 'mstatus' [-Wunused-variable] char mstatus; ^ diag.c:517:18: warning: unused variable 'cons_maxd' [-Wunused-variable] int maxd,maxd2,cons_maxd; ^ diag.c:518:7: warning: unused variable 'score1' [-Wunused-variable] int score1=0,score2 = 0; ^ 5 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o alig.o alig.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' alig.c:144:20: warning: unused variable 'o_apos' [-Wunused-variable] struct algn_pos *o_apos; ^ alig.c:145:20: warning: unused variable 'tpos' [-Wunused-variable] struct algn_pos *tpos; ^ alig.c:593:21: warning: unused variable 'dgc' [-Wunused-variable] struct diag_cont *dgc, *dgc_next; ^ alig.c:579:8: warning: unused variable 'c2n' [-Wunused-variable] int *c2n = smatrix->char2num; ^ alig.c:582:9: warning: unused variable 'data2' [-Wunused-variable] char *data2 = dg->seq_p2.sq->data; ^ alig.c:593:27: warning: unused variable 'dgc_next' [-Wunused-variable] struct diag_cont *dgc, *dgc_next; ^ alig.c:594:10: warning: unused variable 'ttim' [-Wunused-variable] double ttim; ^ alig.c:580:8: warning: unused variable 'sdata' [-Wunused-variable] int *sdata = smatrix ->data; ^ alig.c:583:7: warning: unused variable 'smatrixlen' [-Wunused-variable] int smatrixlen = smatrix->length; ^ alig.c:581:9: warning: unused variable 'data1' [-Wunused-variable] char *data1 = dg->seq_p1.sq->data; ^ alig.c:584:7: warning: unused variable 'a1' [-Wunused-variable] int a1,a2; ^ alig.c:584:10: warning: unused variable 'a2' [-Wunused-variable] int a1,a2; ^ alig.c:585:7: warning: unused variable 'score1' [-Wunused-variable] int score1; ^ 13 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o assemble.o assemble.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' assemble.c:106:7: warning: unused variable 'ep1' [-Wunused-variable] int ep1 = sp1+dg->length-1; ^ assemble.c:854:19: warning: unused variable 'l' [-Wunused-variable] int i,j,si,sj,k,l, l1,l2; ^ assemble.c:854:22: warning: unused variable 'l1' [-Wunused-variable] int i,j,si,sj,k,l, l1,l2; ^ assemble.c:854:25: warning: unused variable 'l2' [-Wunused-variable] int i,j,si,sj,k,l, l1,l2; ^ assemble.c:912:7: warning: unused variable 'survive' [-Wunused-variable] int survive; ^ assemble.c:866:8: warning: unused variable 'changed' [-Wunused-variable] char changed; ^ assemble.c:1327:16: warning: unused variable 'dg' [-Wunused-variable] struct diag *dg, *tdg; ^ assemble.c:1327:21: warning: unused variable 'tdg' [-Wunused-variable] struct diag *dg, *tdg; ^ 8 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o prob.o prob.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' prob.c:158:18: warning: variable 'sq2' is uninitialized when used here [-Wuninitialized] dg.seq_p2.sq = sq2; ^~~ prob.c:126:24: note: initialize the variable 'sq2' to silence this warning struct seq *sq1, *sq2; ^ = NULL prob.c:157:18: warning: variable 'sq1' is uninitialized when used here [-Wuninitialized] dg.seq_p1.sq = sq1; ^~~ prob.c:126:18: note: initialize the variable 'sq1' to silence this warning struct seq *sq1, *sq2; ^ = NULL 2 warnings generated. gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o orf.o orf.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o translate.o translate.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' translate.c:453:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ translate.c:464:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ translate.c:599:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 3 warnings generated. rm -f ./museq gcc -o ./museq \ ./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o \ -pipe -Wall -lm ./diag.o: In function `find_all_diags': /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/diag.c:1845: undefined reference to `find_diags_dialign' /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/diag.c:1913: undefined reference to `calc_ov_weight' ./diag.o: In function `old_find_all_diags': /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/diag.c:1997: undefined reference to `find_diags_dialign' /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/diag.c:2100: undefined reference to `calc_ov_weight' ./assemble.o: In function `simple_aligner': /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/assemble.c:459: undefined reference to `calc_weight' /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/assemble.c:476: undefined reference to `calc_weight' /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/assemble.c:532: undefined reference to `align_diag' ./assemble.o: In function `guided_aligner_rec': /build/dialign-t-g9kNVX/dialign-t-1.0.2/source/assemble.c:1128: undefined reference to `confl_diag' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [museq] Error 1 make[1]: Leaving directory `/build/dialign-t-g9kNVX/dialign-t-1.0.2/source' make: *** [debian/stamp-makefile-build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0236 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-e14b3b7a-236d-44ce-8fbf-64a0311eaccb/build/dialign-t-g9kNVX Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 6276 Build-Time: 5 Distribution: lsid64b Fail-Stage: build Install-Time: 6 Job: dialign-t_1.0.2-2 Package: dialign-t Package-Time: 31 Source-Version: 1.0.2-2 Space: 6276 Status: attempted Version: 1.0.2-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0236 Build needed 00:00:31, 6276k disc space DC-Build-Status: Failed 209.444298s ### Content of /var/log/daemon.log ### Jan 12 21:02:50 stremi-32 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:03:05 stremi-32 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:03:57 stremi-32 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Jan 12 21:04:10 stremi-32 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:21 stremi-32 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:32 stremi-32 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:48 stremi-32 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:05:20 stremi-32 approx: Concurrent download of debian/dists/sid/Release is taking too long Jan 12 21:05:33 stremi-32 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 209.444298 versus expected 39 (r/m: 4.37036661538462 ; m: 39.0) DC-Build-Network: USED. See /tmp/rulesafter.PJdzJm ! ************************************************************ # Generated by iptables-save v1.4.8 on Fri Jan 13 02:36:48 2012 *filter :INPUT ACCEPT [3976906:23642952203] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [1738575:20423356712] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [331593:106603179] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT [40636:5387692] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [237:14160] -A OUTPUT -j LD [237:14160] -A LD -j LOG [237:14160] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Fri Jan 13 02:36:48 2012 ************************************************************ --- /tmp/rulesbefore.wUx2PQ 2012-01-13 02:33:18.588923992 +0100 +++ /tmp/rulesafter.PJdzJm 2012-01-13 02:36:48.041007368 +0100 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Fri Jan 13 02:33:18 2012 +# Generated by iptables-save v1.4.8 on Fri Jan 13 02:36:48 2012 *filter -:INPUT ACCEPT [3903868:22965584503] +:INPUT ACCEPT [3976906:23642952203] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[1689632:19760238817] -A OUTPUT -o lo -j ACCEPT +[1738575:20423356712] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,11 +16,11 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[326792:103889399] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[331593:106603179] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT -[40225:5335048] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[40636:5387692] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [237:14160] -A OUTPUT -j LD [237:14160] -A LD -j LOG [237:14160] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Fri Jan 13 02:33:18 2012 +# Completed on Fri Jan 13 02:36:48 2012 ************************************************************ [10446.039637] ffff88033e561c40 0000000000000082 0000000000000000 ffff88064ac15780 [10446.048044] ffff88033e582a60 ffffffff812fb320 000000000000f9e0 ffff8808a1e45fd8 [10446.056445] 0000000000015780 0000000000015780 ffff8808fb213170 ffff8808fb213468 [10446.064843] Call Trace: [10446.067622] [] ? thread_return+0x79/0xe0 [10446.073896] [] ? get_request+0x7e/0x2ba [10446.080077] [] ? io_schedule+0x73/0xb7 [10446.086166] [] ? get_request_wait+0xf0/0x188 [10446.092834] [] ? autoremove_wake_function+0x0/0x2e [10446.100085] [] ? __make_request+0x2f7/0x428 [10446.106661] [] ? generic_make_request+0x299/0x2f9 [10446.113820] [] ? submit_bio+0xd6/0xf2 [10446.119810] [] ? end_swap_bio_read+0x0/0x60 [10446.126382] [] ? bio_alloc+0x10/0x1f [10446.132270] [] ? get_swap_bio+0x4a/0x9a [10446.138452] [] ? swap_readpage+0x4f/0x53 [10446.144728] [] ? read_swap_cache_async+0xb3/0xf3 [10446.151790] [] ? swapin_readahead+0x57/0x98 [10446.158365] [] ? handle_mm_fault+0x47f/0x80f [10446.165038] [] ? do_page_fault+0x2e0/0x2fc [10446.171502] [] ? page_fault+0x25/0x30 [10446.177486] INFO: task gcc:12660 blocked for more than 120 seconds. [10446.184546] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [10446.193380] gcc D 0000000000000000 0 12660 12646 0x00000000 [10446.201140] ffff88063e45f100 0000000000000082 0000000000000000 ffff880c35deca80 [10446.209549] ffff88063d42b400 ffffffff8118b96e 000000000000f9e0 ffff880b75f2ffd8 [10446.217977] 0000000000015780 0000000000015780 ffff880be1c88000 ffff880be1c882f8 [10446.226387] Call Trace: [10446.229152] [] ? cfq_dispatch_requests+0x106/0x420 [10446.236411] [] ? get_request+0x7e/0x2ba [10446.242598] [] ? io_schedule+0x73/0xb7 [10446.248685] [] ? get_request_wait+0xf0/0x188 [10446.255348] [] ? autoremove_wake_function+0x0/0x2e [10446.262601] [] ? __make_request+0x2f7/0x428 [10446.269176] [] ? generic_make_request+0x299/0x2f9 [10446.276331] [] ? submit_bio+0xd6/0xf2 [10446.282314] [] ? end_swap_bio_read+0x0/0x60 [10446.288885] [] ? bio_alloc+0x10/0x1f [10446.294778] [] ? get_swap_bio+0x4a/0x9a [10446.300962] [] ? swap_readpage+0x4f/0x53 [10446.307236] [] ? read_swap_cache_async+0xb3/0xf3 [10446.314298] [] ? swapin_readahead+0x57/0x98 [10446.320874] [] ? handle_mm_fault+0x47f/0x80f [10446.327547] [] ? do_page_fault+0x2e0/0x2fc [10446.334025] [] ? page_fault+0x25/0x30 [19077.165717] IN= OUT=eth0 SRC=172.16.160.32 DST=66.151.234.53 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=41938 DF PROTO=TCP SPT=47983 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [19080.180035] IN= OUT=eth0 SRC=172.16.160.32 DST=66.151.234.53 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=41939 DF PROTO=TCP SPT=47983 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [19379.633711] IN= OUT=eth0 SRC=172.16.160.32 DST=224.0.0.22 LEN=40 TOS=0x00 PREC=0xC0 TTL=1 ID=0 DF PROTO=2 [19379.685541] IN= OUT=eth0 SRC=172.16.160.32 DST=224.0.0.22 LEN=40 TOS=0x00 PREC=0xC0 TTL=1 ID=0 DF PROTO=2 [19385.073531] IN= OUT=eth0 SRC=172.16.160.32 DST=224.0.0.22 LEN=40 TOS=0x00 PREC=0xC0 TTL=1 ID=0 DF PROTO=2 ************************************************************