DC-Build-Header: epcr 2.3.12-2 / Fri Jan 13 03:17:54 +0100 2012 Another build requested exclusive access to the build node sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-28.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ epcr 2.3.12-2 (amd64) 13 Jan 2012 03:18 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: epcr Version: 2.3.12-2 Source Version: 2.3.12-2 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 (4171 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: 'epcr' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-epcr/trunk/ Need to get 85.5 kB of source archives. Get:1 http://localhost/debian/ sid/main epcr 2.3.12-2 (dsc) [1375 B] Get:2 http://localhost/debian/ sid/main epcr 2.3.12-2 (tar) [76.4 kB] Get:3 http://localhost/debian/ sid/main epcr 2.3.12-2 (diff) [7784 B] Fetched 85.5 kB in 0s (1207 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/epcr-QYaLzx/resolver-akys4P/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-e80d9266-6c32-4be3-85e0-dc2525cb1f0d/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 (>= 7.1), quilt (>= 0.47) 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 (>= 7.1), quilt (>= 0.47) dpkg-deb: building package `sbuild-build-depends-epcr-dummy' in `/build/epcr-QYaLzx/resolver-6Cn9uv/apt_archive/sbuild-build-depends-epcr-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install epcr 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 debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-epcr-dummy 0 upgraded, 20 newly installed, 0 to remove and 10 not upgraded. Need to get 9922 kB/9923 kB of archives. After this operation, 26.9 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 html2text gettext intltool-debian po-debconf debhelper diffstat quilt sbuild-build-depends-epcr-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 html2text amd64 1.3.2a-15 [103 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:15 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:18 http://localhost/debian/ sid/main diffstat amd64 1.55-2 [29.9 kB] Get:19 http://localhost/debian/ sid/main quilt all 0.50-2 [381 kB] Preconfiguring packages ... Fetched 9922 kB in 0s (41.4 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 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 diffstat. Unpacking diffstat (from .../diffstat_1.55-2_amd64.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ... Selecting previously unselected package sbuild-build-depends-epcr-dummy. Unpacking sbuild-build-depends-epcr-dummy (from .../sbuild-build-depends-epcr-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 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 diffstat (1.55-2) ... Setting up quilt (0.50-2) ... Setting up sbuild-build-depends-epcr-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 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 diffstat_1.55-2 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 quilt_0.50-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-epcr-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 Tue Feb 22 11:57:36 2011 CET using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./epcr_2.3.12-2.dsc dpkg-source: info: extracting epcr in epcr-2.3.12 dpkg-source: info: unpacking epcr_2.3.12.orig.tar.gz dpkg-source: info: unpacking epcr_2.3.12-2.debian.tar.gz dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying fix_header_location.patch dpkg-source: info: applying ensure_build_options.patch Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package epcr dpkg-buildpackage: source version 2.3.12-2 dpkg-source --before-build epcr-2.3.12 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with quilt dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' rm -fr epcr rm -f *_depend.mk rm -f libepcr.a *.o rm -f e-PCR famap fahash re-PCR make[1]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' dh_quilt_unpatch Removing patch ensure_build_options.patch Restoring Makefile Removing patch fix_header_location.patch Restoring faread.cpp Removing patch fix_clean_target.patch Restoring stand/config.mk No patches applied dh_clean dpkg-source -b epcr-2.3.12 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: patches are not applied, applying them now dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying fix_header_location.patch dpkg-source: info: applying ensure_build_options.patch dpkg-source: info: building epcr using existing ./epcr_2.3.12.orig.tar.gz dpkg-source: info: building epcr in epcr_2.3.12-2.debian.tar.gz dpkg-source: info: building epcr in epcr_2.3.12-2.dsc debian/rules build dh build --with quilt dh_testdir dh_quilt_patch File series fully applied, ends at patch ensure_build_options.patch dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' /usr/bin/make links depend all OPTIMIZE=6 \ CFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' \ LDFLAGS=-L. make[2]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \ /usr/bin/make -ef ./stand/Makefile.$i CXXFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' links ; \ done make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "epcr" ; then \ test -L epcr || ln -s . epcr ; \ fi make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \ /usr/bin/make -ef ./stand/Makefile.$i CXXFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' depend ; \ done make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./faread.cpp ./fast_seqio_read.cpp ./fast_seqio_write.cpp ./hashset.cpp ./mmap.cpp ./align.cpp ./stsmatch_i.cpp ./stsmatch_m.cpp ./stsfilter.cpp ./stsmatch.cpp ./fahash_create.cpp ./fahash_create1.cpp ./fahash_create2.cpp ./fahash_lookup.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./libepcr_depend.mk make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./e-PCR_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdepcr_depend.mk make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./famap_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdfamap_depend.mk make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./fahash_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdfahash_depend.mk make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./re-PCR_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdrpcr_depend.mk make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \ /usr/bin/make -ef ./stand/Makefile.$i CXXFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' all ; \ done make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "epcr" ; then \ test -L epcr || ln -s . epcr ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c faread.cpp -o faread.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c fast_seqio_read.cpp -o fast_seqio_read.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c fast_seqio_write.cpp -o fast_seqio_write.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c hashset.cpp -o hashset.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c mmap.cpp -o mmap.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c align.cpp -o align.o In file included from align.cpp:33: In file included from ./epcr/align.hpp:34: ./epcr/minilcs.hpp:308:9: error: call to function 'memset' that is neither visible in the template definition nor found by argument-dependent lookup memset(m_Data[i],0,(m_Size+m_MaxGaps+1)*sizeof(TDataType)); ^ align.cpp:261:37: note: in instantiation of member function 'ncbi::pcr_tools::CLcsMatrix::CLcsMatrix' requested here m_MaxMismatch(mm),m_MaxGaps(gg),m_Matrix(256,gg) ^ /usr/include/string.h:65:14: note: 'memset' should be declared prior to the call site extern void *memset (void *__s, int __c, size_t __n) __THROW __nonnull ((1)); ^ In file included from align.cpp:33: In file included from ./epcr/align.hpp:34: ./epcr/minilcs.hpp:310:9: error: call to function 'memset' that is neither visible in the template definition nor found by argument-dependent lookup memset(m_Path[i],0,(m_Size+m_MaxGaps+1)*sizeof(TDataType)); ^ /usr/include/string.h:65:14: note: 'memset' should be declared prior to the call site extern void *memset (void *__s, int __c, size_t __n) __THROW __nonnull ((1)); ^ 2 errors generated. make[3]: *** [align.o] Error 1 make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c e-PCR_main.cpp -o e-PCR_main.o e-PCR_main.cpp:377:72: warning: incomplete format specifier [-Wformat] if(m_Flags&fSequencePercent) fprintf(stderr,"%5.1lf% ",(pos*100.0)/m_SeqLen); ^~ 1 warning generated. make[3]: *** No rule to make target `libepcr.a', needed by `e-PCR'. Stop. make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c famap_main.cpp -o famap_main.o make[3]: *** No rule to make target `libepcr.a', needed by `famap'. Stop. make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c fahash_main.cpp -o fahash_main.o fahash_main.cpp:257:9: warning: enumeration value 'eNone' not handled in switch [-Wswitch-enum] switch(command) { ^ fahash_main.cpp:261:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ fahash_main.cpp:303:41: warning: conversion specifies type 'long long' but the argument has type 'unsigned long' [-Wformat] fprintf(out,"%d\t%d\t%s\t%lld\t%lf\n",wd,i,wtype, ~~~^ %lu 3 warnings generated. make[3]: *** No rule to make target `libepcr.a', needed by `fahash'. Stop. make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[3]: Entering directory `/build/epcr-QYaLzx/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c re-PCR_main.cpp -o re-PCR_main.o re-PCR_main.cpp:345:9: warning: enumeration value 'eNone' not handled in switch [-Wswitch-enum] switch(command) { ^ re-PCR_main.cpp:349:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ re-PCR_main.cpp:487:58: warning: conversion specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat] fprintf(stderr,"= File %s, STSes %u-%u\n", ~^ %lu re-PCR_main.cpp:501:50: warning: conversion specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat] fprintf(stderr,"= File %s, STSes %u-%u\n", ~^ %lu 4 warnings generated. make[3]: *** No rule to make target `libepcr.a', needed by `re-PCR'. Stop. make[3]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[2]: *** [all] Error 2 make[2]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/build/epcr-QYaLzx/epcr-2.3.12' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0318 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-e80d9266-6c32-4be3-85e0-dc2525cb1f0d/build/epcr-QYaLzx Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 2432 Build-Time: 6 Distribution: lsid64b Fail-Stage: build Install-Time: 7 Job: epcr_2.3.12-2 Package: epcr Package-Time: 27 Source-Version: 2.3.12-2 Space: 2432 Status: attempted Version: 2.3.12-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0318 Build needed 00:00:27, 2432k disc space DC-Message: Failed, but took only 58.415481. Retrying, you never know. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. 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-28.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ epcr 2.3.12-2 (amd64) 13 Jan 2012 03:26 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: epcr Version: 2.3.12-2 Source Version: 2.3.12-2 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 3s (5473 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: 'epcr' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-epcr/trunk/ Need to get 85.5 kB of source archives. Get:1 http://localhost/debian/ sid/main epcr 2.3.12-2 (dsc) [1375 B] Get:2 http://localhost/debian/ sid/main epcr 2.3.12-2 (tar) [76.4 kB] Get:3 http://localhost/debian/ sid/main epcr 2.3.12-2 (diff) [7784 B] Fetched 85.5 kB in 0s (7028 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/epcr-q389rA/resolver-xOXw0t/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-23735575-aecb-4bf5-9e62-4b45ed82afed/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 (>= 7.1), quilt (>= 0.47) 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 (>= 7.1), quilt (>= 0.47) dpkg-deb: building package `sbuild-build-depends-epcr-dummy' in `/build/epcr-q389rA/resolver-bHbiP2/apt_archive/sbuild-build-depends-epcr-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install epcr 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 debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-epcr-dummy 0 upgraded, 20 newly installed, 0 to remove and 10 not upgraded. Need to get 9922 kB/9923 kB of archives. After this operation, 26.9 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 html2text gettext intltool-debian po-debconf debhelper diffstat quilt sbuild-build-depends-epcr-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 html2text amd64 1.3.2a-15 [103 kB] Get:14 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:15 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:17 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:18 http://localhost/debian/ sid/main diffstat amd64 1.55-2 [29.9 kB] Get:19 http://localhost/debian/ sid/main quilt all 0.50-2 [381 kB] Preconfiguring packages ... Fetched 9922 kB in 0s (41.8 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 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 diffstat. Unpacking diffstat (from .../diffstat_1.55-2_amd64.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ... Selecting previously unselected package sbuild-build-depends-epcr-dummy. Unpacking sbuild-build-depends-epcr-dummy (from .../sbuild-build-depends-epcr-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 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 diffstat (1.55-2) ... Setting up quilt (0.50-2) ... Setting up sbuild-build-depends-epcr-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 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 diffstat_1.55-2 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 quilt_0.50-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-epcr-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 Tue Feb 22 11:57:36 2011 CET using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./epcr_2.3.12-2.dsc dpkg-source: info: extracting epcr in epcr-2.3.12 dpkg-source: info: unpacking epcr_2.3.12.orig.tar.gz dpkg-source: info: unpacking epcr_2.3.12-2.debian.tar.gz dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying fix_header_location.patch dpkg-source: info: applying ensure_build_options.patch Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package epcr dpkg-buildpackage: source version 2.3.12-2 dpkg-source --before-build epcr-2.3.12 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with quilt dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' rm -fr epcr rm -f *_depend.mk rm -f libepcr.a *.o rm -f e-PCR famap fahash re-PCR make[1]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' dh_quilt_unpatch Removing patch ensure_build_options.patch Restoring Makefile Removing patch fix_header_location.patch Restoring faread.cpp Removing patch fix_clean_target.patch Restoring stand/config.mk No patches applied dh_clean dpkg-source -b epcr-2.3.12 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: patches are not applied, applying them now dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying fix_header_location.patch dpkg-source: info: applying ensure_build_options.patch dpkg-source: info: building epcr using existing ./epcr_2.3.12.orig.tar.gz dpkg-source: info: building epcr in epcr_2.3.12-2.debian.tar.gz dpkg-source: info: building epcr in epcr_2.3.12-2.dsc debian/rules build dh build --with quilt dh_testdir dh_quilt_patch File series fully applied, ends at patch ensure_build_options.patch dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' /usr/bin/make links depend all OPTIMIZE=6 \ CFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' \ LDFLAGS=-L. make[2]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \ /usr/bin/make -ef ./stand/Makefile.$i CXXFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' links ; \ done make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "epcr" ; then \ test -L epcr || ln -s . epcr ; \ fi make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \ /usr/bin/make -ef ./stand/Makefile.$i CXXFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' depend ; \ done make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./faread.cpp ./fast_seqio_read.cpp ./fast_seqio_write.cpp ./hashset.cpp ./mmap.cpp ./align.cpp ./stsmatch_i.cpp ./stsmatch_m.cpp ./stsfilter.cpp ./stsmatch.cpp ./fahash_create.cpp ./fahash_create1.cpp ./fahash_create2.cpp ./fahash_lookup.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./libepcr_depend.mk make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./e-PCR_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdepcr_depend.mk make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./famap_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdfamap_depend.mk make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./fahash_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdfahash_depend.mk make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -M ./re-PCR_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdrpcr_depend.mk make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \ /usr/bin/make -ef ./stand/Makefile.$i CXXFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1' all ; \ done make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "epcr" ; then \ test -L epcr || ln -s . epcr ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c faread.cpp -o faread.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c fast_seqio_read.cpp -o fast_seqio_read.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c fast_seqio_write.cpp -o fast_seqio_write.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c hashset.cpp -o hashset.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c mmap.cpp -o mmap.o g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c align.cpp -o align.o In file included from align.cpp:33: In file included from ./epcr/align.hpp:34: ./epcr/minilcs.hpp:308:9: error: call to function 'memset' that is neither visible in the template definition nor found by argument-dependent lookup memset(m_Data[i],0,(m_Size+m_MaxGaps+1)*sizeof(TDataType)); ^ align.cpp:261:37: note: in instantiation of member function 'ncbi::pcr_tools::CLcsMatrix::CLcsMatrix' requested here m_MaxMismatch(mm),m_MaxGaps(gg),m_Matrix(256,gg) ^ /usr/include/string.h:65:14: note: 'memset' should be declared prior to the call site extern void *memset (void *__s, int __c, size_t __n) __THROW __nonnull ((1)); ^ In file included from align.cpp:33: In file included from ./epcr/align.hpp:34: ./epcr/minilcs.hpp:310:9: error: call to function 'memset' that is neither visible in the template definition nor found by argument-dependent lookup memset(m_Path[i],0,(m_Size+m_MaxGaps+1)*sizeof(TDataType)); ^ /usr/include/string.h:65:14: note: 'memset' should be declared prior to the call site extern void *memset (void *__s, int __c, size_t __n) __THROW __nonnull ((1)); ^ 2 errors generated. make[3]: *** [align.o] Error 1 make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c e-PCR_main.cpp -o e-PCR_main.o e-PCR_main.cpp:377:72: warning: incomplete format specifier [-Wformat] if(m_Flags&fSequencePercent) fprintf(stderr,"%5.1lf% ",(pos*100.0)/m_SeqLen); ^~ 1 warning generated. make[3]: *** No rule to make target `libepcr.a', needed by `e-PCR'. Stop. make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c famap_main.cpp -o famap_main.o make[3]: *** No rule to make target `libepcr.a', needed by `famap'. Stop. make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c fahash_main.cpp -o fahash_main.o fahash_main.cpp:257:9: warning: enumeration value 'eNone' not handled in switch [-Wswitch-enum] switch(command) { ^ fahash_main.cpp:261:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ fahash_main.cpp:303:41: warning: conversion specifies type 'long long' but the argument has type 'unsigned long' [-Wformat] fprintf(out,"%d\t%d\t%s\t%lld\t%lf\n",wd,i,wtype, ~~~^ %lu 3 warnings generated. make[3]: *** No rule to make target `libepcr.a', needed by `fahash'. Stop. make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[3]: Entering directory `/build/epcr-q389rA/epcr-2.3.12' if test -n "" ; then \ test -L || ln -s . ; \ fi g++ -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1 -c re-PCR_main.cpp -o re-PCR_main.o re-PCR_main.cpp:345:9: warning: enumeration value 'eNone' not handled in switch [-Wswitch-enum] switch(command) { ^ re-PCR_main.cpp:349:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ re-PCR_main.cpp:487:58: warning: conversion specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat] fprintf(stderr,"= File %s, STSes %u-%u\n", ~^ %lu re-PCR_main.cpp:501:50: warning: conversion specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat] fprintf(stderr,"= File %s, STSes %u-%u\n", ~^ %lu 4 warnings generated. make[3]: *** No rule to make target `libepcr.a', needed by `re-PCR'. Stop. make[3]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[2]: *** [all] Error 2 make[2]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/build/epcr-q389rA/epcr-2.3.12' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120113-0327 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-23735575-aecb-4bf5-9e62-4b45ed82afed/build/epcr-q389rA Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 2432 Build-Time: 6 Distribution: lsid64b Fail-Stage: build Install-Time: 6 Job: epcr_2.3.12-2 Package: epcr Package-Time: 25 Source-Version: 2.3.12-2 Space: 2432 Status: attempted Version: 2.3.12-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120113-0327 Build needed 00:00:25, 2432k disc space DC-Build-Status: Failed 565.10581s ### Content of /var/log/daemon.log ### Jan 12 21:03:14 stremi-28 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:01 stremi-28 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:12 stremi-28 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:32 stremi-28 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:48 stremi-28 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Jan 12 21:04:49 stremi-28 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:05:00 stremi-28 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:05:27 stremi-28 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Jan 12 21:05:31 stremi-28 approx: Concurrent download of debian/dists/sid/Release is taking too long Jan 12 21:06:00 stremi-28 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long Jan 12 22:36:11 stremi-28 approx: Concurrent download of debian/pool/main/c/chromium-browser/chromium-browser_16.0.912.75~r116452.orig.tar.bz2 is taking too long Jan 13 03:20:54 stremi-28 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: 565.10581 versus expected 27 (r/m: 19.9298448148148 ; m: 27.0) DC-Build-Network: USED. See /tmp/rulesafter.1iOyLv ! ************************************************************ # Generated by iptables-save v1.4.8 on Fri Jan 13 03:27:19 2012 *filter :INPUT ACCEPT [5031638:32773521574] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [2314412:27460958775] -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 [479428:160050915] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT [46659:6183200] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [14:840] -A OUTPUT -j LD [14:840] -A LD -j LOG [14:840] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Fri Jan 13 03:27:19 2012 ************************************************************ --- /tmp/rulesbefore.bfO00V 2012-01-13 03:17:54.081487216 +0100 +++ /tmp/rulesafter.1iOyLv 2012-01-13 03:27:19.197828305 +0100 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Fri Jan 13 03:17:54 2012 +# Generated by iptables-save v1.4.8 on Fri Jan 13 03:27:19 2012 *filter -:INPUT ACCEPT [4714917:29739363349] +:INPUT ACCEPT [5031638:32773521574] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[2086018:24593496790] -A OUTPUT -o lo -j ACCEPT +[2314412:27460958775] -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 -[444689:149233372] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[479428:160050915] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT -[45474:6029364] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[46659:6183200] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [14:840] -A OUTPUT -j LD [14:840] -A LD -j LOG [14:840] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Fri Jan 13 03:17:54 2012 +# Completed on Fri Jan 13 03:27:19 2012 ************************************************************ [16926.147391] [] ? bio_alloc+0x10/0x1f [16926.153276] [] ? get_swap_bio+0x4a/0x9a [16926.159454] [] ? swap_readpage+0x4f/0x53 [16926.165728] [] ? read_swap_cache_async+0xb3/0xf3 [16926.172780] [] ? swapin_readahead+0x57/0x98 [16926.179346] [] ? handle_mm_fault+0x47f/0x80f [16926.186008] [] ? do_page_fault+0x2e0/0x2fc [16926.192474] [] ? page_fault+0x25/0x30 [16926.198453] [] ? copy_user_generic_string+0x2d/0x40 [16926.205789] [] ? save_i387_xstate+0x12f/0x1b2 [16926.212547] [] ? do_notify_resume+0x289/0x73f [16926.219307] [] ? sys_wait4+0xa0/0xb0 [16926.225191] [] ? int_signal+0x12/0x17 [16926.231172] INFO: task gcc:5370 blocked for more than 120 seconds. [16926.238124] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [16926.246950] gcc D ffff880c3d1062e0 0 5370 5351 0x00000000 [16926.254706] ffff880c3d1062e0 0000000000000086 0000000000000673 ffff8801ded48380 [16926.263099] ffffffff810c78a0 ffffea00093668a0 000000000000f9e0 ffff880543729fd8 [16926.271487] 0000000000015780 0000000000015780 ffff8805df8f4db0 ffff8805df8f50a8 [16926.279862] Call Trace: [16926.282632] [] ? zone_statistics+0x3c/0x5d [16926.289109] [] ? alloc_io_context+0x16/0x84 [16926.295673] [] ? current_io_context+0x1b/0x29 [16926.302433] [] ? read_tsc+0xa/0x20 [16926.308125] [] ? get_request+0x7e/0x2ba [16926.314297] [] ? io_schedule+0x73/0xb7 [16926.320379] [] ? get_request_wait+0xf0/0x188 [16926.327042] [] ? autoremove_wake_function+0x0/0x2e [16926.334287] [] ? __make_request+0x2f7/0x428 [16926.340854] [] ? generic_make_request+0x299/0x2f9 [16926.348008] [] ? submit_bio+0xd6/0xf2 [16926.353992] [] ? end_swap_bio_read+0x0/0x60 [16926.360556] [] ? bio_alloc+0x10/0x1f [16926.366441] [] ? get_swap_bio+0x4a/0x9a [16926.372618] [] ? swap_readpage+0x4f/0x53 [16926.378889] [] ? read_swap_cache_async+0xb3/0xf3 [16926.385942] [] ? swapin_readahead+0x57/0x98 [16926.392509] [] ? handle_mm_fault+0x47f/0x80f [16926.399174] [] ? do_page_fault+0x2e0/0x2fc [16926.405643] [] ? page_fault+0x25/0x30 [16926.411627] [] ? copy_user_generic_string+0x2d/0x40 [16926.418970] [] ? save_i387_xstate+0x12f/0x1b2 [16926.425731] [] ? do_notify_resume+0x289/0x73f [16926.432488] [] ? sys_wait4+0xa0/0xb0 [16926.438368] [] ? int_signal+0x12/0x17 [20309.318187] vgrep[21349]: segfault at d8 ip 00002b5750e64d0f sp 00007fff45460310 error 6 in libc-2.13.so[2b5750da6000+17a000] [20309.561431] vgrep[21693]: segfault at d8 ip 00002b9b4ddedd0f sp 00007fff92584e20 error 6 in libc-2.13.so[2b9b4dd2f000+17a000] [20309.577175] vgrep[21741]: segfault at d8 ip 00002b66d9ba9d0f sp 00007fff8689a2f0 error 6 in libc-2.13.so[2b66d9aeb000+17a000] [20310.044379] vgrep[22255]: segfault at d8 ip 00002aba9bbc0d0f sp 00007fff29c349b0 error 6 in libc-2.13.so[2aba9bb02000+17a000] [20310.070883] vgrep[22433]: segfault at d8 ip 00002b69ea26fd0f sp 00007fffb292f190 error 6 in libc-2.13.so[2b69ea1b1000+17a000] ************************************************************