Your message dated Thu, 20 Aug 2015 07:34:13 +0000 with message-id <e1zskmx-0004sz...@franck.debian.org> and subject line Bug#795847: fixed in jellyfish 2.2.3-2 has caused the Debian Bug report #795847, regarding jellyfish: FTBFS: error: 'struct std::__cxx11::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 795847: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=795847 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: jellyfish Version: 2.2.3-1 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org Dear Maintainer, jellyfish fails to build from source on unstable/amd64: [..] g++ -DHAVE_CONFIG_H -I. -Dprotected=public -Dprivate=public -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc In file included from ./unit_tests/gtest/gtest.h:308:0, from unit_tests/test_main.cc:20: /usr/include/c++/5/sstream:300:7: error: 'struct std::__cxx11::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access struct __xfer_bufptrs ^ Makefile:1369: recipe for target 'unit_tests/bin_test_all-test_main.o' failed make[4]: *** [unit_tests/bin_test_all-test_main.o] Error 1 make[4]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' Makefile:2319: recipe for target 'check-am' failed make[3]: *** [check-am] Error 2 make[3]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' Makefile:1875: recipe for target 'check-recursive' failed make[2]: *** [check-recursive] Error 1 make[2]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' Makefile:2322: recipe for target 'check' failed make[1]: *** [check] Error 2 make[1]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' dh_auto_test: make -j1 check returned exit code 2 debian/rules:8: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 [..] The full build log is attached or can be viewed here: https://reproducible.debian.net/logs/unstable/amd64/jellyfish_2.2.3-1.build1.log.gz Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-I: using fakeroot in build. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 10 14:59:19 GMT+12 2015 I: pbuilder-time-stamp: 1439261959 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: creating local configuration I: copying local configuration I: mounting /proc filesystem I: mounting /run/shm filesystem I: mounting /dev/pts filesystem I: Mounting /dev/shm I: Mounting /sys I: policy-rc.d already exists I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team <pbuilder-ma...@lists.alioth.debian.org> Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 9), dh-autoreconf, d-shlibs, yaggo, pkg-config, bc, time, procps, valgrind dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20247 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on dh-autoreconf; however: Package dh-autoreconf is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on yaggo; however: Package yaggo is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on valgrind; however: Package valgrind is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} ca-certificates{a} d-shlibs{a} dh-autoreconf{a} libc6-dbg{a} libruby2.1{a} libsigsegv2{a} libssl1.0.0{a} libtool{a} libyaml-0-2{a} m4{a} openssl{a} pkg-config{a} ruby{a} ruby2.1{a} rubygems-integration{a} time{a} valgrind{a} yaggo{a} 0 packages upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 28.5 MB of archives. After unpacking 154 MB will be used. Writing extended state information... Get: 1 http://ftp.de.debian.org/debian/ unstable/main libsigsegv2 amd64 2.10-4+b1 [29.2 kB] Get: 2 http://ftp.de.debian.org/debian/ unstable/main libyaml-0-2 amd64 0.1.6-3 [50.4 kB] Get: 3 http://ftp.de.debian.org/debian/ unstable/main libssl1.0.0 amd64 1.0.2d-1 [1274 kB] Get: 4 http://reproducible.alioth.debian.org/debian/ ./ autopoint 0.19.5.1-1.0~reproducible1 [426 kB] Get: 5 http://ftp.de.debian.org/debian/ unstable/main bc amd64 1.06.95-9 [103 kB] Get: 6 http://ftp.de.debian.org/debian/ unstable/main m4 amd64 1.4.17-4 [254 kB] Get: 7 http://ftp.de.debian.org/debian/ unstable/main time amd64 1.7-25.1 [31.0 kB] Get: 8 http://ftp.de.debian.org/debian/ unstable/main autoconf all 2.69-8 [340 kB] Get: 9 http://ftp.de.debian.org/debian/ unstable/main autotools-dev all 20140911.1 [70.5 kB] Get: 10 http://ftp.de.debian.org/debian/ unstable/main automake all 1:1.15-2 [735 kB] Get: 11 http://ftp.de.debian.org/debian/ unstable/main openssl amd64 1.0.2d-1 [695 kB] Get: 12 http://ftp.de.debian.org/debian/ unstable/main ca-certificates all 20150426 [208 kB] Get: 13 http://ftp.de.debian.org/debian/ unstable/main d-shlibs all 0.62 [16.9 kB] Get: 14 http://ftp.de.debian.org/debian/ unstable/main libtool all 2.4.2-1.11 [190 kB] Get: 15 http://ftp.de.debian.org/debian/ unstable/main dh-autoreconf all 10 [15.2 kB] Get: 16 http://ftp.de.debian.org/debian/ unstable/main pkg-config amd64 0.28-1 [57.5 kB] Get: 17 http://ftp.de.debian.org/debian/ unstable/main rubygems-integration all 1.9 [4754 B] Get: 18 http://ftp.de.debian.org/debian/ unstable/main libruby2.1 amd64 2.1.5-4 [3280 kB] Get: 19 http://ftp.de.debian.org/debian/ unstable/main ruby2.1 amd64 2.1.5-4 [276 kB] Get: 20 http://ftp.de.debian.org/debian/ unstable/main ruby all 1:2.1.5.1 [9756 B] Get: 21 http://ftp.de.debian.org/debian/ unstable/main libc6-dbg amd64 2.19-19 [3438 kB] Get: 22 http://ftp.de.debian.org/debian/ unstable/main valgrind amd64 1:3.10.1-4 [17.0 MB] Get: 23 http://ftp.de.debian.org/debian/ unstable/main yaggo all 1.5.4-1 [17.6 kB] Fetched 28.5 MB in 1s (20.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libsigsegv2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20247 files and directories currently installed.) Preparing to unpack .../libsigsegv2_2.10-4+b1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-4+b1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../libyaml-0-2_0.1.6-3_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.1.6-3) ... Selecting previously unselected package libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.2d-1_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.2d-1) ... Selecting previously unselected package bc. Preparing to unpack .../bc_1.06.95-9_amd64.deb ... Unpacking bc (1.06.95-9) ... Selecting previously unselected package m4. Preparing to unpack .../archives/m4_1.4.17-4_amd64.deb ... Unpacking m4 (1.4.17-4) ... Selecting previously unselected package time. Preparing to unpack .../time_1.7-25.1_amd64.deb ... Unpacking time (1.7-25.1) ... Selecting previously unselected package autoconf. Preparing to unpack .../autoconf_2.69-8_all.deb ... Unpacking autoconf (2.69-8) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../autotools-dev_20140911.1_all.deb ... Unpacking autotools-dev (20140911.1) ... Selecting previously unselected package automake. Preparing to unpack .../automake_1%3a1.15-2_all.deb ... Unpacking automake (1:1.15-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../autopoint_0.19.5.1-1.0~reproducible1_all.deb ... Unpacking autopoint (0.19.5.1-1.0~reproducible1) ... Selecting previously unselected package openssl. Preparing to unpack .../openssl_1.0.2d-1_amd64.deb ... Unpacking openssl (1.0.2d-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../ca-certificates_20150426_all.deb ... Unpacking ca-certificates (20150426) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../archives/d-shlibs_0.62_all.deb ... Unpacking d-shlibs (0.62) ... Selecting previously unselected package libtool. Preparing to unpack .../libtool_2.4.2-1.11_all.deb ... Unpacking libtool (2.4.2-1.11) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../dh-autoreconf_10_all.deb ... Unpacking dh-autoreconf (10) ... Selecting previously unselected package pkg-config. Preparing to unpack .../pkg-config_0.28-1_amd64.deb ... Unpacking pkg-config (0.28-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../rubygems-integration_1.9_all.deb ... Unpacking rubygems-integration (1.9) ... Selecting previously unselected package libruby2.1:amd64. Preparing to unpack .../libruby2.1_2.1.5-4_amd64.deb ... Unpacking libruby2.1:amd64 (2.1.5-4) ... Selecting previously unselected package ruby2.1. Preparing to unpack .../ruby2.1_2.1.5-4_amd64.deb ... Unpacking ruby2.1 (2.1.5-4) ... Selecting previously unselected package ruby. Preparing to unpack .../ruby_1%3a2.1.5.1_all.deb ... Unpacking ruby (1:2.1.5.1) ... Selecting previously unselected package libc6-dbg:amd64. Preparing to unpack .../libc6-dbg_2.19-19_amd64.deb ... Unpacking libc6-dbg:amd64 (2.19-19) ... Selecting previously unselected package valgrind. Preparing to unpack .../valgrind_1%3a3.10.1-4_amd64.deb ... Unpacking valgrind (1:3.10.1-4) ... Selecting previously unselected package yaggo. Preparing to unpack .../archives/yaggo_1.5.4-1_all.deb ... Unpacking yaggo (1.5.4-1) ... Processing triggers for man-db (2.7.0.2-5) ... Setting up libsigsegv2:amd64 (2.10-4+b1) ... Setting up libyaml-0-2:amd64 (0.1.6-3) ... Setting up libssl1.0.0:amd64 (1.0.2d-1) ... Setting up bc (1.06.95-9) ... Setting up m4 (1.4.17-4) ... Setting up time (1.7-25.1) ... Setting up autoconf (2.69-8) ... Setting up autotools-dev (20140911.1) ... Setting up automake (1:1.15-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.5.1-1.0~reproducible1) ... Setting up openssl (1.0.2d-1) ... Setting up ca-certificates (20150426) ... Setting up d-shlibs (0.62) ... Setting up libtool (2.4.2-1.11) ... Setting up dh-autoreconf (10) ... Setting up pkg-config (0.28-1) ... Setting up rubygems-integration (1.9) ... Setting up libruby2.1:amd64 (2.1.5-4) ... Setting up ruby2.1 (2.1.5-4) ... Setting up ruby (1:2.1.5.1) ... Setting up libc6-dbg:amd64 (2.19-19) ... Setting up valgrind (1:3.10.1-4) ... Setting up yaggo (1.5.4-1) ... Processing triggers for libc-bin (2.19-19) ... Processing triggers for ca-certificates (20150426) ... Updating certificates in /etc/ssl/certs... 180 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Copying source file I: copying [jellyfish_2.2.3-1.dsc] I: copying [./jellyfish_2.2.3.orig.tar.gz] I: copying [./jellyfish_2.2.3-1.debian.tar.xz] I: Extracting source gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jul 3 06:12:49 2015 GMT+12 using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./jellyfish_2.2.3-1.dsc dpkg-source: info: extracting jellyfish in jellyfish-2.2.3 dpkg-source: info: unpacking jellyfish_2.2.3.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.2.3-1.debian.tar.xz I: Building the package I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: source package jellyfish dpkg-buildpackage: source version 2.2.3-1 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Andreas Tille <ti...@debian.org> dpkg-source --before-build jellyfish-2.2.3 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean debian/rules override_dh_clean make[1]: Entering directory '/tmp/buildd/jellyfish-2.2.3' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh make[1]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' debian/rules build dh build --with autoreconf dh_testdir dh_autoreconf libtoolize: putting auxiliary files in `.'. libtoolize: copying file `./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'. libtoolize: copying file `m4/libtool.m4' libtoolize: copying file `m4/ltoptions.m4' libtoolize: copying file `m4/ltsugar.m4' libtoolize: copying file `m4/ltversion.m4' libtoolize: copying file `m4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for __int128... yes checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for siginfo_t.si_int... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode debian/rules override_dh_auto_build make[1]: Entering directory '/tmp/buildd/jellyfish-2.2.3' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build make -j1 make[2]: Entering directory '/tmp/buildd/jellyfish-2.2.3' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo make all-recursive make[3]: Entering directory '/tmp/buildd/jellyfish-2.2.3' Making all in . make[4]: Entering directory '/tmp/buildd/jellyfish-2.2.3' /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/rectangular_binary_matrix.cc -o lib/rectangular_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/mer_dna.lo lib/mer_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/mer_dna.cc -fPIC -DPIC -o lib/.libs/mer_dna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/mer_dna.cc -o lib/mer_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/storage.lo lib/storage.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 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g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/allocators_mmap.cc -o lib/allocators_mmap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/misc.lo lib/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/misc.cc -fPIC -DPIC -o lib/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 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-I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/time.cc -fPIC -DPIC -o lib/.libs/time.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/time.cc -o lib/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/generator_manager.lo lib/generator_manager.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/generator_manager.cc -fPIC -DPIC -o lib/.libs/generator_manager.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c lib/generator_manager.cc -o lib/generator_manager.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:0 -Wl,-z,relro -o libjellyfish-2.0.la -rpath /usr/lib/x86_64-linux-gnu lib/rectangular_binary_matrix.lo lib/mer_dna.lo lib/storage.lo lib/allocators_mmap.lo lib/misc.lo lib/int128.lo lib/thread_exec.lo lib/jsoncpp.lo lib/time.lo lib/generator_manager.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o lib/.libs/rectangular_binary_matrix.o lib/.libs/mer_dna.o lib/.libs/storage.o lib/.libs/allocators_mmap.o lib/.libs/misc.o lib/.libs/int128.o lib/.libs/thread_exec.o lib/.libs/jsoncpp.o lib/.libs/time.o lib/.libs/generator_manager.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -O3 -O2 -Wl,-z -Wl,relro -Wl,-soname -Wl,libjellyfish-2.0.so.2 -o .libs/libjellyfish-2.0.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so.2" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so.2") libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so") libtool: link: ar cru .libs/libjellyfish-2.0.a lib/rectangular_binary_matrix.o lib/mer_dna.o lib/storage.o lib/allocators_mmap.o lib/misc.o lib/int128.o lib/thread_exec.o lib/jsoncpp.o lib/time.o lib/generator_manager.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libjellyfish-2.0.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" ) g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/count_main.o sub_commands/count_main.cc sub_commands/count_main.cc: In function 'int count_main(int, char**)': sub_commands/count_main.cc:248:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<jellyfish::dumper_t<mer_array> > dumper; ^ In file included from /usr/include/c++/5/memory:81:0, from sub_commands/count_main.cc:28: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/mem_main.o sub_commands/mem_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/merge_files.o jellyfish/merge_files.cc jellyfish/merge_files.cc:38:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] typedef std::auto_ptr<binary_reader> binary_reader_ptr; ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from /usr/include/c++/5/iomanip:43, from ./include/jellyfish/err.hpp:21, from ./jellyfish/merge_files.hpp:21, from jellyfish/merge_files.cc:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ jellyfish/merge_files.cc:39:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] typedef std::auto_ptr<text_reader> text_reader_ptr; ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from /usr/include/c++/5/iomanip:43, from ./include/jellyfish/err.hpp:21, from ./jellyfish/merge_files.hpp:21, from jellyfish/merge_files.cc:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ jellyfish/merge_files.cc:50:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr; ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from /usr/include/c++/5/iomanip:43, from ./include/jellyfish/err.hpp:21, from ./jellyfish/merge_files.hpp:21, from jellyfish/merge_files.cc:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ /bin/bash ./libtool --tag=CXX --mode=link g++ -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o libjellyfish-2.0.la libtool: link: g++ -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -o bin/.libs/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o -lpthread ./.libs/libjellyfish-2.0.so make[4]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' make[3]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' make[2]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' make[1]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' dh_auto_test make -j1 check make[1]: Entering directory '/tmp/buildd/jellyfish-2.2.3' make check-recursive make[2]: Entering directory '/tmp/buildd/jellyfish-2.2.3' Making check in . make[3]: Entering directory '/tmp/buildd/jellyfish-2.2.3' make libgtest.la libgtest_main.la bin/generate_sequence bin/test_all make[4]: Entering directory '/tmp/buildd/jellyfish-2.2.3' /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cru .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/tmp/buildd/jellyfish-2.2.3/./.libs/libgtest.a") libtool: link: ar cru .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libgtest_main.a libtool: link: rm -fr .libs/libgtest_main.lax libtool: link: ( cd ".libs" && rm -f "libgtest_main.la" && ln -s "../libgtest_main.la" "libgtest_main.la" ) g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.o jellyfish/dbg.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la libtool: link: g++ -std=c++0x -g -O3 -Werror -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o -lpthread ./.libs/libjellyfish-2.0.so g++ -DHAVE_CONFIG_H -I. -Dprotected=public -Dprivate=public -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc In file included from ./unit_tests/gtest/gtest.h:308:0, from unit_tests/test_main.cc:20: /usr/include/c++/5/sstream:300:7: error: 'struct std::__cxx11::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access struct __xfer_bufptrs ^ Makefile:1369: recipe for target 'unit_tests/bin_test_all-test_main.o' failed make[4]: *** [unit_tests/bin_test_all-test_main.o] Error 1 make[4]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' Makefile:2319: recipe for target 'check-am' failed make[3]: *** [check-am] Error 2 make[3]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' Makefile:1875: recipe for target 'check-recursive' failed make[2]: *** [check-recursive] Error 1 make[2]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' Makefile:2322: recipe for target 'check' failed make[1]: *** [check] Error 2 make[1]: Leaving directory '/tmp/buildd/jellyfish-2.2.3' dh_auto_test: make -j1 check returned exit code 2 debian/rules:8: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 E: Failed autobuilding of package I: unmounting /sys filesystem I: unmounting /dev/shm filesystem I: unmounting dev/pts filesystem I: unmounting run/shm filesystem I: unmounting proc filesystem I: cleaning the build env I: removing directory /var/cache/pbuilder/build//33131 and its subdirectories
--- End Message ---
--- Begin Message ---Source: jellyfish Source-Version: 2.2.3-2 We believe that the bug you reported is fixed in the latest version of jellyfish, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 795...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated jellyfish package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 20 Aug 2015 09:07:18 +0200 Source: jellyfish Binary: jellyfish libjellyfish-2.0-2 libjellyfish-2.0-dev jellyfish-examples Architecture: source amd64 Version: 2.2.3-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing) libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish) libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish) Closes: 795847 Changes: jellyfish (2.2.3-2) unstable; urgency=medium . [ Charles Plessy ] * Patch with Upstream commit a3c491a for GCC5; closes: #795847. . [ Andreas Tille ] * Do not mention removed file from d/copyright Checksums-Sha1: 649f3edafd03b7080aa8902d638e7ed30eb54bef 2299 jellyfish_2.2.3-2.dsc 61b570fb6f026e03a04c664f21b4206475560687 7012 jellyfish_2.2.3-2.debian.tar.xz ddbde51da619eb6e49cf8d552fa2e17572868b66 447814 jellyfish-examples_2.2.3-2_amd64.deb 63be260f07b49d5a4ba651c3065e7e5eccffeab3 347138 jellyfish_2.2.3-2_amd64.deb b19987f0497bd0d58efaa945e9d7b06fcc33e38a 60626 libjellyfish-2.0-2_2.2.3-2_amd64.deb 7491cf4fc1f35cdb572baa90688f2ece32e7bb0b 115188 libjellyfish-2.0-dev_2.2.3-2_amd64.deb Checksums-Sha256: 246fa0630675cac3b9394c7ac48f62fb32586bb9c63f0d3c4f55f2df9c86fb49 2299 jellyfish_2.2.3-2.dsc f1ef5b56e48d893b6cbc7f419c35c108dd20f4077971fb88e6c6f767ee4cb95b 7012 jellyfish_2.2.3-2.debian.tar.xz 946c76d8e639f76ff0e24fb6337a93e7a4eb33f6e273ade604afd05b1bd6232b 447814 jellyfish-examples_2.2.3-2_amd64.deb 3d591eafb77d9258af05f77cb02039b00f714bf3ffcc93c18cadc668153bb230 347138 jellyfish_2.2.3-2_amd64.deb 98ef1bfe3c162f5e03265eb1b26d72ea503ce54dab90161c81cbcf0417c95dec 60626 libjellyfish-2.0-2_2.2.3-2_amd64.deb a235288e49af577e585771f53d7cf1b2c3dba1b1f3dfe5278b5981b95a08ec55 115188 libjellyfish-2.0-dev_2.2.3-2_amd64.deb Files: 8add237435731aa8b74b5298ef154a59 2299 science optional jellyfish_2.2.3-2.dsc da7b58fcc8703519d7e37c7d1a74496f 7012 science optional jellyfish_2.2.3-2.debian.tar.xz e2f11b01d694dd9b4e63de2a8d5aa41d 447814 science optional jellyfish-examples_2.2.3-2_amd64.deb 877b94c448f89a1f9d645b900e520613 347138 science optional jellyfish_2.2.3-2_amd64.deb 5074992dfa7582327fc4e4e577ccfc93 60626 libs optional libjellyfish-2.0-2_2.2.3-2_amd64.deb f9063fda7d6aa56de0a30a3e4e2d1850 115188 libdevel optional libjellyfish-2.0-dev_2.2.3-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJV1X7vAAoJEFeKBJTRxkbR32AP/Re/GhVJElsxueowywlC5f3C De6i/oUtarwDEHfSE93maCIJpJ6suqE8n38vf59F6vcAW7vMR8iIwCtSNp0hmoYV zA1DXGhdFA6Q9CdJsO05+Qezm//Uwa7ujxw0pnsrx1XY5oliAEwtiJHhtzdICvkM G/PgrZpF9HXlEB9TuUuTH8GVw9L5vwgQjZ5n1Obc67/ngZQ7MOFIG/5T9lKq50hH W0GeUKHpcOxDU9O0MQBavvrSfS58Ggvbv+KDu5wuUo4QqjUeh/HRSXe4tSLUgkY2 zuYJyRFGh8gp26zZCFwk2hGEieD6nz8GkIpdX9ES362JNXLxQrCT+v/lE4RdMAfV ZB1Duq4YXpgJ6UjNQjo8odnIpG/X7eL+81jXrcmXBrnHseOjBiCX5DYO7KAzMTMT dAfnFuMjtLFY37qVQ64HNfS6yd5PwBIdC7zTuMYHvY4mcquWw7CfCUF0jnt48K8a axyCzf74L+Pb5cAztGO5ngzO4Gzm4VakhKK/Nlev69xjD3lw+GesFzvUXqVVh665 oKLoM2vdb927jmrsnxGRGIxI7WJ1lBZjn8z+V73bq6kU5KiTbW6VycImPuBtetqf FM8UMwKdaLi3J6i4R74PfPjNDf9OzP/hEFmzs8NlumCK4quE/Ky0HhImUFQXnZ2a giti5cTCXsb1p/2w0Qlt =qU/a -----END PGP SIGNATURE-----
--- End Message ---
