Date: Sat, 29 Oct 2016 16:42:55 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110arm64-quarterly][biology/jellyfish] Failed for jellyfish-2.2.4 in build Message-ID: <201610291642.u9TGgt2r039639@thunderx1.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: bacon4000@gmail.com Last committer: mat@FreeBSD.org Ident: $FreeBSD: branches/2016Q4/biology/jellyfish/Makefile 412344 2016-04-01 13:29:15Z mat $ Log URL: http://thunderx1.nyi.freebsd.org/data/110arm64-quarterly/424729/logs/jellyfish-2.2.4.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-quarterly&build=424729 Log: ====>> Building biology/jellyfish build started at Sat Oct 29 16:37:50 UTC 2016 port directory: /usr/ports/biology/jellyfish building for: FreeBSD 110arm64-quarterly-job-22 11.0-RELEASE-p1 FreeBSD 11.0-RELEASE-p1 arm64 maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: branches/2016Q4/biology/jellyfish/Makefile 412344 2016-04-01 13:29:15Z mat $ Poudriere version: 3.1.14 Host OSVERSION: 1100121 Jail OSVERSION: 1100122 !!! Jail is newer than host. (Jail: 1100122, Host: 1100121) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_v=FreeBSD 11.0-RELEASE-p1 UNAME_r=11.0-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=aarch64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110arm64-quarterly/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=jellyfish-2.2.4 OSREL=11.0 _OSRELEASE=11.0-RELEASE-p1 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=48 PWD=/usr/local/poudriere/data/.m/110arm64-quarterly/ref/.p/pool MASTERNAME=110arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100122 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --without-sse --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jellyfish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jellyfish/work HOME=/wrkdirs/usr/ports/biology/jellyfish/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jellyfish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jellyfish/work HOME=/wrkdirs/usr/ports/biology/jellyfish/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/jellyfish" EXAMPLESDIR="share/examples/jellyfish" DATADIR="share/jellyfish" WWWDIR="www/jellyfish" ETCDIR="etc/jellyfish" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/jellyfish DOCSDIR=/usr/local/share/doc/jellyfish EXAMPLESDIR=/usr/local/share/examples/jellyfish WWWDIR=/usr/local/www/jellyfish ETCDIR=/usr/local/etc/jellyfish --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License GPLv3+ accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> jellyfish-2.2.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz [110arm64-quarterly-job-22] Installing pkg-1.8.7_3... [110arm64-quarterly-job-22] Extracting pkg-1.8.7_3: .......... done ===> jellyfish-2.2.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of jellyfish-2.2.4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by jellyfish-2.2.4 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by jellyfish-2.2.4 for building => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.4_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by jellyfish-2.2.4 for building ===> Extracting for jellyfish-2.2.4 => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.4_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for jellyfish-2.2.4 ===> Applying FreeBSD patches for jellyfish-2.2.4 =========================================================================== =======================<phase: build-depends >============================ ===> jellyfish-2.2.4 depends on executable: yaggo - not found ===> Installing existing package /packages/All/yaggo-1.5.9.txz [110arm64-quarterly-job-22] Installing yaggo-1.5.9... [110arm64-quarterly-job-22] `-- Installing ruby-2.2.5_1,1... [110arm64-quarterly-job-22] | `-- Installing libffi-3.2.1... [110arm64-quarterly-job-22] | | `-- Installing indexinfo-0.2.5... [110arm64-quarterly-job-22] | | `-- Extracting indexinfo-0.2.5: .... done [110arm64-quarterly-job-22] | `-- Extracting libffi-3.2.1: .......... done [110arm64-quarterly-job-22] | `-- Installing libyaml-0.1.6_2... [110arm64-quarterly-job-22] | `-- Extracting libyaml-0.1.6_2: ......... done [110arm64-quarterly-job-22] | `-- Installing libedit-3.1.20150325_2,1... [110arm64-quarterly-job-22] | `-- Extracting libedit-3.1.20150325_2,1: .......... done [110arm64-quarterly-job-22] `-- Extracting ruby-2.2.5_1,1: .......... done [110arm64-quarterly-job-22] Extracting yaggo-1.5.9: ...... done Message from ruby-2.2.5_1,1: ==== Some of the standard commands are provided as separate ports for ease of upgrading: devel/ruby-gems: gem - RubyGems package manager devel/rubygem-rake: rake - Ruby Make And some of the standard libraries are provided as separate ports since they require extra dependencies: databases/ruby-gdbm: GDBM module Install them as occasion demands. ==== ===> jellyfish-2.2.4 depends on executable: yaggo - found ===> Returning to build of jellyfish-2.2.4 ===> jellyfish-2.2.4 depends on executable: autoconf-2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_1.txz [110arm64-quarterly-job-22] Installing autoconf-2.69_1... [110arm64-quarterly-job-22] `-- Installing autoconf-wrapper-20131203... [110arm64-quarterly-job-22] `-- Extracting autoconf-wrapper-20131203: ........ done [110arm64-quarterly-job-22] `-- Installing perl5-5.20.3_15... [110arm64-quarterly-job-22] `-- Extracting perl5-5.20.3_15: .......... done [110arm64-quarterly-job-22] `-- Installing m4-1.4.17_1,1... [110arm64-quarterly-job-22] `-- Extracting m4-1.4.17_1,1: .......... done [110arm64-quarterly-job-22] Extracting autoconf-2.69_1: .......... done Message from perl5-5.20.3_15: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl <snip> ===> jellyfish-2.2.4 depends on executable: aclocal-1.15 - not found ===> Installing existing package /packages/All/automake-1.15_1.txz [110arm64-quarterly-job-22] Installing automake-1.15_1... [110arm64-quarterly-job-22] `-- Installing automake-wrapper-20131203... [110arm64-quarterly-job-22] `-- Extracting automake-wrapper-20131203: ... done [110arm64-quarterly-job-22] Extracting automake-1.15_1: .......... done ===> jellyfish-2.2.4 depends on executable: aclocal-1.15 - found ===> Returning to build of jellyfish-2.2.4 ===> jellyfish-2.2.4 depends on executable: automake-1.15 - found ===> jellyfish-2.2.4 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6.txz [110arm64-quarterly-job-22] Installing libtool-2.4.6... [110arm64-quarterly-job-22] Extracting libtool-2.4.6: .......... done ===> jellyfish-2.2.4 depends on executable: libtoolize - found ===> Returning to build of jellyfish-2.2.4 ===> jellyfish-2.2.4 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz [110arm64-quarterly-job-22] Installing gmake-4.2.1_1... [110arm64-quarterly-job-22] `-- Installing gettext-runtime-0.19.8.1... [110arm64-quarterly-job-22] `-- Extracting gettext-runtime-0.19.8.1: .......... done [110arm64-quarterly-job-22] Extracting gmake-4.2.1_1: .......... done ===> jellyfish-2.2.4 depends on executable: gmake - found ===> Returning to build of jellyfish-2.2.4 ===> jellyfish-2.2.4 depends on package: pkgconf>=0.9.10 - not found ===> Installing existing package /packages/All/pkgconf-1.0.1.txz [110arm64-quarterly-job-22] Installing pkgconf-1.0.1... [110arm64-quarterly-job-22] Extracting pkgconf-1.0.1: .......... done ===> jellyfish-2.2.4 depends on package: pkgconf>=0.9.10 - found ===> Returning to build of jellyfish-2.2.4 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for jellyfish-2.2.4 libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, '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' configure: loading site script /usr/ports/Templates/config.site checking build system type... aarch64-portbld-freebsd11.0 checking host system type... aarch64-portbld-freebsd11.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking whether gmake supports nested variables... (cached) yes checking how to print strings... printf checking for style of include used by gmake... GNU checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /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 checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking how to convert aarch64-portbld-freebsd11.0 file names to aarch64-portbld-freebsd11.0 format... func_convert_file_noop checking how to convert aarch64-portbld-freebsd11.0 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... no 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... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd11.0 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 whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd11.0 ld.so checking how to hardcode library paths into programs... immediate checking for md5sum... no checking for md5... md5 -r checking for yaggo... /usr/local/bin/yaggo checking pkg-config is at least version 0.9.0... yes checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... no checking for siginfo_t.si_int... no 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 =========================================================================== =======================<phase: build >============================ ===> Building for jellyfish-2.2.4 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4' /usr/local/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo gmake all-am gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4' depbase=`echo lib/rectangular_binary_matrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -std=c++0x -g -O3 -Werror -std=c++0x -O2 -pipe -fno-strict-aliasing -MT lib/rectangular_binary_matrix.lo -MD -MP -MF $depbase.Tpo -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -std=c++0x -g -O3 -Werror -std=c++0x -O2 -pipe -fno-strict-aliasing -MT lib/rectangular_binary_matrix.lo -MD -MP -MF lib/.deps/rectangular_binary_matrix.Tpo -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o In file included from lib/rectangular_binary_matrix.cc:22: ./include/jellyfish/rectangular_binary_matrix.hpp:348:17: error: variable 'res' is uninitialized when used within its own initialization [-Werror,-Wuninitialized] u128 res = res ^ res; ~~~ ^~~ ./include/jellyfish/rectangular_binary_matrix.hpp:142:14: note: in instantiation of function template specialization 'jellyfish::RectangularBinaryMatrix::times_128<unsigned long *>' requested here return times_128(v); ^ lib/rectangular_binary_matrix.cc:83:24: note: in instantiation of function template specialization 'jellyfish::RectangularBinaryMatrix::times<unsigned long *>' requested here res.get(i) = this->times(&v[0]); ^ 1 error generated. gmake[2]: *** [Makefile:1626: lib/rectangular_binary_matrix.lo] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4' gmake[1]: *** [Makefile:943: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4' *** Error code 1 Stop. make: stopped in /usr/ports/biology/jellyfish
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