Date: Tue, 18 Jun 2019 06:43:49 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120powerpc64-quarterly][biology/jellyfish] Failed for jellyfish-2.2.6_4 in build Message-ID: <201906180643.x5I6hngc098141@pylon.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: jwb@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: branches/2019Q2/biology/jellyfish/Makefile 487272 2018-12-12 01:35:33Z gerald $ Log URL: http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/504456/logs/jellyfish-2.2.6_4.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=504456 Log: =>> Building biology/jellyfish build started at Tue Jun 18 06:40:09 UTC 2019 port directory: /usr/ports/biology/jellyfish package name: jellyfish-2.2.6_4 building for: FreeBSD 120powerpc64-quarterly-job-20 12.0-RELEASE-p5 FreeBSD 12.0-RELEASE-p5 1200086 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q2/biology/jellyfish/Makefile 487272 2018-12-12 01:35:33Z gerald $ Poudriere version: 3.2.8-4-g701d8fe1 Host OSVERSION: 1300012 Jail OSVERSION: 1200086 Job Id: 20 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p5 1200086 UNAME_r=12.0-RELEASE-p5 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-4-g701d8fe1 MASTERMNT=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --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" PATH=/wrkdirs/usr/ports/biology/jellyfish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" 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" PATH=/wrkdirs/usr/ports/biology/jellyfish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc8" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAG S="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- VER=2.2.6 OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /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 # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p5 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv3+ accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> jellyfish-2.2.6_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120powerpc64-quarterly-job-20] Installing pkg-1.10.5_5... [120powerpc64-quarterly-job-20] Extracting pkg-1.10.5_5: .......... done ===> jellyfish-2.2.6_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of jellyfish-2.2.6_4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by jellyfish-2.2.6_4 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by jellyfish-2.2.6_4 for building => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.6_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by jellyfish-2.2.6_4 for building ===> Extracting for jellyfish-2.2.6_4 => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.6_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for jellyfish-2.2.6_4 ===> Applying FreeBSD patches for jellyfish-2.2.6_4 =========================================================================== =======================<phase: build-depends >============================ ===> jellyfish-2.2.6_4 depends on executable: yaggo - not found ===> Installing existing package /packages/All/yaggo-1.5.9.txz [120powerpc64-quarterly-job-20] Installing yaggo-1.5.9... [120powerpc64-quarterly-job-20] `-- Installing ruby-2.4.5_1,1... [120powerpc64-quarterly-job-20] | `-- Installing gcc8-8.3.0_2... [120powerpc64-quarterly-job-20] | | `-- Installing binutils-2.32,1... [120powerpc64-quarterly-job-20] | | `-- Installing gettext-runtime-0.19.8.1_2... [120powerpc64-quarterly-job-20] | | | `-- Installing indexinfo-0.3.1... [120powerpc64-quarterly-job-20] | | | `-- Extracting indexinfo-0.3.1: .... done [120powerpc64-quarterly-job-20] | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [120powerpc64-quarterly-job-20] | | `-- Extracting binutils-2.32,1: .......... done [120powerpc64-quarterly-job-20] | | `-- Installing gmp-6.1.2_1... [120powerpc64-quarterly-job-20] | | `-- Extracting gmp-6.1.2_1: .......... done [120powerpc64-quarterly-job-20] | | `-- Installing mpc-1.1.0_2... <snip> =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for jellyfish-2.2.6_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... powerpc64-portbld-freebsd12.0 checking host system type... powerpc64-portbld-freebsd12.0 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 whether gmake supports the include directive... yes (GNU style) checking for gcc... gcc8 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 gcc8 accepts -g... yes checking for gcc8 option to accept ISO C89... none needed checking whether gcc8 understands -c and -o together... yes checking dependency style of gcc8... 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 gcc8... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm checking the name lister (/usr/local/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 powerpc64-portbld-freebsd12.0 file names to powerpc64-portbld-freebsd12.0 format... func_convert_file_noop checking how to convert powerpc64-portbld-freebsd12.0 file names to toolchain format... func_convert_file_noop checking for /usr/local/bin/ld option to reload object files... -r checking for objdump... /usr/local/bin/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 archiver @FILE support... @ checking for strip... strip checking for ranlib... /usr/local/bin/ranlib checking command to parse /usr/local/bin/nm output from gcc8 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... cpp8 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 gcc8 supports -fno-rtti -fno-exceptions... no checking for gcc8 option to produce PIC... -fPIC -DPIC checking if gcc8 PIC flag -fPIC -DPIC works... yes checking if gcc8 static flag -static works... yes checking if gcc8 supports -c -o file.o... yes checking if gcc8 supports -c -o file.o... (cached) yes checking whether the gcc8 linker (/usr/local/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd12.0 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 g++8 accepts -g... yes checking dependency style of g++8... gcc3 checking how to run the C++ preprocessor... g++8 -E checking for ld used by g++8... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking whether the g++8 linker (/usr/local/bin/ld) supports shared libraries... yes checking for g++8 option to produce PIC... -fPIC -DPIC checking if g++8 PIC flag -fPIC -DPIC works... yes checking if g++8 static flag -static works... yes checking if g++8 supports -c -o file.o... yes checking if g++8 supports -c -o file.o... (cached) yes checking whether the g++8 linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd12.0 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>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes 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-2.2.6_4 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.6' /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-2.2.6' depbase=`echo sub_commands/jellyfish.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++8 -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -std=c++0x -g -O3 -Werror -std=c++0x -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -MT sub_commands/jellyfish.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/count_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++8 -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -g -O3 -std=c++0x -g -O3 -Werror -std=c++0x -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -MT sub_commands/count_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/count_main.o sub_commands/count_main.cc &&\ mv -f $depbase.Tpo $depbase.Po sub_commands/count_main.cc: In function 'jellyfish::mer_dna_bloom_counter* load_bloom_filter(const char*)': sub_commands/count_main.cc:197:82: error: 'new' of type 'jellyfish::mer_dna_bloom_counter' {aka 'jellyfish::bloom_counter2<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0> >'} with extended alignment 16 [-Werror=aligned-new=] auto res = new mer_dna_bloom_counter(header.size(), header.nb_hashes(), in, fns); ^ sub_commands/count_main.cc:197:82: note: uses 'void* operator new(std::size_t)', which does not have an alignment parameter sub_commands/count_main.cc:197:82: note: use '-faligned-new' to enable C++17 over-aligned new support sub_commands/count_main.cc: In function 'int count_main(int, char**)': sub_commands/count_main.cc:285:71: error: 'new' of type 'jellyfish::mer_dna_bloom_filter' {aka 'jellyfish::bloom_filter<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0> >'} with extended alignment 16 [-Werror=aligned-new=] bf.reset(new mer_dna_bloom_filter(args.bf_fp_arg, args.bf_size_arg)); ^ sub_commands/count_main.cc:285:71: note: uses 'void* operator new(std::size_t)', which does not have an alignment parameter sub_commands/count_main.cc:285:71: note: use '-faligned-new' to enable C++17 over-aligned new support sub_commands/count_main.cc:333:28: error: catching polymorphic type 'class MergeError' by value [-Werror=catch-value=] } catch(MergeError e) { ^ In file included from sub_commands/count_main.cc:33: ./include/jellyfish/hash_counter.hpp: In instantiation of 'jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::hash_counter(size_t, uint16_t, uint16_t, uint16_t, uint16_t, const size_t*) [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint16_t = short unsigned int]': sub_commands/count_main.cc:244:110: required from here ./include/jellyfish/hash_counter.hpp:64:10: error: 'new' of type 'jellyfish::cooperative::hash_counter<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0> >::array' {aka 'jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int, atomic::gcc, allocators::mmap>'} with extended alignment 16 [-Werror=aligned-new=] ary_(new array(size, key_len, val_len, reprobe_limit, reprobes)), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./include/jellyfish/hash_counter.hpp:64:10: note: uses 'void* operator new(std::size_t)', which does not have an alignment parameter ./include/jellyfish/hash_counter.hpp:64:10: note: use '-faligned-new' to enable C++17 over-aligned new support ./include/jellyfish/hash_counter.hpp: In instantiation of 'bool jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::double_size(bool) [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]': ./include/jellyfish/hash_counter.hpp:189:28: required from 'bool jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::handle_full_ary() [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' ./include/jellyfish/hash_counter.hpp:167:7: required from 'bool jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::update_add(const Key&, uint64_t, Key&) [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; uint64_t = long unsigned int]' sub_commands/count_main.cc:173:11: required from 'void mer_counter_base<PathIterator, MerIteratorType, ParserType>::start(int) [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*> >; MerIteratorType = mer_qual_iterator; ParserType = sequence_qual_parser]' sub_commands/count_main.cc:148:16: required from here ./include/jellyfish/hash_counter.hpp:207:22: error: 'new' of type 'jellyfish::cooperative::hash_counter<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0> >::array' {aka 'jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int, atomic::gcc, allocators::mmap>'} with extended alignment 16 [-Werror=aligned-new=] new_ary_ = new array(ary_->size() * 2, ary_->key_len(), ary_->val_len(), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ary_->max_reprobe(), ary_->reprobes()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./include/jellyfish/hash_counter.hpp:207:22: note: uses 'void* operator new(std::size_t)', which does not have an alignment parameter ./include/jellyfish/hash_counter.hpp:207:22: note: use '-faligned-new' to enable C++17 over-aligned new support ./include/jellyfish/hash_counter.hpp:209:10: error: catching polymorphic type 'class jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int, atomic::gcc, allocators::mmap> >::ErrorAllocation' by value [-Werror=catch-value=] } catch(typename array::ErrorAllocation e) { ^~~~~ cc1plus: all warnings being treated as errors gmake[2]: *** [Makefile:1671: sub_commands/count_main.o] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.6' gmake[1]: *** [Makefile:998: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.6' *** Error code 1 Stop. make: stopped in /usr/ports/biology/jellyfish
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