Skip site navigation (1)Skip section navigation (2)
Date:      Tue, 19 Feb 2019 10:42:49 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-powerpc64-default][biology/jellyfish] Failed for jellyfish-2.2.6_4 in build
Message-ID:  <201902191042.x1JAgn0I020049@pylon.nyi.freebsd.org>

next in thread | raw e-mail | index | archive | help

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: head/biology/jellyfish/Makefile 487272 2018-12-12 01:35:33Z gerald $
Log URL:        http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p492815_s343942/logs/jellyfish-2.2.6_4.log
Build URL:      http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p492815_s343942
Log:

=>> Building biology/jellyfish
build started at Tue Feb 19 10:40:59 UTC 2019
port directory: /usr/ports/biology/jellyfish
package name: jellyfish-2.2.6_4
building for: FreeBSD head-powerpc64-default-job-03 13.0-CURRENT FreeBSD 13.0-CURRENT 1300010 powerpc
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/jellyfish/Makefile 487272 2018-12-12 01:35:33Z gerald $
Poudriere version: 3.2.8-1-g2a843cca
Host OSVERSION: 1300012
Jail OSVERSION: 1300010
Job Id: 03

---Begin Environment---
SHELL=/bin/csh
OSVERSION=1300010
UNAME_v=FreeBSD 13.0-CURRENT 1300010
UNAME_r=13.0-CURRENT
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=3.2.8-1-g2a843cca
MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=vt100
PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-powerpc64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-default/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=13.0 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=13.0-CURRENT
OSREL=13.0
OSVERSION=1300010
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
[head-powerpc64-default-job-03] Installing pkg-1.10.5_5...
[head-powerpc64-default-job-03] 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
[head-powerpc64-default-job-03] Installing yaggo-1.5.9...
[head-powerpc64-default-job-03] `-- Installing ruby-2.4.5_1,1...
[head-powerpc64-default-job-03] |   `-- Installing gcc8-8.2.0_4...
[head-powerpc64-default-job-03] |   | `-- Installing binutils-2.32,1...
[head-powerpc64-default-job-03] |   |   `-- Installing gettext-runtime-0.19.8.1_2...
[head-powerpc64-default-job-03] |   |   | `-- Installing indexinfo-0.3.1...
[head-powerpc64-default-job-03] |   |   | `-- Extracting indexinfo-0.3.1: .... done
[head-powerpc64-default-job-03] |   |   `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[head-powerpc64-default-job-03] |   | `-- Extracting binutils-2.32,1: .......... done
[head-powerpc64-default-job-03] |   | `-- Installing gcc5-5.5.0_6...
[head-powerpc64-default-job-03] |   |   `-- Installing gmp-6.1.2_1...
[head-powerpc64-default-job-03] |   |   `-- Extracting gmp-6.1.2_1: .......... done
<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-freebsd13.0
checking host system type... powerpc64-portbld-freebsd13.0
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-freebsd13.0 file names to powerpc64-portbld-freebsd13.0 format... func_convert_file_noop
checking how to convert powerpc64-portbld-freebsd13.0 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... freebsd13.0 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... freebsd13.0 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



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201902191042.x1JAgn0I020049>