[package - main-amd64-default][biology/abyss] Failed for abyss-2.3.1 in build
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Date: Wed, 08 Dec 2021 00:40:45 UTC
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: yuri@FreeBSD.org
Log URL: http://beefy18.nyi.freebsd.org/data/main-amd64-default/p7539e33f88ff_s169b368a62/logs/abyss-2.3.1.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=p7539e33f88ff_s169b368a62
Log:
=>> Building biology/abyss
build started at Wed Dec 8 00:39:56 UTC 2021
port directory: /usr/ports/biology/abyss
package name: abyss-2.3.1
building for: FreeBSD main-amd64-default-job-03 14.0-CURRENT FreeBSD 14.0-CURRENT 1400043 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400042
Jail OSVERSION: 1400043
Job Id: 03
!!! Jail is newer than host. (Jail: 1400043, Host: 1400042) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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POUDRIEREPATH=/usr/local/bin/poudriere
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PORT_FLAGS=
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DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for abyss-2.3.1:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/abyss/work/.cache HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/abyss/work/.cache HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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--
PORTDOCS="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
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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
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#### /usr/ports/Mk/Scripts/ports_env.sh ####
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#### Misc Poudriere ####
GID=0
UID=0
---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 >============================
===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[main-amd64-default-job-03] Installing pkg-1.17.5...
[main-amd64-default-job-03] Extracting pkg-1.17.5: .......... done
===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of abyss-2.3.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.1 for building
=> SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.1 for building
===> Extracting for abyss-2.3.1
=> SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for abyss-2.3.1
===> Applying FreeBSD patches for abyss-2.3.1 from /usr/ports/biology/abyss/files
===========================================================================
=======================<phase: build-depends >============================
===> abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - not found
===> Installing existing package /packages/All/boost-libs-1.72.0_6.pkg
[main-amd64-default-job-03] Installing boost-libs-1.72.0_6...
[main-amd64-default-job-03] `-- Installing icu-70.1_1,1...
[main-amd64-default-job-03] `-- Extracting icu-70.1_1,1: .......... done
<snip>
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for dlfcn.h... (cached) yes
checking for fcntl.h... (cached) yes
checking for float.h... (cached) yes
checking for limits.h... (cached) yes
checking for stddef.h... (cached) yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for stdbool.h that conforms to C99... (cached) yes
checking for _Bool... (cached) yes
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... (cached) yes
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checking for std::hash<int>... yes
checking for std::tr1::hash<int>... no
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checking for dup2... (cached) yes
checking for gethostname... (cached) yes
checking for getopt_long... yes
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checking for memset... (cached) yes
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checking for strtoul... (cached) yes
checking for vfork.h... (cached) no
checking for fork... (cached) yes
checking for vfork... (cached) yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... (cached) yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... no
checking build system type... amd64-portbld-freebsd14.0
checking host system type... amd64-portbld-freebsd14.0
checking if compiler needs -Werror to reject unknown flags... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... c++ -std=c++11 -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... no
checking tr1/functional presence... no
checking for tr1/functional... no
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... no
checking google/sparse_hash_map presence... no
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checking unordered_map usability... yes
checking unordered_map presence... yes
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checking tr1/unordered_map usability... no
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checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... no
checking tr1/unordered_set presence... no
checking for tr1/unordered_set... no
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for c++ -std=c++11 option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating vendor/gtest-1.7.0/Makefile
config.status: creating RResolver/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating vendor/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build >============================
===> Building for abyss-2.3.1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1'
gmake all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1'
Making all in bin
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/bin'
cp ../bin/abyss-nompi ABYSS-P
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/bin'
Making all in doc
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/doc'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/doc'
Making all in Common
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Common'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-ContigID.o -MD -MP -MF .deps/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Histogram.o -MD -MP -MF .deps/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Kmer.o -MD -MP -MF .deps/libcommon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Log.o -MD -MP -MF .deps/libcommon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
Kmer.cpp:120:9: error: reference to 'bitset' is ambiguous
typedef bitset<2 * MAX_KMER> Seq;
^
/usr/include/sys/_bitset.h:64:17: note: candidate found by name lookup is 'bitset'
__BITSET_DEFINE(bitset, 1);
^
/usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset'
class _LIBCPP_TEMPLATE_VIS bitset
^
1 error generated.
gmake[3]: *** [Makefile:486: libcommon_a-Kmer.o] Error 1
gmake[3]: *** Waiting for unfinished jobs....
mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Common'
gmake[2]: *** [Makefile:490: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1'
gmake[1]: *** [Makefile:410: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/abyss