[package - 134releng-armv7-default][biology/stacks] Failed for stacks-2.68 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Fri, 24 Jan 2025 00:55:12 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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere3/data/134releng-armv7-default/86e28c84a7e0/logs/stacks-2.68.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=134releng-armv7-default&build=86e28c84a7e0
Log:
=>> Building biology/stacks
build started at Fri Jan 24 00:53:03 UTC 2025
port directory: /usr/ports/biology/stacks
package name: stacks-2.68
building for: FreeBSD 134releng-armv7-default-job-02 13.4-RELEASE-p2 FreeBSD 13.4-RELEASE-p2 1304000 arm
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 476 Jan 18 01:09 /usr/ports/biology/stacks/Makefile
Ports top last git commit: 86e28c84a7e
Ports top unclean checkout: no
Port dir last git commit: e3e3bee1992
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500028
Jail OSVERSION: 1304000
Job Id: 02
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1304000
UNAME_v=FreeBSD 13.4-RELEASE-p2 1304000
UNAME_r=13.4-RELEASE-p2
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/134releng-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/134releng-armv7-default/02/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=134releng-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/134releng-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stacks/work/.cache HOME=/wrkdirs/usr/ports/biology/stacks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stacks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stacks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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/stacks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stacks/work/.cache HOME=/wrkdirs/usr/ports/biology/stacks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stacks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stacks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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 064
4" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/stacks" EXAMPLESDIR="share/examples/stacks" DATADIR="share/stacks" WWWDIR="www/stacks" ETCDIR="etc/stacks"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/stacks DOCSDIR=/usr/local/share/doc/stacks EXAMPLESDIR=/usr/local/share/examples/stacks WWWDIR=/usr/local/www/stacks ETCDIR=/usr/local/etc/stacks
--End SUB_LIST--
---Begin 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 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
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) 524288
stack size (kbytes, -s) 65536
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) 8192
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 >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> stacks-2.68 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[134releng-armv7-default-job-02] Installing pkg-1.21.3...
[134releng-armv7-default-job-02] Extracting pkg-1.21.3: .......... done
===> stacks-2.68 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of stacks-2.68
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by stacks-2.68 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by stacks-2.68 for building
=> SHA256 Checksum OK for stacks-2.68.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by stacks-2.68 for building
===> Extracting for stacks-2.68
=> SHA256 Checksum OK for stacks-2.68.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for stacks-2.68
===> Applying FreeBSD patches for stacks-2.68 from /usr/ports/biology/stacks/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> stacks-2.68 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[134releng-armv7-default-job-02] Installing gmake-4.4.1...
[134releng-armv7-default-job-02] `-- Installing gettext-runtime-0.23.1...
[134releng-armv7-default-job-02] | `-- Installing indexinfo-0.3.1...
[134releng-armv7-default-job-02] | `-- Extracting indexinfo-0.3.1: .... done
[134releng-armv7-default-job-02] `-- Extracting gettext-runtime-0.23.1: .......... done
[134releng-armv7-default-job-02] Extracting gmake-4.4.1: .......... done
===> stacks-2.68 depends on package: gmake>=4.4.1 - found
===> Returning to build of stacks-2.68
===> stacks-2.68 depends on file: /usr/local/bin/python3.11 - not found
===> Installing existing package /packages/All/python311-3.11.11.pkg
[134releng-armv7-default-job-02] Installing python311-3.11.11...
[134releng-armv7-default-job-02] `-- Installing libffi-3.4.6...
[134releng-armv7-default-job-02] `-- Extracting libffi-3.4.6: .......... done
[134releng-armv7-default-job-02] `-- Installing mpdecimal-4.0.0...
[134releng-armv7-default-job-02] `-- Extracting mpdecimal-4.0.0: .......... done
[134releng-armv7-default-job-02] `-- Installing readline-8.2.13_2...
[134releng-armv7-default-job-02] `-- Extracting readline-8.2.13_2: .......... done
<snip>
187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {}
| ^
| std::
src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
216 | void add(SRead&& r) {reads_.push_back(move(r));}
| ^
| std::
src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));}
| ^
| std::
In file included from src/process_radtags.cc:31:
In file included from src/process_radtags.h:43:
In file included from src/clean.h:31:
In file included from src/kmers.h:36:
src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {}
| ^
| std::
src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {}
| ^
| std::
src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {}
| ^
| std::
src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {}
| ^
| std::
src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
216 | void add(SRead&& r) {reads_.push_back(move(r));}
| ^
| std::
src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));}
| ^
| std::
src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
245 | void ref(DNASeq4&& s) {ref_ = move(s);}
| ^
| std::
src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
308 | reads_.push_back(move(r));
| ^
| std::
src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
245 | void ref(DNASeq4&& s) {ref_ = move(s);}
| ^
| std::
src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
308 | reads_.push_back(move(r));
| ^
| std::
In file included from src/process_radtags.cc:31:
In file included from src/process_radtags.h:43:
In file included from src/clean.h:31:
In file included from src/kmers.h:37:
src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
92 | , utags (move(o.utags))
| ^
| std::
src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
93 | , remtags (move(o.remtags))
| ^
| std::
src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
95 | , dist (move(o.dist))
| ^
| std::
src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
96 | , alns (move(o.alns))
| ^
| std::
src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
99 | , loc (move(o.loc))
| ^
| std::
src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
100 | , snps (move(o.snps))
| ^
| std::
src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
101 | , alleles (move(o.alleles))
| ^
| std::
src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
102 | , gaps (move(o.gaps))
| ^
| std::
In file included from src/sstacks.cc:29:
In file included from src/catalog_utils.h:32:
src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
452 | ++cloc->alleles[move(hap)];
| ^
| std::
src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
454 | ++cloc->alleles[move(hap)];
| ^
| std::
src/process_radtags.cc:764:5: error: unknown type name 'omp_lock_t'
764 | omp_lock_t inpbuf_lock[num_worker_threads];
| ^
In file included from src/sstacks.cc:34:
In file included from src/sstacks.h:50:
In file included from src/kmers.h:37:
src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
92 | , utags (move(o.utags))
| ^
| std::
src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
93 | , remtags (move(o.remtags))
| ^
| std::
src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
95 | , dist (move(o.dist))
| ^
| std::
src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
96 | , alns (move(o.alns))
| ^
| std::
src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
99 | , loc (move(o.loc))
| ^
| std::
src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
100 | , snps (move(o.snps))
| ^
| std::
src/process_radtags.cc:765:5: error: unknown type name 'omp_lock_t'
765 | omp_lock_t outbuf_lock[num_worker_threads];
| ^
src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
101 | , alleles (move(o.alleles))
| ^
| std::
src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
102 | , gaps (move(o.gaps))
| ^
| std::
In file included from src/sstacks.cc:34:
In file included from src/sstacks.h:53:
src/GappedAln.h:42:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
42 | this->cigar = move(cigar);
| ^
| std::
src/GappedAln.h:49:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
49 | this->cigar = move(cigar);
| ^
| std::
src/process_radtags.cc:826:18: error: use of undeclared identifier 'omp_get_thread_num'
826 | int thread_no = omp_get_thread_num();
| ^
src/GappedAln.h:778:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
778 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len)));
| ^
| std::
src/GappedAln.h:924:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
924 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len), (uint) j));
| ^
| std::
src/process_radtags.cc:1007:6: error: unknown type name 'omp_lock_t'
1007 | omp_lock_t &thread_inpbuf_lock = inpbuf_lock[thread_index];
| ^
src/process_radtags.cc:1009:6: error: unknown type name 'omp_lock_t'
1009 | omp_lock_t &thread_outbuf_lock = outbuf_lock[thread_index];
| ^
src/process_radtags.cc:1374:5: error: unknown type name 'omp_lock_t'
1374 | omp_lock_t inpbuf_lock[num_worker_threads];
| ^
src/process_radtags.cc:1375:5: error: unknown type name 'omp_lock_t'
1375 | omp_lock_t outbuf_lock[num_worker_threads];
| ^
src/process_radtags.cc:1433:18: error: use of undeclared identifier 'omp_get_thread_num'
1433 | int thread_no = omp_get_thread_num();
| ^
src/process_radtags.cc:1576:6: error: unknown type name 'omp_lock_t'
1576 | omp_lock_t &thread_inpbuf_lock = inpbuf_lock[thread_index];
| ^
src/process_radtags.cc:1578:6: error: unknown type name 'omp_lock_t'
1578 | omp_lock_t &thread_outbuf_lock = outbuf_lock[thread_index];
| ^
25 warnings and 10 errors generated.
gmake[2]: *** [Makefile:1100: src/process_radtags.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
29 warnings generated.
31 warnings generated.
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68'
gmake[1]: *** [Makefile:1122: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68'
gmake: *** [Makefile:762: all] Error 2
===> 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/stacks