[package - main-amd64-default][biology/stacks] Failed for stacks-2.4_2 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Tue, 23 Apr 2024 12:12:30 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/beefy18/data/main-amd64-default/pddece660bc1b_sc0f02dcd4c9/logs/stacks-2.4_2.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pddece660bc1b_sc0f02dcd4c9
Log:
=>> Building biology/stacks
build started at Tue Apr 23 12:11:37 UTC 2024
port directory: /usr/ports/biology/stacks
package name: stacks-2.4_2
building for: FreeBSD main-amd64-default-job-11 15.0-CURRENT FreeBSD 15.0-CURRENT 1500018 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 671 Sep 8 2022 /usr/ports/biology/stacks/Makefile
Ports top last git commit: ddece660bc1
Ports top unclean checkout: no
Port dir last git commit: fb16dfecae4
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500006
Jail OSVERSION: 1500018
Job Id: 11
!!! Jail is newer than host. (Jail: 1500018, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500018
UNAME_v=FreeBSD 15.0-CURRENT 1500018
UNAME_r=15.0-CURRENT
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=3.4.1-30-g79e3edcd
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-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/main-amd64-default/11/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd
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=gmake PYTHON="/usr/local/bin/python3.9" 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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=15.0 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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) 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) 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-2.4_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.2.pkg
[main-amd64-default-job-11] Installing pkg-1.21.2...
[main-amd64-default-job-11] Extracting pkg-1.21.2: .......... done
===> stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of stacks-2.4_2
===========================================================================
=======================<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-2.4_2 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-2.4_2 for building
=> SHA256 Checksum OK for stacks-2.4.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-2.4_2 for building
===> Extracting for stacks-2.4_2
=> SHA256 Checksum OK for stacks-2.4.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-2.4_2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> stacks-2.4_2 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-amd64-default-job-11] Installing gmake-4.4.1...
[main-amd64-default-job-11] `-- Installing gettext-runtime-0.22.5...
[main-amd64-default-job-11] | `-- Installing indexinfo-0.3.1...
[main-amd64-default-job-11] | `-- Extracting indexinfo-0.3.1: .... done
[main-amd64-default-job-11] `-- Extracting gettext-runtime-0.22.5: .......... done
[main-amd64-default-job-11] Extracting gmake-4.4.1: .......... done
===> stacks-2.4_2 depends on package: gmake>=4.4.1 - found
===> Returning to build of stacks-2.4_2
<snip>
| std::
depbase=`echo src/MetaPopInfo.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/MetaPopInfo.o -MD -MP -MF $depbase.Tpo -c -o src/MetaPopInfo.o src/MetaPopInfo.cc &&\
mv -f $depbase.Tpo $depbase.Po
25 warnings generated.
depbase=`echo src/models.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/models.o -MD -MP -MF $depbase.Tpo -c -o src/models.o src/models.cc &&\
mv -f $depbase.Tpo $depbase.Po
In file included from src/MetaPopInfo.cc:10:
In file included from src/input.h:34:
In file included from src/stacks.h:40:
src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();}
| ^
| std::
src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;}
| ^
| std::
In file included from src/MetaPopInfo.cc:10:
In file included from src/input.h:34:
src/stacks.h:269:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
269 | : seq(move(s)), name(move(n))
| ^
| std::
src/stacks.h:269:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
269 | : seq(move(s)), name(move(n))
| ^
| std::
src/MetaPopInfo.cc:427:30: error: non-constant-expression cannot be narrowed from type 'size_t' (aka 'unsigned long') to 'const int' in initializer list [-Wc++11-narrowing-const-reference]
427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} );
| ^
4 warnings and 1 error generated.
gmake[2]: *** [Makefile:1031: src/MetaPopInfo.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
In file included from src/models.cc:30:
In file included from src/models.h:26:
src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();}
| ^
| std::
src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;}
| ^
| std::
In file included from src/models.cc:30:
In file included from src/models.h:27:
src/stacks.h:269:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
269 | : seq(move(s)), name(move(n))
| ^
| std::
src/stacks.h:269:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
269 | : seq(move(s)), name(move(n))
| ^
| std::
In file included from src/models.cc:30:
In file included from src/models.h:28:
In file included from src/locus.h:34:
src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {}
| ^
| std::
src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {}
| ^
| std::
src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
223 | return AlnRead(Read(move(seq), move(name)), move(cig));
| ^
| std::
src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
223 | return AlnRead(Read(move(seq), move(name)), move(cig));
| ^
| std::
src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
223 | return AlnRead(Read(move(seq), move(name)), move(cig));
| ^
| std::
In file included from src/models.cc:30:
In file included from src/models.h:28:
src/locus.h:186:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
186 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {}
| ^
| std::
src/locus.h:192:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
192 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {}
| ^
| std::
src/locus.h:193:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
193 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {}
| ^
| std::
src/locus.h:193:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
193 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {}
| ^
| std::
src/locus.h:222:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
222 | void add(SRead&& r) {reads_.push_back(move(r));}
| ^
| std::
src/locus.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
223 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));}
| ^
| std::
src/locus.h:251:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
251 | void ref(DNASeq4&& s) {ref_ = move(s);}
| ^
| std::
src/locus.h:314:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
314 | reads_.push_back(move(r));
| ^
| std::
In file included from src/models.cc:30:
In file included from src/models.h:29:
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/models.cc:30:
src/models.h:115:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
115 | : alleles_(move(alleles))
| ^
| std::
src/models.h:117:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
117 | , sample_calls_(move(sample_calls))
| ^
| std::
src/models.h:124:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
124 | : SiteCall(move(alleles), -1, move(sample_calls)) {}
| ^
| std::
src/models.h:124:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
124 | : SiteCall(move(alleles), -1, move(sample_calls)) {}
| ^
| std::
src/models.cc:515:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
515 | return SiteCall(move(allele_freqs), move(sample_calls));
| ^
| std::
src/models.cc:515:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
515 | return SiteCall(move(allele_freqs), move(sample_calls));
| ^
| std::
src/models.cc:709:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
709 | return SiteCall(move(allele_freqs), move(sample_calls));
| ^
| std::
src/models.cc:709:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
709 | return SiteCall(move(allele_freqs), move(sample_calls));
| ^
| std::
src/models.cc:1007:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1007 | return SiteCall(move(allele_freqs), dimorph_qual, move(sample_calls));
| ^
| std::
src/models.cc:1007:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1007 | return SiteCall(move(allele_freqs), dimorph_qual, move(sample_calls));
| ^
| std::
22 warnings generated.
35 warnings generated.
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4'
gmake[1]: *** [Makefile:1053: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4'
gmake: *** [Makefile:704: 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