[package - main-i386-default][biology/ngs-sdk] Failed for ngs-sdk-3.0.1 in build
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Date: Sat, 27 Apr 2024 07:41:12 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p9476d3e04f44_s4ba444de708/logs/ngs-sdk-3.0.1.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p9476d3e04f44_s4ba444de708
Log:
=>> Building biology/ngs-sdk
build started at Sat Apr 27 07:41:04 UTC 2024
port directory: /usr/ports/biology/ngs-sdk
package name: ngs-sdk-3.0.1
building for: FreeBSD main-i386-default-job-08 15.0-CURRENT FreeBSD 15.0-CURRENT 1500018 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1650 Feb 3 01:01 /usr/ports/biology/ngs-sdk/Makefile
Ports top last git commit: 9476d3e04f4
Ports top unclean checkout: no
Port dir last git commit: 076c40f6357
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1500018
Job Id: 08
---Begin Environment---
SHELL=/bin/sh
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
OSVERSION=1500018
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
UNAME_m=i386
UNAME_p=i386
UNAME_r=15.0-CURRENT
LOCALBASE=/usr/local
UNAME_v=FreeBSD 15.0-CURRENT 1500018
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-i386-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
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OUTPUT_REDIRECTED_STDERR=4
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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--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix="/wrkdirs/usr/ports/biology/ngs-sdk/work/stage/usr/local" --build-prefix="/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build"
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work/.cache HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ngs-sdk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ngs-sdk/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work/.cache HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ngs-sdk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ngs-sdk/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=" -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_DAT
A="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/ngs" EXAMPLESDIR="share/examples/ngs" DATADIR="share/ngs" WWWDIR="www/ngs" ETCDIR="etc/ngs"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ngs DOCSDIR=/usr/local/share/doc/ngs EXAMPLESDIR=/usr/local/share/examples/ngs WWWDIR=/usr/local/www/ngs ETCDIR=/usr/local/etc/ngs
--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
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### ####
# 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 PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> ngs-sdk-3.0.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.2.pkg
[main-i386-default-job-08] Installing pkg-1.21.2...
[main-i386-default-job-08] Extracting pkg-1.21.2: .......... done
===> ngs-sdk-3.0.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ngs-sdk-3.0.1
===========================================================================
=======================<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 PD accepted by the user
===> Fetching all distfiles required by ngs-sdk-3.0.1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD accepted by the user
===> Fetching all distfiles required by ngs-sdk-3.0.1 for building
=> SHA256 Checksum OK for ncbi-ngs-3.0.1_GH0.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 PD accepted by the user
===> Fetching all distfiles required by ngs-sdk-3.0.1 for building
===> Extracting for ngs-sdk-3.0.1
=> SHA256 Checksum OK for ncbi-ngs-3.0.1_GH0.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 ngs-sdk-3.0.1
===> Applying FreeBSD patches for ngs-sdk-3.0.1 from /usr/ports/biology/ngs-sdk/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> ngs-sdk-3.0.1 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-i386-default-job-08] Installing gmake-4.4.1...
[main-i386-default-job-08] `-- Installing gettext-runtime-0.22.5...
[main-i386-default-job-08] | `-- Installing indexinfo-0.3.1...
[main-i386-default-job-08] | `-- Extracting indexinfo-0.3.1: .... done
[main-i386-default-job-08] `-- Extracting gettext-runtime-0.22.5: .......... done
[main-i386-default-job-08] Extracting gmake-4.4.1: .......... done
===> ngs-sdk-3.0.1 depends on package: gmake>=4.4.1 - found
===> Returning to build of ngs-sdk-3.0.1
===> ngs-sdk-3.0.1 depends on package: perl5>=5.36<5.37 - not found
===> Installing existing package /packages/All/perl5-5.36.3_1.pkg
[main-i386-default-job-08] Installing perl5-5.36.3_1...
[main-i386-default-job-08] Extracting perl5-5.36.3_1: .......... done
===> ngs-sdk-3.0.1 depends on package: perl5>=5.36<5.37 - found
===> Returning to build of ngs-sdk-3.0.1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for ngs-sdk-3.0.1
CONFIGURING ngs-sdk
Configuring NGS-SDK package
checking system type... FreeBSD
checking machine architecture... i386
checking for supported architecture... i386 (32 bits) is supported
checking for supported OS... FreeBSD (FreeBSD) is supported
checking for supported tool chain... clang tool chain is supported
checking for clang... FreeBSD clang version 18.1.4 (https://github.com/llvm/llvm-project.git llvmorg-18.1.4-0-ge6c3289804a6)
checking for clang++... yes
checking for Python 3... skipped
configure: creating 'Makefile.config.FreeBSD.i386'
configure: creating 'Makefile.config'
configure: creating 'reconfigure'
build type: release
build prefix: /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk
build output path: /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel
includedir: /wrkdirs/usr/ports/biology/ngs-sdk/work/stage/usr/local/include
bindir: /wrkdirs/usr/ports/biology/ngs-sdk/work/stage/usr/local/bin
libdir: /wrkdirs/usr/ports/biology/ngs-sdk/work/stage/usr/local/lib
sharedir: /wrkdirs/usr/ports/biology/ngs-sdk/work/stage/usr/local/share
CC = clang -c
CPP = clang++
configured with: "'--prefix=/wrkdirs/usr/ports/biology/ngs-sdk/work/stage/usr/local' '--build-prefix=/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build'"
CONFIGURING ngs-java
Configuring NGS-JAVA package
checking system type... unrecognized OS 'FreeBSD' at konfigure.perl line 353.
FreeBSD
checking machine architecture... i386
checking for supported architecture... i386 (32 bits) is supported
checking for supported OS...
CONFIGURING ngs-python
Configuring NGS-PYTHON package
checking system type... unrecognized OS 'FreeBSD' at konfigure.perl line 353.
FreeBSD
checking machine architecture... i386
checking for supported architecture... i386 (32 bits) is supported
checking for supported OS...
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for ngs-sdk-3.0.1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/dispatch'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/adapter'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/language'
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/language/c++'
mkdir -p /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/ilib
mkdir -p /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/dispatch
clang++ -c -mmacosx-version-min=10.10 -std=c++11 -o /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/dispatch/ReadCollectionItf.pic.o ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/dispatch -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/ngs/unix/i386 -MD -arch i386
mkdir -p /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/lib
mkdir -p /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/language/c++
mkdir -p /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/adapter
clang++ -c -mmacosx-version-min=10.10 -std=c++11 -o /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/language/c++/ReadCollection.pic.o ReadCollection.cpp -fPIC -DNDEBUG -O3 -I. -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/language/c++ -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/ngs/unix/i386 -MD -arch i386
clang++ -c -mmacosx-version-min=10.10 -std=c++11 -o /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/adapter/ReadCollectionItf.pic.o ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/adapter -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/ngs/unix/i386 -MD -arch i386
clang++: warning: argument unused during compilation: '-mmacosx-version-min=10.10' [-Wunused-command-line-argument]
clang++: error: unsupported option '-arch' for target 'i386-unknown-freebsd15.0'
clang++: warning: argument unused during compilation: '-mmacosx-version-min=10.10' [-Wunused-command-line-argument]
clang++: error: unsupported option '-arch' for target 'i386-unknown-freebsd15.0'
clang++: warning: argument unused during compilation: '-mmacosx-version-min=10.10' [-Wunused-command-line-argument]
clang++: error: unsupported option '-arch' for target 'i386-unknown-freebsd15.0'
gmake[2]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/./Makefile.config.FreeBSD.i386:109: /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/dispatch/ReadCollectionItf.pic.o] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/dispatch'
gmake[3]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/./Makefile.config.FreeBSD.i386:109: /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/language/c++/ReadCollection.pic.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/language/c++'
gmake[1]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/Makefile.rules:31: dispatch] Error 2
gmake[1]: *** Waiting for unfinished jobs....
clang++ -c -mmacosx-version-min=10.10 -std=c++11 -o /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/adapter/PileupItf.pic.o PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/adapter -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/ngs/unix/i386 -MD -arch i386
gmake[2]: *** [Makefile:46: c++] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/language'
gmake[1]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/Makefile.rules:31: language] Error 2
gmake[2]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/./Makefile.config.FreeBSD.i386:109: /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/adapter/ReadCollectionItf.pic.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
clang++: warning: argument unused during compilation: '-mmacosx-version-min=10.10' [-Wunused-command-line-argument]
clang++: error: unsupported option '-arch' for target 'i386-unknown-freebsd15.0'
gmake[2]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/./Makefile.config.FreeBSD.i386:109: /wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/build/ngs-sdk/FreeBSD/clang/i386/rel/obj/adapter/PileupItf.pic.o] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/adapter'
gmake[1]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk/Makefile.rules:31: adapter] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-3.0.1/ngs-sdk'
gmake: *** [Makefile:54: ngs-sdk] 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/ngs-sdk