[package - 124i386-quarterly][biology/pooler] Failed for pooler-1.86 in build
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Date: Tue, 22 Aug 2023 16:34:13 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: ssb22@cam.ac.uk
Log URL: https://pkg-status.freebsd.org/beefy4/data/124i386-quarterly/f3d8c4bf5c40/logs/pooler-1.86.log
Build URL: https://pkg-status.freebsd.org/beefy4/build.html?mastername=124i386-quarterly&build=f3d8c4bf5c40
Log:
=>> Building biology/pooler
build started at Tue Aug 22 16:34:07 UTC 2023
port directory: /usr/ports/biology/pooler
package name: pooler-1.86
building for: FreeBSD 124i386-quarterly-job-06 12.4-RELEASE-p4 FreeBSD 12.4-RELEASE-p4 i386
maintained by: ssb22@cam.ac.uk
Makefile ident:
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Host OSVERSION: 1400089
Jail OSVERSION: 1204000
Job Id: 06
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ssb22@cam.ac.uk
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XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pooler/work/.cache HOME=/wrkdirs/usr/ports/biology/pooler/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pooler/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pooler/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pooler/work/.cache HOME=/wrkdirs/usr/ports/biology/pooler/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pooler/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pooler/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 -fopenmp -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fopenmp -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" B
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--SUB_LIST--
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=======================<phase: check-sanity >============================
===> License APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> pooler-1.86 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.2.pkg
[124i386-quarterly-job-06] Installing pkg-1.19.2...
[124i386-quarterly-job-06] Extracting pkg-1.19.2: .......... done
===> pooler-1.86 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of pooler-1.86
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by pooler-1.86 for building
===========================================================================
=======================<phase: checksum >============================
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by pooler-1.86 for building
=> SHA256 Checksum OK for ssb22-PrimerPooler-v1.86_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by pooler-1.86 for building
===> Extracting for pooler-1.86
=> SHA256 Checksum OK for ssb22-PrimerPooler-v1.86_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for pooler-1.86
===========================================================================
=======================<phase: build-depends >============================
===> pooler-1.86 depends on executable: update-desktop-database - not found
===> Installing existing package /packages/All/desktop-file-utils-0.26_1.pkg
[124i386-quarterly-job-06] Installing desktop-file-utils-0.26_1...
[124i386-quarterly-job-06] `-- Installing gettext-runtime-0.21.1...
[124i386-quarterly-job-06] | `-- Installing indexinfo-0.3.1...
[124i386-quarterly-job-06] | `-- Extracting indexinfo-0.3.1: .... done
[124i386-quarterly-job-06] `-- Extracting gettext-runtime-0.21.1: .......... done
[124i386-quarterly-job-06] `-- Installing glib-2.76.4_1,2...
[124i386-quarterly-job-06] | `-- Installing libffi-3.4.4...
[124i386-quarterly-job-06] | `-- Extracting libffi-3.4.4: .......... done
[124i386-quarterly-job-06] | `-- Installing libiconv-1.17...
[124i386-quarterly-job-06] | `-- Extracting libiconv-1.17: .......... done
[124i386-quarterly-job-06] | `-- Installing libxml2-2.10.4...
[124i386-quarterly-job-06] | | `-- Installing readline-8.2.1...
[124i386-quarterly-job-06] | | `-- Extracting readline-8.2.1: .......... done
[124i386-quarterly-job-06] | `-- Extracting libxml2-2.10.4: .......... done
[124i386-quarterly-job-06] | `-- Installing pcre2-10.42...
[124i386-quarterly-job-06] | `-- Extracting pcre2-10.42: .......... done
[124i386-quarterly-job-06] | `-- Installing python39-3.9.17...
[124i386-quarterly-job-06] | | `-- Installing mpdecimal-2.5.1...
[124i386-quarterly-job-06] | | `-- Extracting mpdecimal-2.5.1: .......... done
[124i386-quarterly-job-06] | `-- Extracting python39-3.9.17: .......... done
[124i386-quarterly-job-06] `-- Extracting glib-2.76.4_1,2: .......... done
[124i386-quarterly-job-06] Extracting desktop-file-utils-0.26_1: .......... done
Building cache database of MIME types
Building cache database of MIME types
Generating GIO modules cache
Compiling glib schemas
No schema files found: doing nothing.
=====
Message from python39-3.9.17:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> pooler-1.86 depends on executable: update-desktop-database - found
===> Returning to build of pooler-1.86
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for pooler-1.86
===========================================================================
=======================<phase: build >============================
===> Building for pooler-1.86
--- 32.h ---
--- 128.h ---
--- 32.h ---
chmod +w 32.h 2>/dev/null || true
--- 128.h ---
chmod +w 128.h 2>/dev/null || true
--- 32.h ---
sed -e s/64/32/g < 64.h > 32.h
--- 128.h ---
sed -e s/64/128/g < 64.h > 128.h
--- 32.h ---
chmod -w 32.h
--- 32-64.h ---
chmod +w 32-64.h 2>/dev/null || true
--- 128.h ---
chmod -w 128.h
--- 32-64.h ---
sed -e s/64/32/g -e s/128/64/g < 64-128.h > 32-64.h
chmod -w 32-64.h
--- pooler ---
$(sh -c 'case "$OSTYPE" in darwin*) [ "cc" = cc ] && gcc --version 2>/dev/null >/dev/null ;; *) false ;; esac' && echo gcc || echo "cc") -O2 -pipe -fopenmp -fstack-protector-strong -fno-strict-aliasing $(echo 'int main(){}' > _test.c; if $(sh -c 'case "$OSTYPE" in darwin*) [ "cc" = cc ] && gcc --version 2>/dev/null >/dev/null ;; *) false ;; esac' && echo gcc || echo "cc") -fopenmp _test.c -o /dev/null 2>/dev/null; then echo -fopenmp; fi; rm _test.c) *.c -o pooler -lm
Bus error (core dumped)
Bus error (core dumped)
*** [pooler] Error code 138
make[1]: stopped in /wrkdirs/usr/ports/biology/pooler/work/PrimerPooler-1.86/pooler
1 error
make[1]: stopped in /wrkdirs/usr/ports/biology/pooler/work/PrimerPooler-1.86/pooler
===> 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/pooler