[package - 13stable-armv7-quarterly][biology/pooler] Failed for pooler-1.75 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Jan 30 16:53:52 UTC 2021
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 at cam.ac.uk
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: branches/2021Q1/biology/pooler/Makefile 555418 2020-11-15 18:50:17Z jwb $
Log URL: http://beefy12.nyi.freebsd.org/data/13stable-armv7-quarterly/562611/logs/pooler-1.75.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=13stable-armv7-quarterly&build=562611
Log:
=>> Building biology/pooler
build started at Sat Jan 30 16:53:23 UTC 2021
port directory: /usr/ports/biology/pooler
package name: pooler-1.75
building for: FreeBSD 13stable-armv7-quarterly-job-01 13.0-ALPHA2 FreeBSD 13.0-ALPHA2 1300136 arm
maintained by: ssb22 at cam.ac.uk
Makefile ident: $FreeBSD: branches/2021Q1/biology/pooler/Makefile 555418 2020-11-15 18:50:17Z jwb $
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1300134
Jail OSVERSION: 1300136
Job Id: 01
!!! Jail is newer than host. (Jail: 1300136, Host: 1300134) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---End OPTIONS List---
--MAINTAINER--
ssb22 at cam.ac.uk
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work 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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work 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 NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc9" CFLAGS="-O2 -pipe -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing " CPP="cpp9" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -L/u
sr/local/lib/gcc9 " LIBS="" CXX="g++9" CXXFLAGS="-O2 -pipe -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 " 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"
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--PLIST_SUB--
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--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pooler DOCSDIR=/usr/local/share/doc/pooler EXAMPLESDIR=/usr/local/share/examples/pooler WWWDIR=/usr/local/www/pooler ETCDIR=/usr/local/etc/pooler
--End SUB_LIST--
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# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
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#### /usr/ports/Mk/Scripts/ports_env.sh ####
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locked memory (kbytes, -l) unlimited
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=======================<phase: check-sanity >============================
===> License APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> pooler-1.75 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.1.txz
[13stable-armv7-quarterly-job-01] Installing pkg-1.16.1...
[13stable-armv7-quarterly-job-01] Extracting pkg-1.16.1: .......... done
===> pooler-1.75 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of pooler-1.75
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License APACHE20 accepted by the user
=> ssb22-PrimerPooler-v1.75_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.75?dummy=/ssb22-PrimerPooler-v1.75_GH0.tar.gz
fetch: https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.75?dummy=/ssb22-PrimerPooler-v1.75_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.75?dummy=/ssb22-PrimerPooler-v1.75_GH0.tar.gz: size of remote file is not known
ssb22-PrimerPooler-v1.75_GH0.tar.gz 123 kB 6186 kBps 00s
===> Fetching all distfiles required by pooler-1.75 for building
===========================================================================
=======================<phase: checksum >============================
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by pooler-1.75 for building
=> SHA256 Checksum OK for ssb22-PrimerPooler-v1.75_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by pooler-1.75 for building
===> Extracting for pooler-1.75
=> SHA256 Checksum OK for ssb22-PrimerPooler-v1.75_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for pooler-1.75
===========================================================================
=======================<phase: build-depends >============================
===> pooler-1.75 depends on executable: gcc9 - not found
===> Installing existing package /packages/All/gcc9-9.3.0_1.txz
[13stable-armv7-quarterly-job-01] Installing gcc9-9.3.0_1...
[13stable-armv7-quarterly-job-01] `-- Installing binutils-2.33.1_4,1...
[13stable-armv7-quarterly-job-01] | `-- Installing gettext-runtime-0.21...
[13stable-armv7-quarterly-job-01] | | `-- Installing indexinfo-0.3.1...
[13stable-armv7-quarterly-job-01] | | `-- Extracting indexinfo-0.3.1: .... done
[13stable-armv7-quarterly-job-01] | `-- Extracting gettext-runtime-0.21: .......... done
[13stable-armv7-quarterly-job-01] `-- Extracting binutils-2.33.1_4,1: .......... done
[13stable-armv7-quarterly-job-01] `-- Installing gmp-6.2.1...
[13stable-armv7-quarterly-job-01] `-- Extracting gmp-6.2.1: .......... done
[13stable-armv7-quarterly-job-01] `-- Installing mpc-1.1.0_2...
[13stable-armv7-quarterly-job-01] | `-- Installing mpfr-4.1.0...
[13stable-armv7-quarterly-job-01] | `-- Extracting mpfr-4.1.0: .......... done
[13stable-armv7-quarterly-job-01] `-- Extracting mpc-1.1.0_2: ......... done
[13stable-armv7-quarterly-job-01] Extracting gcc9-9.3.0_1: .......... done
=====
Message from gcc9-9.3.0_1:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc9
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> pooler-1.75 depends on executable: gcc9 - found
===> Returning to build of pooler-1.75
===> pooler-1.75 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for pooler-1.75
===========================================================================
=======================<phase: build >============================
===> Building for pooler-1.75
chmod +w 128.h 32.h 32-64.h 2>/dev/null || true
sed -e s/64/128/g < 64.h > 128.h
sed -e s/64/32/g < 64.h > 32.h
sed -e s/64/32/g -e s/128/64/g < 64-128.h > 32-64.h
chmod -w 128.h 32.h 32-64.h
/nxb-bin/usr/bin/cc -O2 -pipe -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing *.c -o pooler -lm
In file included from bit-common.c:63:
In file included from ./bit-choice.h:23:
In file included from ./triangle.h:44:
./openmp.h:19:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from genome.c:28:
./openmp.h:19:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from pool-split.c:25:
./openmp.h:19:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/pooler/work/PrimerPooler-1.75/pooler
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/pooler
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