[package - 130releng-armv7-default][biology/star] Failed for rna-STAR-2.7.9.a in build
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Date: Sat, 23 Jul 2022 21:29:44 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: http://ampere3.nyi.freebsd.org/data/130releng-armv7-default/a51002eeb3d0/logs/rna-STAR-2.7.9.a.log
Build URL: http://ampere3.nyi.freebsd.org/build.html?mastername=130releng-armv7-default&build=a51002eeb3d0
Log:
=>> Building biology/star
build started at Sat Jul 23 21:29:19 UTC 2022
port directory: /usr/ports/biology/star
package name: rna-STAR-2.7.9.a
building for: FreeBSD 130releng-armv7-default-job-09 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 1300139 arm
maintained by: jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> rna-STAR-2.7.9.a depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.3.pkg
[130releng-armv7-default-job-09] Installing pkg-1.18.3...
[130releng-armv7-default-job-09] Extracting pkg-1.18.3: .......... done
===> rna-STAR-2.7.9.a depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rna-STAR-2.7.9.a
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.9.a for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.9.a for building
=> SHA256 Checksum OK for alexdobin-STAR-2.7.9a_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.9.a for building
===> Extracting for rna-STAR-2.7.9.a
=> SHA256 Checksum OK for alexdobin-STAR-2.7.9a_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for rna-STAR-2.7.9.a
===> Applying FreeBSD patches for rna-STAR-2.7.9.a from /usr/ports/biology/star/files
/bin/rm -f -rf /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/htslib
/usr/bin/sed -i.bak -e 's|"htslib/htslib/sam.h"|<htslib/sam.h>|g' -e 's|"htslib/htslib/kstring.h"|<htslib/kstring.h>|g' -e 's|"htslib/htslib/bgzf.h"|<htslib/bgzf.h>|g' /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/BAMfunctions.cpp /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/IncludeDefine.h /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/STAR.cpp /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/bamRemoveDuplicates.cpp /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/bam_cat.c /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/bam_cat.h /wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source/signalFromBAM.h
===========================================================================
=======================<phase: build-depends >============================
===> rna-STAR-2.7.9.a depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[130releng-armv7-default-job-09] Installing gmake-4.3_2...
[130releng-armv7-default-job-09] `-- Installing gettext-runtime-0.21...
[130releng-armv7-default-job-09] | `-- Installing indexinfo-0.3.1...
[130releng-armv7-default-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv7-default-job-09] `-- Extracting gettext-runtime-0.21: .......... done
[130releng-armv7-default-job-09] Extracting gmake-4.3_2: .......... done
===> rna-STAR-2.7.9.a depends on package: gmake>=4.3 - found
===> Returning to build of rna-STAR-2.7.9.a
===========================================================================
=======================<phase: lib-depends >============================
===> rna-STAR-2.7.9.a depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.15.pkg
[130releng-armv7-default-job-09] Installing htslib-1.15...
[130releng-armv7-default-job-09] `-- Installing curl-7.84.0...
[130releng-armv7-default-job-09] | `-- Installing ca_root_nss-3.80...
<snip>
In file included from Transcriptome_geneFullAlignOverlap.cpp:1:
In file included from ./Transcriptome.h:6:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from Transcriptome_quantAlign.cpp:1:
In file included from ./Transcriptome.h:6:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from Variation.cpp:1:
In file included from ./Variation.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from bamRemoveDuplicates.cpp:2:
In file included from ./bamRemoveDuplicates.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from bamSortByCoordinate.cpp:1:
In file included from ./bamSortByCoordinate.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from binarySearch2.cpp:1:
In file included from ./binarySearch2.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from blocksOverlap.cpp:1:
In file included from ./blocksOverlap.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from extendAlign.cpp:1:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from genomeParametersWrite.cpp:1:
In file included from ./genomeParametersWrite.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from genomeSAindex.cpp:1:
In file included from ./genomeSAindex.h:3:
In file included from ./PackedArray.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from genomeScanFastaFiles.cpp:1:
In file included from ./genomeScanFastaFiles.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from insertSeqSA.cpp:5:
In file included from ./insertSeqSA.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from mapThreadsSpawn.cpp:1:
In file included from ./mapThreadsSpawn.h:3:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from outputSJ.cpp:1:
In file included from ./ReadAlignChunk.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from readLoad.cpp:1:
In file included from ./readLoad.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from samHeaders.cpp:1:
In file included from ./samHeaders.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from serviceFuns.cpp:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from signalFromBAM.cpp:1:
In file included from ./signalFromBAM.h:6:
In file included from ./Stats.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from sjAlignSplit.cpp:1:
In file included from ./sjAlignSplit.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from sjdbBuildIndex.cpp:1:
In file included from ./sjdbBuildIndex.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from sjdbInsertJunctions.cpp:1:
In file included from ./sjdbInsertJunctions.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from sjdbLoadFromFiles.cpp:1:
In file included from ./sjdbLoadFromFiles.h:5:
In file included from ./SjdbClass.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from sjdbLoadFromStream.cpp:1:
In file included from ./sjdbLoadFromStream.h:5:
In file included from ./SjdbClass.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from sjdbPrepare.cpp:1:
In file included from ./sjdbPrepare.h:4:
In file included from ./SjdbClass.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from soloInputFeatureUMI.cpp:1:
In file included from ./soloInputFeatureUMI.h:7:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from stitchAlignToTranscript.cpp:1:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from stitchGapIndel.cpp:1:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from stitchWindowAligns.cpp:1:
In file included from ./stitchWindowAligns.h:1:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from streamFuns.cpp:1:
In file included from ./streamFuns.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
In file included from twoPassRunPass1.cpp:1:
In file included from ./twoPassRunPass1.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
gmake[1]: *** [Makefile:130: Depend.list] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.9a/source'
===> 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/star