[package - 130releng-armv7-quarterly][biology/star] Failed for rna-STAR-2.7.3.a_1 in build
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Date: Thu, 16 Sep 2021 09:10:35 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://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/5744604f85d8/logs/rna-STAR-2.7.3.a_1.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=5744604f85d8
Log:
=>> Building biology/star
build started at Thu Sep 16 09:10:07 UTC 2021
port directory: /usr/ports/biology/star
package name: rna-STAR-2.7.3.a_1
building for: FreeBSD 130releng-armv7-quarterly-job-13 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 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-2.7.3.a_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[130releng-armv7-quarterly-job-13] Installing pkg-1.16.3...
[130releng-armv7-quarterly-job-13] Extracting pkg-1.16.3: .......... done
===> rna-STAR-2.7.3.a_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rna-STAR-2.7.3.a_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.3.a_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.3.a_1 for building
=> SHA256 Checksum OK for alexdobin-STAR-2.7.3a_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.3.a_1 for building
===> Extracting for rna-STAR-2.7.3.a_1
=> SHA256 Checksum OK for alexdobin-STAR-2.7.3a_GH0.tar.gz.
===========================================================================
<snip>
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_geneCountsAddAlign.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_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 alignSmithWaterman.cpp:1:
./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 loadGTF.cpp:1:
In file included from ./loadGTF.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 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 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:
./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 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.
Makefile:104: Depend.list: No such file or directory
gmake[1]: *** [Makefile:103: Depend.list] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/star