[package - 141amd64-default][biology/sra-tools] Failed for sra-tools-3.0.6 in package
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Date: Thu, 14 Nov 2024 04:49:52 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: https://pkg-status.freebsd.org/beefy22/data/141amd64-default/dfee61567d9e/logs/sra-tools-3.0.6.log
Build URL: https://pkg-status.freebsd.org/beefy22/build.html?mastername=141amd64-default&build=dfee61567d9e
Log:
=>> Building biology/sra-tools
build started at Thu Nov 14 04:41:46 UTC 2024
port directory: /usr/ports/biology/sra-tools
package name: sra-tools-3.0.6
building for: FreeBSD 141amd64-default-job-33 14.1-RELEASE-p6 FreeBSD 14.1-RELEASE-p6 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2155 May 21 01:01 /usr/ports/biology/sra-tools/Makefile
Ports top last git commit: dfee61567d
Ports top unclean checkout: no
Port dir last git commit: a40e262549
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1401000
Job Id: 33
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PORT_FLAGS=
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MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for sra-tools-3.0.6:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/sra-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/sra-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/sra-tools/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--
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--End PLIST_SUB--
--SUB_LIST--
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PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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.
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# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
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UID=0
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max memory size (kbytes, -m) unlimited
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max user processes (-u) 89999
open files (-n) 8192
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--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD LGPL21+ accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> sra-tools-3.0.6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[141amd64-default-job-33] Installing pkg-1.21.3...
[141amd64-default-job-33] Extracting pkg-1.21.3: .......... done
===> sra-tools-3.0.6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of sra-tools-3.0.6
===========================================================================
=======================<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 LGPL21+ accepted by the user
===> Fetching all distfiles required by sra-tools-3.0.6 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD LGPL21+ accepted by the user
===> Fetching all distfiles required by sra-tools-3.0.6 for building
=> SHA256 Checksum OK for ncbi-sra-tools-3.0.6_GH0.tar.gz.
=> SHA256 Checksum OK for ncbi-ncbi-vdb-3.0.6_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 LGPL21+ accepted by the user
===> Fetching all distfiles required by sra-tools-3.0.6 for building
===> Extracting for sra-tools-3.0.6
=> SHA256 Checksum OK for ncbi-sra-tools-3.0.6_GH0.tar.gz.
=> SHA256 Checksum OK for ncbi-ncbi-vdb-3.0.6_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 sra-tools-3.0.6
===> Applying FreeBSD patches for sra-tools-3.0.6 from /usr/ports/biology/sra-tools/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> sra-tools-3.0.6 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.2.37.pkg
[141amd64-default-job-33] Installing bash-5.2.37...
[141amd64-default-job-33] `-- Installing gettext-runtime-0.22.5...
[141amd64-default-job-33] | `-- Installing indexinfo-0.3.1...
[141amd64-default-job-33] | `-- Extracting indexinfo-0.3.1: .... done
[141amd64-default-job-33] `-- Extracting gettext-runtime-0.22.5: .......... done
[141amd64-default-job-33] `-- Installing readline-8.2.13_2...
[141amd64-default-job-33] `-- Extracting readline-8.2.13_2: .......... done
[141amd64-default-job-33] Extracting bash-5.2.37: .......... done
===> sra-tools-3.0.6 depends on executable: bash - found
===> Returning to build of sra-tools-3.0.6
===> sra-tools-3.0.6 depends on file: /usr/local/openjdk17/bin/java - not found
===> Installing existing package /packages/All/openjdk17-17.0.13+11.1.pkg
[141amd64-default-job-33] Installing openjdk17-17.0.13+11.1...
[141amd64-default-job-33] `-- Installing alsa-lib-1.2.12...
[141amd64-default-job-33] `-- Extracting alsa-lib-1.2.12: .......... done
[141amd64-default-job-33] `-- Installing fontconfig-2.15.0_3,1...
[141amd64-default-job-33] | `-- Installing expat-2.6.3...
[141amd64-default-job-33] | `-- Extracting expat-2.6.3: .......... done
<snip>
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/itf/VTable.h
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/itf/ErrorMsg.hpp
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/itf/ReadGroupItf.hpp
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/itf/ReadItf.h
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReadCollection.hpp
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Package.hpp
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ErrorMsg.hpp
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/jar/ngs-java.jar
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/AlignTest.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/AlignSliceTest.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/FragTest.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/PileupTest.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/RefTest.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/ReadGroupTest.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/examples/DumpReferenceFASTA.java
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/Makefile
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/README.txt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java/expected.txt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/jar/ngs-examples.jar
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/package-search-index.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Pileup.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/PileupEvent.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Fragment.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/package-tree.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ReadGroup.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Package.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Statistics.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ReadIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/PileupEventIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ReferenceIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/FragmentIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ReadCollection.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/AlignmentIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ErrorMsg.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/package-summary.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/PileupIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Reference.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ReadGroupIterator.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/ReferenceSequence.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Read.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/ngs/Alignment.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/index.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/type-search-index.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/allpackages-index.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/serialized-form.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/element-list
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/index-all.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/help-doc.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/module-search-index.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/constant-values.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/member-search-index.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/allclasses-index.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/stylesheet.css
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/search.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/overview-summary.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm/ncbi
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/tag-search-index.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/legal
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/legal/jquery.md
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/legal/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/legal/ASSEMBLY_EXCEPTION
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/legal/jqueryUI.md
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/resources
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/resources/glass.png
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/resources/x.png
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/jquery-ui.overrides.css
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/overview-tree.html
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery-3.7.1.min.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery-ui.min.css
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery-ui.min.js
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/jar/ngs-doc.jar
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/jar/ngs-src.jar
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/AlignTest.py
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/AlignSliceTest.py
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/FragTest.py
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/PileupTest.py
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/RefTest.py
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/expected.txt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/Makefile
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python/README.txt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/prefetch
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/prefetch.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/prefetch-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/prefetch.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-config.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-config.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-config
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fastq-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fastq-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fastq-dump-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fastq-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sff-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sff-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sff-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/illumina-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/illumina-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/illumina-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/abi-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/abi-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/abi-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-pileup
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-pileup.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-pileup-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-pileup.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sam-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sam-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sam-dump-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sam-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fasterq-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fasterq-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fasterq-dump-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/fasterq-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-dump
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-dump.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-dump-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-dump.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-validate.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-validate.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-validate
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/check-corrupt.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/check-corrupt.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/check-corrupt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-decrypt.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-decrypt.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-decrypt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-encrypt.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-encrypt.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-encrypt
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath-orig.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-stat.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-stat.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-stat
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ngs-pileup.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ngs-pileup.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ngs-pileup
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/rcexplain.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/rcexplain.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/rcexplain
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/kdbmeta.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/kdbmeta.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/kdbmeta
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/align-info.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/align-info.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/align-info
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ref-variation.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ref-variation.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ref-variation
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/var-expand.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/var-expand.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/var-expand
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-search.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-search.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-search
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/test-sra.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/test-sra.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/test-sra
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/cache-mgr.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/cache-mgr.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/cache-mgr
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info.3.0.6
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info.3
-- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info
/usr/bin/strip /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/*.3.0.6
/bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-sratools
/bin/mkdir -p /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools
/bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-sratools/* /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools
/bin/rmdir /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-sratools
/bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-java /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/java
/bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples-python /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/python
====> Compressing man pages (compress-man)
===> Installing ldconfig configuration file
===========================================================================
=======================<phase: package >============================
===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-11-14T04:41:46+0000' 'PKG_NOTE_ports_top_git_hash=dfee61567d' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=a40e262549' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building packages for sra-tools-3.0.6
===> Building sra-tools-3.0.6
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery-3.6.1.min.js:No such file or directory
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/sra-tools