[package - 133amd64-default][biology/gatk] Failed for gatk-4.6.0.0 in checksum
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Date: Sun, 14 Jul 2024 12:32:08 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy16/data/133amd64-default/a71eaeb3e54e/logs/gatk-4.6.0.0.log
Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=133amd64-default&build=a71eaeb3e54e
Log:
=>> Building biology/gatk
build started at Sun Jul 14 12:09:35 UTC 2024
port directory: /usr/ports/biology/gatk
package name: gatk-4.6.0.0
building for: FreeBSD 133amd64-default-job-09 13.3-RELEASE-p4 FreeBSD 13.3-RELEASE-p4 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 3943 Jul 13 01:02 /usr/ports/biology/gatk/Makefile
Ports top last git commit: a71eaeb3e54
Ports top unclean checkout: no
Port dir last git commit: 290983fbb4b
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500019
Jail OSVERSION: 1303001
Job Id: 09
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1303001
UNAME_v=FreeBSD 13.3-RELEASE-p4
UNAME_r=13.3-RELEASE-p4
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
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POUDRIERE_VERSION=3.4.1-30-g79e3edcd
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OUTPUT_REDIRECTED_STDERR=4
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OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=133amd64-default
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OLDPWD=/usr/local/poudriere/data/.m/133amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for gatk-4.6.0.0:
WITH_LARGE_FILES=on: Download large LFS files needed for build and tests
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/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 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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="i
nstall -m 444"
--End MAKE_ENV--
--PLIST_SUB--
JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=13.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gatk" EXAMPLESDIR="share/examples/gatk" DATADIR="share/gatk" WWWDIR="www/gatk" ETCDIR="etc/gatk"
--End PLIST_SUB--
--SUB_LIST--
PORTVERSION=4.6.0.0 JAVA=/usr/local/openjdk17/bin/java JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gatk DOCSDIR=/usr/local/share/doc/gatk EXAMPLESDIR=/usr/local/share/examples/gatk WWWDIR=/usr/local/www/gatk ETCDIR=/usr/local/etc/gatk
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
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.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 2048
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gatk-4.6.0.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[133amd64-default-job-09] Installing pkg-1.21.3...
[133amd64-default-job-09] Extracting pkg-1.21.3: .......... done
===> gatk-4.6.0.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gatk-4.6.0.0
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gatk-4.6.0.0 depends on executable: git - not found
===> Installing existing package /packages/All/git-2.45.2_1.pkg
[133amd64-default-job-09] Installing git-2.45.2_1...
[133amd64-default-job-09] `-- Installing curl-8.8.0...
[133amd64-default-job-09] | `-- Installing libnghttp2-1.62.1...
[133amd64-default-job-09] | `-- Extracting libnghttp2-1.62.1: .......... done
[133amd64-default-job-09] | `-- Installing libpsl-0.21.5_1...
[133amd64-default-job-09] | | `-- Installing libidn2-2.3.7...
[133amd64-default-job-09] | | `-- Installing indexinfo-0.3.1...
[133amd64-default-job-09] | | `-- Extracting indexinfo-0.3.1: .... done
[133amd64-default-job-09] | | `-- Installing libunistring-1.2...
[133amd64-default-job-09] | | `-- Extracting libunistring-1.2: .......... done
[133amd64-default-job-09] | | `-- Extracting libidn2-2.3.7: .......... done
[133amd64-default-job-09] | `-- Extracting libpsl-0.21.5_1: .......... done
[133amd64-default-job-09] | `-- Installing libssh2-1.11.0_1,3...
[133amd64-default-job-09] | `-- Extracting libssh2-1.11.0_1,3: .......... done
[133amd64-default-job-09] `-- Extracting curl-8.8.0: .......... done
[133amd64-default-job-09] `-- Installing expat-2.6.2...
[133amd64-default-job-09] `-- Extracting expat-2.6.2: .......... done
[133amd64-default-job-09] `-- Installing gettext-runtime-0.22.5...
[133amd64-default-job-09] `-- Extracting gettext-runtime-0.22.5: .......... done
[133amd64-default-job-09] `-- Installing p5-Authen-SASL-2.17...
[133amd64-default-job-09] | `-- Installing p5-Digest-HMAC-1.04...
[133amd64-default-job-09] | | `-- Installing perl5-5.36.3_1...
[133amd64-default-job-09] | | `-- Extracting perl5-5.36.3_1: .......... done
[133amd64-default-job-09] | `-- Extracting p5-Digest-HMAC-1.04: .......... done
[133amd64-default-job-09] | `-- Installing p5-GSSAPI-0.28_2...
[133amd64-default-job-09] | `-- Extracting p5-GSSAPI-0.28_2: .......... done
[133amd64-default-job-09] `-- Extracting p5-Authen-SASL-2.17: .......... done
[133amd64-default-job-09] `-- Installing p5-CGI-4.66...
[133amd64-default-job-09] | `-- Installing p5-HTML-Parser-3.82...
[133amd64-default-job-09] | | `-- Installing p5-HTML-Tagset-3.24...
[133amd64-default-job-09] | | `-- Extracting p5-HTML-Tagset-3.24: ....... done
[133amd64-default-job-09] | | `-- Installing p5-HTTP-Message-6.46...
[133amd64-default-job-09] | | `-- Installing p5-Clone-0.46...
[133amd64-default-job-09] | | `-- Extracting p5-Clone-0.46: ......... done
[133amd64-default-job-09] | | `-- Installing p5-Encode-Locale-1.05...
[133amd64-default-job-09] | | `-- Extracting p5-Encode-Locale-1.05: ....... done
[133amd64-default-job-09] | | `-- Installing p5-HTTP-Date-6.06...
[133amd64-default-job-09] | | | `-- Installing p5-TimeDate-2.33,1...
[133amd64-default-job-09] | | | `-- Extracting p5-TimeDate-2.33,1: .......... done
[133amd64-default-job-09] | | `-- Extracting p5-HTTP-Date-6.06: ....... done
[133amd64-default-job-09] | | `-- Installing p5-IO-HTML-1.004...
[133amd64-default-job-09] | | `-- Extracting p5-IO-HTML-1.004: ....... done
[133amd64-default-job-09] | | `-- Installing p5-LWP-MediaTypes-6.04...
[133amd64-default-job-09] | | `-- Extracting p5-LWP-MediaTypes-6.04: ........ done
[133amd64-default-job-09] | | `-- Installing p5-URI-5.28...
[133amd64-default-job-09] | | `-- Extracting p5-URI-5.28: .......... done
[133amd64-default-job-09] | | `-- Extracting p5-HTTP-Message-6.46: .......... done
[133amd64-default-job-09] | `-- Extracting p5-HTML-Parser-3.82: .......... done
[133amd64-default-job-09] `-- Extracting p5-CGI-4.66: .......... done
[133amd64-default-job-09] `-- Installing p5-Error-0.17029...
[133amd64-default-job-09] `-- Extracting p5-Error-0.17029: ......... done
[133amd64-default-job-09] `-- Installing p5-IO-Socket-SSL-2.087...
[133amd64-default-job-09] | `-- Installing p5-IO-Socket-IP-0.42...
<snip>
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-with-missing-sites.allelicCounts.tsv (2.2 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv (2.2 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-with-missing-sites.allelicCounts.tsv (2.2 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv (191 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-with-missing-intervals.denoisedCR.tsv (190 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv (2.2 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv (191 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-gencode-transcripts.dragen.tab.gz (1.7 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-human_g1k_v37.20.21.dragen.tab.gz (1.6 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-human_g1k_v37_20.21.dragen.zip (1.5 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/compose-str-table-file-human_v38.20.21.dragen.tab.gz (1.7 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/dragstr/dragen-param-estimator-expected-output.txt (2.7 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.pos.annot.hdf5 (30 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.pos.vcf (171 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.indel.pos.vcf.idx (114 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.pos.annot.hdf5 (147 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.pos.vcf (193 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.posUn.unlabeled.annot.hdf5 (32 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snp.posUn.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.AS.snpIndel.pos.annot.hdf5 (174 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.pos.annot.hdf5 (31 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.pos.vcf (171 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.indel.posUn.unlabeled.annot.hdf5 (33 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.pos.annot.hdf5 (181 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.pos.vcf.idx (114 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/extract.nonAS.snpIndel.posUn.annot.hdf5 (181 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf (2.0 MB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf.idx (5.4 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz (128 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz.tbi (2.1 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz (132 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz.tbi (2.5 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz (46 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz.tbi (2.0 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz (50 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz.tbi (2.5 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/score/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp.annot.hdf5 (737 KB)
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Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.scorer.pkl (249 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.trainingScores.hdf5 (2.9 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB)
Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB)
===> Fetching all distfiles required by gatk-4.6.0.0 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.6.0.0 for building
/usr/ports/Mk/Scripts/checksum.sh: cannot open gatk-4.6.0.0-deps.tar.gz: No such file or directory
*** Error code 2
Stop.
make: stopped in /usr/ports/biology/gatk