[package - main-amd64-default][biology/gatk] Failed for gatk-4.6.2.0 in checksum

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From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 16 Sep 2025 17:17:58 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/beefy18/data/main-amd64-default/p118fb2971704_s4ab64e34911/logs/gatk-4.6.2.0.log
Build URL:      https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p118fb2971704_s4ab64e34911
Log:

=>> Building biology/gatk
build started at Tue Sep 16 11:51:58 UTC 2025
port directory: /usr/ports/biology/gatk
package name: gatk-4.6.2.0
building for: FreeBSD main-amd64-default-job-03 16.0-CURRENT FreeBSD 16.0-CURRENT 1600000 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 5132 Sep  6 01:01 /usr/ports/biology/gatk/Makefile
Ports top last git commit: 118fb297170
Ports top unclean checkout: no
Port dir last git commit: 803f55e390e
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1500061
Jail OSVERSION: 1600000
Job Id: 03




!!! Jail is newer than host. (Jail: 1600000, Host: 1500061) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/sh
OSVERSION=1600000
UNAME_v=FreeBSD 16.0-CURRENT 1600000
UNAME_r=16.0-CURRENT
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
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.3
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-amd64-default/03/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.3
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-4.6.2.0:
     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--
PYTHON="/usr/local/bin/python3.11" 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=" " 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="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
 JAVASHAREDIR="share/java"  JAVAJARDIR="share/java/classes" PYTHON_INCLUDEDIR=include/python3.11  PYTHON_LIBDIR=lib/python3.11  PYTHON_PLATFORM=freebsd16  PYTHON_SITELIBDIR=lib/python3.11/site-packages  PYTHON_SUFFIX=311  PYTHON_BASESUFFIX=311  PYTHON_TAG=.cpython-311  PYTHON_SOABI=.cpython-311  PYTHON_VER=3.11  PYTHON_BASEVER=3.11  PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=16.0 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=4.6.2.0 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" PYTHON_INCLUDEDIR=/usr/local/include/python3.11  PYTHON_LIBDIR=/usr/local/lib/python3.11  PYTHON_PLATFORM=freebsd16  PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages  PYTHON_SUFFIX=311  PYTHON_BASESUFFIX=311  PYTHON_TAG=.cpython-311  PYTHON_SOABI=.cpython-311  PYTHON_VER=3.11  PYTHON_BASEVER=3.11  PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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---
# 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
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
pipebuf                         (-y)  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-4.6.2.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-2.2.2.pkg
[main-amd64-default-job-03] Installing pkg-2.2.2...
[main-amd64-default-job-03] Extracting pkg-2.2.2: .......... done
===>   gatk-4.6.2.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gatk-4.6.2.0
===========================================================================
=======================<phase: fetch-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   gatk-4.6.2.0 depends on executable: git - not found
===>   Installing existing package /packages/All/git-2.51.0.pkg
[main-amd64-default-job-03] Installing git-2.51.0...
[main-amd64-default-job-03] `-- Installing curl-8.15.0...
[main-amd64-default-job-03] |   `-- Installing brotli-1.1.0,1...
[main-amd64-default-job-03] |   `-- Extracting brotli-1.1.0,1: .......... done
[main-amd64-default-job-03] |   `-- Installing libidn2-2.3.8...
[main-amd64-default-job-03] |   | `-- Installing indexinfo-0.3.1_1...
[main-amd64-default-job-03] |   | `-- Extracting indexinfo-0.3.1_1: .... done
[main-amd64-default-job-03] |   | `-- Installing libunistring-1.3...
[main-amd64-default-job-03] |   | `-- Extracting libunistring-1.3: .......... done
[main-amd64-default-job-03] |   `-- Extracting libidn2-2.3.8: .......... done
[main-amd64-default-job-03] |   `-- Installing libnghttp2-1.66.0...
[main-amd64-default-job-03] |   `-- Extracting libnghttp2-1.66.0: .......... done
[main-amd64-default-job-03] |   `-- Installing libpsl-0.21.5_2...
[main-amd64-default-job-03] |   `-- Extracting libpsl-0.21.5_2: .......... done
[main-amd64-default-job-03] |   `-- Installing libssh2-1.11.1,3...
[main-amd64-default-job-03] |   `-- Extracting libssh2-1.11.1,3: .......... done
[main-amd64-default-job-03] |   `-- Installing zstd-1.5.7...
[main-amd64-default-job-03] |   | `-- Installing liblz4-1.10.0,1...
[main-amd64-default-job-03] |   | `-- Extracting liblz4-1.10.0,1: .......... done
[main-amd64-default-job-03] |   `-- Extracting zstd-1.5.7: .......... done
[main-amd64-default-job-03] `-- Extracting curl-8.15.0: .......... done
[main-amd64-default-job-03] `-- Installing expat-2.7.1...
[main-amd64-default-job-03] `-- Extracting expat-2.7.1: .......... done
[main-amd64-default-job-03] `-- Installing gettext-runtime-0.23.1...
[main-amd64-default-job-03] `-- Extracting gettext-runtime-0.23.1: .......... done
[main-amd64-default-job-03] `-- Installing p5-Authen-SASL-2.1900...
[main-amd64-default-job-03] |   `-- Installing p5-Crypt-URandom-0.54...
[main-amd64-default-job-03] |   | `-- Installing perl5-5.42.0_1...
[main-amd64-default-job-03] |   | `-- Extracting perl5-5.42.0_1: .......... done
[main-amd64-default-job-03] |   `-- Extracting p5-Crypt-URandom-0.54: ........ done
[main-amd64-default-job-03] |   `-- Installing p5-Digest-HMAC-1.05...
[main-amd64-default-job-03] |   `-- Extracting p5-Digest-HMAC-1.05: .......... done
[main-amd64-default-job-03] `-- Extracting p5-Authen-SASL-2.1900: .......... done
[main-amd64-default-job-03] `-- Installing p5-Error-0.17030...
[main-amd64-default-job-03] `-- Extracting p5-Error-0.17030: ......... done
<snip>
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb (20 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt (17 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac (4.1 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa (8.3 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/ShiftBack.chain (125 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.bed (132 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.bed.idx (283 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed (138 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed.idx (305 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/control_region_shifted.chrM.interval_list (233 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mitochondria_references/non_control_region.chrM.interval_list (211 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/multiSampleSubsetted.bam (32 MB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/multiSampleSubsetted.bam.bai (36 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal.bam (4.4 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal.bam.bai (5.3 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam (3.5 MB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai (33 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam (4.8 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam.bai (33 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_3.bam (20 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_3.bam.bai (40 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_4.bam (29 MB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/normal_4.bam.bai (47 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor.bam (4.8 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor.bam.bai (5.3 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam (3.9 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai (32 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam (5.5 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam.bai (33 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_3.bam (21 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_3.bam.bai (40 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_4.bam (29 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/dream_synthetic_bams/tumor_4.bam.bai (46 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/highDPMTsnippet.bai (96 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/highDPMTsnippet.bam (1.5 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/alleles.vcf (924 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/alleles.vcf.idx (297 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/mito.bam (1.1 MB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/mito.bam.bai (96 B)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/mito_shifted_8000.dict (135 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/mito_shifted_8000.fasta (17 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/mutect/mito/mito_shifted_8000.fasta.fai (21 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20.allelicCounts.tsv (2.2 MB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-with-missing-sites.allelicCounts.tsv (2.2 MB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': 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)
Username for 'https://github.com': Password for 'https://github.com': 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)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.scorer.pkl (687 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.calibrationScores.hdf5 (2.7 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.scorer.pkl (304 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.trainingScores.hdf5 (2.9 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.scorer.pkl (676 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.calibrationScores.hdf5 (2.7 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.scorer.pkl (310 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.trainingScores.hdf5 (2.9 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.calibrationScores.hdf5 (5.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.scorer.pkl (745 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IF.snp.trainingScores.hdf5 (6.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.calibrationScores.hdf5 (5.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.scorer.pkl (702 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snp.posOnly.IFDifferentSeed.snp.trainingScores.hdf5 (6.0 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.calibrationScores.hdf5 (2.7 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.scorer.pkl (336 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.indel.trainingScores.hdf5 (2.9 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.snp.scorer.pkl (745 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/expected/extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IFDifferentSeed.indel.calibrationScores.hdf5 (2.7 KB)
Username for 'https://github.com': Password for 'https://github.com': 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 (321 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': 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)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/train/isolation-forest-hyperparameters-different-seed.json (23 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/readFilter/read_filter_output.sam (5.9 MB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf.idx (3.6 KB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/SVIntegrationTest_hg19.bam.bai (38 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_gaps.bed.gz (136 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_gaps.bed.gz.tbi (157 B)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/SVIntegrationTest_hg19_umap_s50.bed.gz (75 KB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf (224 KB)
Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf (240 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam (116 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf (222 KB)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/testFlowModeFlag_expected.bam (1.1 MB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/testFlowModeFlag_expected.bam.sbi (92 B)
Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/testFlowModeFlag_expected.txt (2.2 KB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/variantRecalling/150292-BC05.vcf.gz (311 KB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': Downloading src/test/resources/large/variantRecalling/chr5.bam1.rename.bam.bai (62 KB)
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Username for 'https://github.com': Password for 'https://github.com': Username for 'https://github.com': Password for 'https://github.com': ===> Fetching all distfiles required by gatk-4.6.2.0 for building
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.6.2.0 for building
=> SHA256 Checksum OK for gatk-4.6.2.0-deps.tar.gz.
=> SHA256 Checksum mismatch for broadinstitute-gatk-4.6.2.0_GH0.tar.gz.
===>  Giving up on fetching files:  broadinstitute-gatk-4.6.2.0_GH0.tar.gz 
Make sure the Makefile and distinfo file (/usr/ports/biology/gatk/distinfo)
are up to date.  If you are absolutely sure you want to override this
check, type "make NO_CHECKSUM=yes [other args]".
*** Error code 1

Stop.
make[1]: stopped making "checksum" in /usr/ports/biology/gatk
*** Error code 1

Stop.
make: stopped making "checksum" in /usr/ports/biology/gatk