[package - main-armv7-default][biology/bio-mocha] Failed for bio-mocha-1.13_1 in stage
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Date: Fri, 07 Jan 2022 08:26:19 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/main-armv7-default/pe2d17ded99d5_s5169832c96/logs/bio-mocha-1.13_1.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=pe2d17ded99d5_s5169832c96
Log:
=>> Building biology/bio-mocha
build started at Fri Jan 7 08:23:58 UTC 2022
port directory: /usr/ports/biology/bio-mocha
package name: bio-mocha-1.13_1
building for: FreeBSD main-armv7-default-job-13 14.0-CURRENT FreeBSD 14.0-CURRENT 1400046 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
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Host OSVERSION: 1400003
Jail OSVERSION: 1400046
Job Id: 13
!!! Jail is newer than host. (Jail: 1400046, Host: 1400003) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bio-mocha-1.13_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[main-armv7-default-job-13] Installing pkg-1.17.5...
[main-armv7-default-job-13] Extracting pkg-1.17.5: .......... done
===> bio-mocha-1.13_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bio-mocha-1.13_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by bio-mocha-1.13_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by bio-mocha-1.13_1 for building
<snip>
=====
Message from ca_root_nss-3.71:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
===> bio-mocha-1.13_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of bio-mocha-1.13_1
===========================================================================
=======================<phase: configure >============================
===> Configuring for bio-mocha-1.13_1
configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals
./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:94: the top level
configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals
./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:94: the top level
configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals
./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:94: the top level
configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals
./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:94: the top level
configure: loading site script /usr/ports/Templates/config.site
checking for gcc... /nxb-bin/usr/bin/cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
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checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /nxb-bin/usr/bin/cc accepts -g... yes
checking for /nxb-bin/usr/bin/cc option to accept ISO C89... none needed
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking location of HTSlib source tree... none found
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking shared library type... plain .so
checking for library containing dlopen... none required
checking if the compiler accepts -rdynamic... yes
checking for zlib.h... (cached) yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
===========================================================================
=======================<phase: build >============================
===> Building for bio-mocha-1.13_1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14'
echo '#define BCFTOOLS_VERSION "1.14"' > version.h
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o main.o main.c
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/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfisec.o vcfisec.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfmerge.o vcfmerge.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfquery.o vcfquery.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcffilter.o vcffilter.c
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/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfview.o vcfview.c
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/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfroh.o vcfroh.c
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/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsort.o vcfsort.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cols.o cols.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o extsort.o extsort.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o dist.o dist.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o abuf.o abuf.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ccall.o ccall.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o em.o em.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o prob1.o prob1.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kmin.o kmin.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o str_finder.o str_finder.c
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c
/nxb-bin/usr/bin/cc -rdynamic -fstack-protector-strong -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -L/usr/local/lib -lpthread
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-rbuf.o test/test-rbuf.c
/nxb-bin/usr/bin/cc -fstack-protector-strong -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib
/nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-regidx.o test/test-regidx.c
/nxb-bin/usr/bin/cc -fstack-protector-strong -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/GTisec.so version.c plugins/GTisec.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/GTsubset.so version.c plugins/GTsubset.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/allele-length.so version.c plugins/allele-length.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/contrast.so version.c plugins/contrast.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/counts.so version.c plugins/counts.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/dosage.so version.c plugins/dosage.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/extendFMT.so version.c plugins/extendFMT.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-tags.so version.c plugins/fill-tags.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fixref.so version.c plugins/fixref.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/frameshifts.so version.c plugins/frameshifts.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/gvcfz.so version.c plugins/gvcfz.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/impute-info.so version.c plugins/impute-info.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/indel-stats.so version.c plugins/indel-stats.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mendelian.so version.c plugins/mendelian.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/missing2ref.so version.c plugins/missing2ref.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mocha.so version.c plugins/mocha.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mochatools.so version.c plugins/mochatools.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/parental-origin.so version.c plugins/parental-origin.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/prune.so version.c plugins/prune.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/scatter.so version.c plugins/scatter.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/score.so version.c plugins/score.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/setGT.so version.c plugins/setGT.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/split-vep.so version.c plugins/split-vep.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/split.so version.c plugins/split.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/tag2tag.so version.c plugins/tag2tag.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-phase.so version.c plugins/trio-phase.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-stats.so version.c plugins/trio-stats.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -L/usr/local/lib
/nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -L/usr/local/lib
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14'
===========================================================================
=======================<phase: run-depends >============================
===> bio-mocha-1.13_1 depends on package: bcftools>=1.13 - not found
===> Installing existing package /packages/All/bcftools-1.14.pkg
[main-armv7-default-job-13] Installing bcftools-1.14...
[main-armv7-default-job-13] `-- Installing gsl-2.7...
[main-armv7-default-job-13] `-- Extracting gsl-2.7: .......... done
[main-armv7-default-job-13] Extracting bcftools-1.14: .......... done
===> bio-mocha-1.13_1 depends on package: bcftools>=1.13 - found
===> Returning to build of bio-mocha-1.13_1
===========================================================================
=======================<phase: stage >============================
===> Staging for bio-mocha-1.13_1
===> Generating temporary packing list
/bin/mkdir -p /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools
install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/extendFMT.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools
install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/mocha.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools
install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/mochatools.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools
install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/score.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools
install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/trio-phase.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools
(cd /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/MoCha && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/share/bio-mocha)
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bio-mocha