[package - 93amd64-default][biology/seqan-apps] Failed for seqan-apps-2.1.1 in stage

Wed Aug 31 01:36:14 UTC 2016

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:     h2+fbsdports at fsfe.org
Last committer: junovitch at FreeBSD.org
Ident:          $FreeBSD: head/biology/seqan-apps/Makefile 414897 2016-05-10 00:52:04Z junovitch $
Log URL:        http://beefy2.nyi.freebsd.org/data/93amd64-default/421100/logs/seqan-apps-2.1.1.log
Build URL:      http://beefy2.nyi.freebsd.org/build.html?mastername=93amd64-default&build=421100
Log:

====>> Building biology/seqan-apps
build started at Wed Aug 31 00:49:46 UTC 2016
port directory: /usr/ports/biology/seqan-apps
building for: FreeBSD 93amd64-default-job-13 9.3-RELEASE-p45 FreeBSD 9.3-RELEASE-p45 amd64
maintained by: h2+fbsdports at fsfe.org
Makefile ident:      $FreeBSD: head/biology/seqan-apps/Makefile 414897 2016-05-10 00:52:04Z junovitch $
Poudriere version: 3.1.14
Host OSVERSION: 1200005
Jail OSVERSION: 903000

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UNAME_v=FreeBSD 9.3-RELEASE-p45
UNAME_r=9.3-RELEASE-p45
BLOCKSIZE=K
MAIL=/var/mail/root
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OPSYS=FreeBSD
ARCH=amd64
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/93amd64-default/ref
UID=0
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
_JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=seqan-apps-2.1.1
OSREL=9.3
_OSRELEASE=9.3-RELEASE-p45
PYTHONBASE=/usr/local
OLDPWD=/
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OSVERSION=903000
---End Environment---

---Begin OPTIONS List---
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work  HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work  HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="gcc49" CFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing"  CPP="cpp49" CPPFLAGS=""  LDFLAGS=" -fstack-protector -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49" LIBS=""  CXX="g++49" CXXFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/loc
 al/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49"  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 444"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
CMAKE_BUILD_TYPE="release"
RM_I386=""
OSREL=9.3
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/seqan-apps"
EXAMPLESDIR="share/examples/seqan-apps"
DATADIR="share/seqan-apps"
WWWDIR="www/seqan-apps"
ETCDIR="etc/seqan-apps"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/seqan-apps
DOCSDIR=/usr/local/share/doc/seqan-apps
EXAMPLESDIR=/usr/local/share/examples/seqan-apps
WWWDIR=/usr/local/www/seqan-apps
ETCDIR=/usr/local/etc/seqan-apps
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/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
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.8.7_1.txz
[93amd64-default-job-13] Installing pkg-1.8.7_1...
[93amd64-default-job-13] Extracting pkg-1.8.7_1: .......... done
===>   seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of seqan-apps-2.1.1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.1.1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.1.1 for building
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.1.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.1.1 for building
===>  Extracting for seqan-apps-2.1.1
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.1.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for seqan-apps-2.1.1
# missing C99 functions in FreeBSD's math.h, use C++ instead
# the other way around (use math.h instead of cmath)
===========================================================================
=======================<phase: build-depends  >============================
===>   seqan-apps-2.1.1 depends on package: boost-libs>0 - not found
===>   Installing existing package /packages/All/boost-libs-1.55.0_12.txz
[93amd64-default-job-13] Installing boost-libs-1.55.0_12...
[93amd64-default-job-13] `-- Installing libiconv-1.14_9...
[93amd64-default-job-13] `-- Extracting libiconv-1.14_9: .......... done
[93amd64-default-job-13] `-- Installing icu-55.1,1...
[93amd64-default-job-13] `-- Extracting icu-55.1,1: .......... done
[93amd64-default-job-13] Extracting boost-libs-1.55.0_12: .......... done
Message from boost-libs-1.55.0_12:
You have built the Boost library with thread support.

Don't forget to add -pthread to your linker options when
linking your code.
===>   seqan-apps-2.1.1 depends on package: boost-libs>0 - found
===>   Returning to build of seqan-apps-2.1.1
===>   seqan-apps-2.1.1 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.6.1.txz
[93amd64-default-job-13] Installing cmake-3.6.1...
[93amd64-default-job-13] `-- Installing expat-2.2.0...
[93amd64-default-job-13] `-- Extracting expat-2.2.0: .......... done
[93amd64-default-job-13] `-- Installing cmake-modules-3.6.1...
[93amd64-default-job-13] `-- Extracting cmake-modules-3.6.1: .......... done
[93amd64-default-job-13] `-- Installing curl-7.50.1...
[93amd64-default-job-13] |   `-- Installing ca_root_nss-3.26...
[93amd64-default-job-13] |   `-- Extracting ca_root_nss-3.26: ....... done
[93amd64-default-job-13] `-- Extracting curl-7.50.1: .......... done
[93amd64-default-job-13] `-- Installing libarchive-3.2.1,1...
[93amd64-default-job-13] |   `-- Installing liblz4-131...
[93amd64-default-job-13] |   `-- Extracting liblz4-131: .......... done
[93amd64-default-job-13] |   `-- Installing lzo2-2.09...
[93amd64-default-job-13] |   `-- Extracting lzo2-2.09: .......... done
[93amd64-default-job-13] `-- Extracting libarchive-3.2.1,1: .......... done
[93amd64-default-job-13] `-- Installing jsoncpp-1.7.3...
[93amd64-default-job-13] `-- Extracting jsoncpp-1.7.3: .......... done
[93amd64-default-job-13] `-- Installing libexecinfo-1.1_3...
[93amd64-default-job-13] `-- Extracting libexecinfo-1.1_3: ..... done
[93amd64-default-job-13] Extracting cmake-3.6.1: .......... done
Message from ca_root_nss-3.26:
********************************* WARNING *********************************

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.

*********************************** NOTE **********************************

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
<snip>
[ 82%] Built target s4_join
/usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake
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[ 84%] Built target s4_search
/usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqan_tcoffee /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake
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[ 86%] Built target seqan_tcoffee
/usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqcons2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake
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cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sgip /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sgip /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake
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[ 90%] Built target sgip
/usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake
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[ 91%] Built target snp_store
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cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/splazers /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/splazers /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake
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[ 93%] Built target splazers
/usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/stellar /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/stellar /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake
/usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build
[ 94%] Built target stellar
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cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/tree_recon /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake
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[ 96%] Built target tree_recon
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cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake
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cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake
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/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles 0
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Installing the project stripped...
/usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/alf
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/example/small.fasta
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bisar
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/casbar
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/four2three
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/dfi
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta1.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta2.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fiona
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/compute_gain
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/example/reads.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fx_bam_coverage
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf_mate_joining
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified_reads.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/stellar.gff
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/insegt
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annoOutput.gff
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annotations.gff
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/readOutput.gff
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/tupleOutput.gff
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_frag_sequencing
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_genome
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_materializer
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_methylation
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_simulator
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_splicing
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_variator
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_frag_sequencing
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_genome
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_materializer
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_methylation
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_simulator
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_splicing
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_variator
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/example/adeno_virus.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/micro_razers
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/genome.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa.result
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bam2roi
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_feature_projection
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_thumbnails
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bed_sort.sh
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gff_sort.sh
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_sort.sh
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_9.sh
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/plot.awk
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/ps2pswLinks.gawk
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.bed
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.gtf
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/example.bam
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.tar.gz
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.zip
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/pair_align
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/param_chooser
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/genome.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads2.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers3
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/genome.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads2.fa
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rep_sep
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/README
/usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 -B/wrkdirs/usr/ports/biology/seqan-apps/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 sak_doc
/usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 -B/wrkdirs/usr/ports/biology/seqan-apps/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles 2
/usr/bin/make -f CMakeFiles/Makefile2 apps/sak/CMakeFiles/sak_doc.dir/all
/usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/seqan_library.dir/DependInfo.cmake
/usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build
[  0%] Built target seqan_library
/usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake
/usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build
[ 50%] Built target sak
/usr/bin/make -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/CMakeFiles/sak_doc.dir/DependInfo.cmake
Scanning dependencies of target sak_doc
/usr/bin/make -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/build
[100%] Generating README.sak.txt
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && ../../bin/sak --export-help=txt > README.sak.txt
*** [apps/sak/README.sak.txt] Signal 11

Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build.
*** [apps/sak/CMakeFiles/sak_doc.dir/all] Error code 1

Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build.
*** [apps/sak/CMakeFiles/sak_doc.dir/rule] Error code 1

Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build.
*** [sak_doc] Error code 1

Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build.
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sak
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/LICENSE
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README
-- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README.sak.txt
CMake Error at apps/sak/cmake_install.cmake:59 (file):
  file INSTALL cannot find
  "/wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/sak.1".
Call Stack (most recent call first):
  apps/cmake_install.cmake:48 (include)
  cmake_install.cmake:32 (include)

*** [install/strip] Error code 1

Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build.
*** [do-install] Error code 1

Stop in /usr/ports/biology/seqan-apps.