Date: Fri, 25 Apr 2014 01:48:08 GMT From: pkg-fallout-builder@FreeBSD.org To: h2+fbsdports@fsfe.org Cc: pkg-fallout@FreeBSD.org Subject: [REL - head-amd64-default][biology/seqan] Failed for seqan-1.3.1_2 in build Message-ID: <201404250148.s3P1m8oe019356@beefy2.isc.freebsd.org>
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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@fsfe.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/biology/seqan/Makefile 347809 2014-03-10 20:55:20Z gerald $ Log URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-04-24_12h15m18s/logs/seqan-1.3.1_2.log Build URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-04-24_12h15m18s Log: ====>> Building biology/seqan build started at Fri Apr 25 01:46:40 UTC 2014 port directory: /usr/ports/biology/seqan building for: FreeBSD head-amd64-default-job-16 11.0-CURRENT FreeBSD 11.0-CURRENT r264257 amd64 maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan/Makefile 347809 2014-03-10 20:55:20Z gerald $ Poudriere version: 3.1-pre Host OSVERSION: 1100013 Jail OSVERSION: 1100018 !!! Jail is newer than host. (Jail: 1100018, Host: 1100013) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- OSVERSION=1100018 UNAME_v=FreeBSD 11.0-CURRENT r264257 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref PKG_EXT=txz tpid=69594 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=seqan-1.3.1_2 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add OLDPWD=/usr/local/poudriere/data/build/head-amd64-default/ref/poudriere/rdeps PWD=/usr/local/poudriere/data/build/head-amd64-default/ref/poudriere/pool MASTERNAME=head-amd64-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" PYTHON="/usr/local/bin/python2.7" TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd11 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_VERSION=python2.7 CMAKE_BUILD_TYPE="release" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local PORTDOCS="" PORTEXAMPLES="" PORTDATA="" LIB32DIR=lib DOCSDIR="share/doc/seqan" EXAMPLESDIR="share/examples/seqan" DATADIR="share/seqan" WWWDIR="www/seqan" ETCDIR="etc/seqan" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan DOCSDIR=/usr/local/share/doc/seqan EXAMPLESDIR=/usr/local/share/examples/seqan WWWDIR=/usr/local/www/seqan ETCDIR=/usr/local/etc/seqan --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 #### WITH_PKGNG=yes NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for seqan-1.3.1_2 =======================<phase: check-sanity >============================ ===> License BSD GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> seqan-1.3.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.2.7_2.txz Installing pkg-1.2.7_2... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of seqan-1.3.1_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_2 for building => SHA256 Checksum OK for seqan-1.3.1.zip. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_2 for building ===> Extracting for seqan-1.3.1_2 => SHA256 Checksum OK for seqan-1.3.1.zip. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for seqan-1.3.1_2 ===> Applying FreeBSD patches for seqan-1.3.1_2 =========================================================================== =======================<phase: build-depends >============================ ===> seqan-1.3.1_2 depends on file: /usr/local/bin/python2.7 - not found ===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27 ===> Installing existing package /packages/All/python27-2.7.6_4.txz Installing python27-2.7.6_4...Installing gettext-0.18.3.1... done done ==== Note that some of the standard modules are provided as separate ports since they require extra dependencies: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Install them as needed. ==== ===> Returning to build of seqan-1.3.1_2 ===> seqan-1.3.1_2 depends on file: /usr/local/bin/cmake - not found ===> Verifying install for /usr/local/bin/cmake in /usr/ports/devel/cmake ===> Installing existing package /packages/All/cmake-2.8.12.1_4.txz Installing cmake-2.8.12.1_4...Installing cmake-modules-2.8.12.1_1... done done ===> Returning to build of seqan-1.3.1_2 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for seqan-1.3.1_2 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan/work/.build -- The C compiler identification is Clang 3.4.0 -- The CXX compiler identification is Clang 3.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PythonInterp: /usr/local/bin/python2.7 (found suitable version "2.7.6", minimum required is "2.7") -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-Qopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-openmp] -- Performing Test OpenMP_FLAG_DETECTED <snip> Linking C static library libbam.a cd /wrkdirs/usr/ports/biology/seqan/work/.build/libs/samtools && /usr/local/bin/cmake -P CMakeFiles/bam.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/seqan/work/.build/libs/samtools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bam.dir/link.txt --verbose=1 /usr/bin/ar cr libbam.a CMakeFiles/bam.dir/bgzf.c.o CMakeFiles/bam.dir/kstring.c.o CMakeFiles/bam.dir/bam_aux.c.o CMakeFiles/bam.dir/bam.c.o CMakeFiles/bam.dir/bam_import.c.o CMakeFiles/bam.dir/sam.c.o CMakeFiles/bam.dir/bam_index.c.o CMakeFiles/bam.dir/bam_pileup.c.o CMakeFiles/bam.dir/bam_lpileup.c.o CMakeFiles/bam.dir/bam_md.c.o CMakeFiles/bam.dir/glf.c.o CMakeFiles/bam.dir/razf.c.o CMakeFiles/bam.dir/faidx.c.o CMakeFiles/bam.dir/knetfile.c.o CMakeFiles/bam.dir/bam_sort.c.o CMakeFiles/bam.dir/sam_header.c.o CMakeFiles/bam.dir/bam_reheader.c.o CMakeFiles/bam.dir/kprobaln.c.o /usr/bin/ranlib libbam.a /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 5 6 7 8 9 10 11 12 13 14 15 16 17 [ 13%] Built target bam /usr/bin/make -f CMakeFiles/Seqan.dir/build.make CMakeFiles/Seqan.dir/depend cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake /wrkdirs/usr/ports/biology/seqan/work/.build /wrkdirs/usr/ports/biology/seqan/work/.build /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles/Seqan.dir/DependInfo.cmake Scanning dependencies of target Seqan /usr/bin/make -f CMakeFiles/Seqan.dir/build.make CMakeFiles/Seqan.dir/build /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles [ 13%] Built target Seqan /usr/bin/make -f apps/CMakeFiles/dfi.dir/build.make apps/CMakeFiles/dfi.dir/depend cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps /wrkdirs/usr/ports/biology/seqan/work/.build /wrkdirs/usr/ports/biology/seqan/work/.build/apps /wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/dfi.dir/DependInfo.cmake Scanning dependencies of target dfi /usr/bin/make -f apps/CMakeFiles/dfi.dir/build.make apps/CMakeFiles/dfi.dir/build /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 18 [ 14%] Building CXX object apps/CMakeFiles/dfi.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp.o cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o CMakeFiles/dfi.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp.o -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/misc/misc_cmdparser.h:37: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/map.h:42: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:74: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78: warning: for loop has empty body [-Wempty-body] for(TSize _xSize = 1; _xSize <= saSize; _xSize *= BlockSize, ++treeLevels) ; ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78: note: put the semicolon on a separate line to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:96: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54: warning: for loop has empty body [-Wempty-body] for(; lcpSize > _xSize; _xSize *= 2, ++treeLevels) ; ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54: note: put the semicolon on a separate line to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:155: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49: warning: for loop has empty body [-Wempty-body] for(_xSize = 1; _xSize < size; _xSize <<= 1) ; ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49: note: put the semicolon on a separate line to silence this warning 4 warnings generated. Linking CXX executable dfi cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 CMakeFiles/dfi.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp.o -o dfi -L/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib -lz -Wl,-rpath,/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib: /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 18 [ 14%] Built target dfi /usr/bin/make -f apps/CMakeFiles/insegt.dir/build.make apps/CMakeFiles/insegt.dir/depend cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps /wrkdirs/usr/ports/biology/seqan/work/.build /wrkdirs/usr/ports/biology/seqan/work/.build/apps /wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/insegt.dir/DependInfo.cmake Scanning dependencies of target insegt /usr/bin/make -f apps/CMakeFiles/insegt.dir/build.make apps/CMakeFiles/insegt.dir/build /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles [ 14%] Building CXX object apps/CMakeFiles/insegt.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp.o cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o CMakeFiles/insegt.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp.o -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp:13: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ 1 warning generated. Linking CXX executable insegt cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 CMakeFiles/insegt.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp.o -o insegt -L/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib -lz -Wl,-rpath,/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib: /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles [ 14%] Built target insegt /usr/bin/make -f apps/CMakeFiles/mason.dir/build.make apps/CMakeFiles/mason.dir/depend cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps /wrkdirs/usr/ports/biology/seqan/work/.build /wrkdirs/usr/ports/biology/seqan/work/.build/apps /wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/mason.dir/DependInfo.cmake Scanning dependencies of target mason /usr/bin/make -f apps/CMakeFiles/mason.dir/build.make apps/CMakeFiles/mason.dir/build /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles [ 14%] Building CXX object apps/CMakeFiles/mason.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp.o cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o CMakeFiles/mason.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp.o -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/find.h:43: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ 1 warning generated. Linking CXX executable mason cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 CMakeFiles/mason.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp.o -o mason -L/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib -lz -Wl,-rpath,/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib: /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles [ 14%] Built target mason /usr/bin/make -f apps/CMakeFiles/micro_razers.dir/build.make apps/CMakeFiles/micro_razers.dir/depend cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps /wrkdirs/usr/ports/biology/seqan/work/.build /wrkdirs/usr/ports/biology/seqan/work/.build/apps /wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/micro_razers.dir/DependInfo.cmake Scanning dependencies of target micro_razers /usr/bin/make -f apps/CMakeFiles/micro_razers.dir/build.make apps/CMakeFiles/micro_razers.dir/build /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 47 [ 15%] Building CXX object apps/CMakeFiles/micro_razers.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp.o cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++ -O2 -pipe -fno-strict-aliasing -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools -I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o CMakeFiles/micro_razers.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp.o -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/find.h:43: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:29: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:74: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78: warning: for loop has empty body [-Wempty-body] for(TSize _xSize = 1; _xSize <= saSize; _xSize *= BlockSize, ++treeLevels) ; ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78: note: put the semicolon on a separate line to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:29: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:96: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54: warning: for loop has empty body [-Wempty-body] for(; lcpSize > _xSize; _xSize *= 2, ++treeLevels) ; ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54: note: put the semicolon on a separate line to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:29: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:155: /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49: warning: for loop has empty body [-Wempty-body] for(_xSize = 1; _xSize < size; _xSize <<= 1) ; ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49: note: put the semicolon on a separate line to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/find.h:43: In file included from /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:54: /usr/include/c++/v1/map:457:17: error: no matching function for call to object of type 'const seqan::RepeatLess_<unsigned int>' {return static_cast<const _Compare&>(*this)(__x.__cc.first, __y.__cc.first);} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__tree:1613:17: note: in instantiation of member function 'std::__1::__map_value_compare<unsigned int, std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> >, seqan::RepeatLess_<unsigned int>, true>::operator()' requested here if (value_comp()(__v, __nd->__value_)) ^ /usr/include/c++/v1/__tree:1867:36: note: in instantiation of function template specialization 'std::__1::__tree<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> >, std::__1::__map_value_compare<unsigned int, std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> >, seqan::RepeatLess_<unsigned int>, true>, std::__1::allocator<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> > > >::__find_equal<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> > >' requested here __node_base_pointer& __child = __find_equal(__parent, __v); ^ /usr/include/c++/v1/map:1043:55: note: in instantiation of member function 'std::__1::__tree<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> >, std::__1::__map_value_compare<unsigned int, std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> >, seqan::RepeatLess_<unsigned int>, true>, std::__1::allocator<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> > > >::__insert_unique' requested here insert(const value_type& __v) {return __tree_.__insert_unique(__v);} ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/repeat_base.h:290:13: note: in instantiation of member function 'std::__1::map<unsigned int, seqan::Repeat<unsigned int, unsigned int>, seqan::RepeatLess_<unsigned int>, std::__1::allocator<std::__1::pair<const unsigned int, seqan::Repeat<unsigned int, unsigned int> > > >::insert' requested here list.insert(::std::pair<TOcc,TRepeat>(rep.beginPosition, rep)); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_swift.h:270:4: note: in instantiation of function template specialization 'seqan::findRepeats<seqan::String<seqan::Repeat<unsigned int, unsigned int>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, int, int>' requested here findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:1614:15: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) TSwiftFinder swiftFinder(genome, options.repeatLength, 1); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:1976:5: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Default_> > >, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_> >, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan ::RazerSSpec<false, false> >' requested here mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:2133:10: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_> > >' requested here return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift<TSwiftSpec>()); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:2192:11: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_> > >' requested here return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>()); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:165:14: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false> >' requested here int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:660:15: note: in instantiation of function template specialization 'mapMicroRNAReads<seqan::RazerSSpec<false, false> >' requested here int result = mapMicroRNAReads(fname[0], fname + 1, errorPrbFileName.c_str(), options); ^ /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/repeat_base.h:97:15: note: candidate function not viable: 'this' argument has type 'const seqan::RepeatLess_<unsigned int>', but method is not marked const inline bool operator() (TPos const &a, TPos const &b) { ^ 4 warnings and 1 error generated. *** Error code 1 Stop. make[3]: stopped in /wrkdirs/usr/ports/biology/seqan/work/.build *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/seqan/work/.build *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/seqan/work/.build *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan ===> Cleaning for seqan-1.3.1_2
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