From owner-freebsd-pkg-fallout@freebsd.org Thu Jun 21 11:51:25 2018 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 51773101BC3A for ; Thu, 21 Jun 2018 11:51:25 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id B5C267921D for ; Thu, 21 Jun 2018 11:51:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 6C545101BC39; Thu, 21 Jun 2018 11:51:24 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 1DF0F101BC38 for ; Thu, 21 Jun 2018 11:51:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id C152A7921B for ; Thu, 21 Jun 2018 11:51:23 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (thunderx1.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fb]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 884A511515 for ; Thu, 21 Jun 2018 11:51:23 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (localhost [127.0.0.1]) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id w5LBpNEp006753 for ; Thu, 21 Jun 2018 11:51:23 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2/Submit) id w5LBpNK5006737; Thu, 21 Jun 2018 11:51:23 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 21 Jun 2018 11:51:23 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201806211151.w5LBpNK5006737@thunderx1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 111arm64-default][biology/freebayes] Failed for freebayes-1.2.0 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.26 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 21 Jun 2018 11:51:25 -0000 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 Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/freebayes/Makefile 467806 2018-04-20 00:07:27Z jwb $ Log URL: http://thunderx1.nyi.freebsd.org/data/111arm64-default/472730/logs/freebayes-1.2.0.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-default&build=472730 Log: =>> Building biology/freebayes build started at Thu Jun 21 11:41:10 UTC 2018 port directory: /usr/ports/biology/freebayes package name: freebayes-1.2.0 building for: FreeBSD 111arm64-default-job-18 11.1-RELEASE FreeBSD 11.1-RELEASE arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/freebayes/Makefile 467806 2018-04-20 00:07:27Z jwb $ Poudriere version: 3.2.7-1-g7087c444 Host OSVERSION: 1200060 Jail OSVERSION: 1101001 Job Id: 18 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1101001 UNAME_v=FreeBSD 11.1-RELEASE UNAME_r=11.1-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.7-1-g7087c444 MASTERMNT=/usr/local/poudriere/data/.m/111arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=111arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing --std=c++11" MANPREFIX="/usr/local" 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-- PORTDOCS="" PORTEXAMPLES="" OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/freebayes" EXAMPLESDIR="share/examples/freebayes" DATADIR="share/freebayes" WWWDIR="www/freebayes" ETCDIR="etc/freebayes" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/freebayes DOCSDIR=/usr/local/share/doc/freebayes EXAMPLESDIR=/usr/local/share/examples/freebayes WWWDIR=/usr/local/www/freebayes ETCDIR=/usr/local/etc/freebayes --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /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 # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=error: invalid value 'c++17' in '-std=c++17' CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=error: invalid value 'gnu++17' in '-std=gnu++17' _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=11.1-RELEASE OSREL=11.1 OSVERSION=1101001 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> freebayes-1.2.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [111arm64-default-job-18] Installing pkg-1.10.5_1... [111arm64-default-job-18] Extracting pkg-1.10.5_1: .......... done ===> freebayes-1.2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of freebayes-1.2.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0 for building => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz. => SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz. => SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0 for building ===> Extracting for freebayes-1.2.0 => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz. => SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz. => SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz. c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Sample.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Result.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c AlleleParser.cpp AlleleParser.cpp:1012:46: warning: '&&' within '||' [-Wlogical-op-parentheses] && (currAllele.isReference() && currAllele.referenceLength <= maxComplexGap ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlleleParser.cpp:1012:46: note: place parentheses around the '&&' expression to silence this warning && (currAllele.isReference() && currAllele.referenceLength <= maxComplexGap ^ ( ) 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Genotype.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c DataLikelihood.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Multinomial.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Ewens.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c ResultData.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Dirichlet.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Marginals.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c split.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c LeftAlign.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c IndelAllele.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Bias.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -c -o Contamination.o Contamination.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c NonCall.cpp c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c SegfaultHandler.cpp cd ../vcflib/smithwaterman && gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/smithwaterman' c++ -O3 -c -o disorder.o disorder.cpp -I. c++ -O3 -c -o smithwaterman.o smithwaterman.cpp -I. c++ -O3 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I. c++ -O3 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I. c++ -O3 -c -o LeftAlign.o LeftAlign.cpp -I. LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses] && (indel.insertion && indel.position == referenceSequence.size() ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning && (indel.insertion && indel.position == referenceSequence.size() ^ ( ) 1 warning generated. c++ -O3 -c -o Repeats.o Repeats.cpp -I. c++ -O3 -c -o IndelAllele.o IndelAllele.cpp -I. c++ -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman ld -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L. #c++ -O3 -c -o smithwaterman.cpp disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -I. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/smithwaterman' c++ -O2 -pipe -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c ../vcflib/src/Variant.cpp ./vcflib/src/Variant.cpp:212:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ ./vcflib/src/Variant.cpp:334:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ ./vcflib/src/Variant.cpp:368:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ ./vcflib/src/Variant.cpp:406:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ 4 warnings generated. cd ../SeqLib && ./configure && gmake checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/missing: Unknown `--is-lightweight' option Try `/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... nawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... none required checking for library containing lzma_code... none required checking for library containing BZ2_bzBuffToBuffDecompress... none required checking for library containing clock_gettime... none required checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/seqtools/Makefile config.status: creating config.h config.status: executing depfiles commands gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' gmake all-recursive gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' Making all in bwa gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/bwa' cc -c -O2 -pipe -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -O2 -pipe -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -O2 -pipe -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o In file included from ksw.c:29: In file included from /usr/bin/../lib/clang/4.0.0/include/emmintrin.h:27: In file included from /usr/bin/../lib/clang/4.0.0/include/xmmintrin.h:27: /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:64:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:143:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:173:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:203:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:230:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:253:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:274:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:301:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:324:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:345:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:366:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:387:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:408:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:430:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:453:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:475:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:497:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:518:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/../lib/clang/4.0.0/include/mmintrin.h:539:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. gmake[5]: *** [Makefile:26: ksw.o] Error 1 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/bwa' gmake[4]: *** [Makefile:358: all-recursive] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' gmake[3]: *** [Makefile:299: all] Error 2 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' gmake[2]: *** [Makefile:53: ../SeqLib/src/libseqlib.a] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src' gmake[1]: *** [Makefile:2: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/freebayes