From owner-freebsd-pkg-fallout@freebsd.org Tue Aug 21 01:22:41 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 D866C1083E4A for ; Tue, 21 Aug 2018 01:22:40 +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 4FA398C386 for ; Tue, 21 Aug 2018 01:22:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 14AA31083E3A; Tue, 21 Aug 2018 01:22:40 +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 E6CB91083E39 for ; Tue, 21 Aug 2018 01:22:39 +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 9D6ED8C385 for ; Tue, 21 Aug 2018 01:22:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy14.nyi.freebsd.org (beefy14.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e1]) (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 7F4621D3D2 for ; Tue, 21 Aug 2018 01:22:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy14.nyi.freebsd.org (localhost [127.0.0.1]) by beefy14.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id w7L1MdAV046061 for ; Tue, 21 Aug 2018 01:22:39 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy14.nyi.freebsd.org (8.15.2/8.15.2/Submit) id w7L1MdhZ046054; Tue, 21 Aug 2018 01:22:39 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 21 Aug 2018 01:22:39 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201808210122.w7L1MdhZ046054@beefy14.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 111mips-quarterly][biology/freebayes] Failed for freebayes-1.2.0 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 21 Aug 2018 01:22:41 -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: linimon@FreeBSD.org Ident: $FreeBSD: branches/2018Q3/biology/freebayes/Makefile 473009 2018-06-21 23:52:37Z linimon $ Log URL: http://beefy14.nyi.freebsd.org/data/111mips-quarterly/477697/logs/freebayes-1.2.0.log Build URL: http://beefy14.nyi.freebsd.org/build.html?mastername=111mips-quarterly&build=477697 Log: =>> Building biology/freebayes build started at Tue Aug 21 01:18:37 UTC 2018 port directory: /usr/ports/biology/freebayes package name: freebayes-1.2.0 building for: FreeBSD 111mips-quarterly-job-03 11.1-RELEASE-p13 FreeBSD 11.1-RELEASE-p13 1101001 mips maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2018Q3/biology/freebayes/Makefile 473009 2018-06-21 23:52:37Z linimon $ Poudriere version: 3.2.7-2-g1cf194be Host OSVERSION: 1200069 Jail OSVERSION: 1101001 Job Id: 03 ---Begin Environment--- POUDRIEREPATH=/usr/local/bin/poudriere SCRIPTPATH=/usr/local/share/poudriere/bulk.sh OLDPWD=/usr/local/poudriere/data/.m/111mips-quarterly/ref/.p SCRIPTPREFIX=/usr/local/share/poudriere MASTERNAME=111mips-quarterly P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/111mips-quarterly/ref/.p/pool SAVED_TERM= PACKAGE_BUILDING=yes POUDRIERE_BUILD_TYPE=bulk MASTERMNT=/usr/local/poudriere/data/.m/111mips-quarterly/ref POUDRIERE_VERSION=3.2.7-2-g1cf194be LIBEXECPREFIX=/usr/local/libexec/poudriere USER=root QEMU_EMULATING=1 LOCALBASE=/usr/local PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin HOME=/root STATUS=1 MAIL=/var/mail/root BLOCKSIZE=K UNAME_r=11.1-RELEASE-p13 UNAME_v=FreeBSD 11.1-RELEASE-p13 1101001 OSVERSION=1101001 ABI_FILE=/usr/lib/crt1.o UNAME_m=mips UNAME_p=mips SHELL=/bin/csh ---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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=mips MACHINE_ARCH=mips ARCH=${MACHINE_ARCH} #### /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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=Using built-in specs. Target: mips-undermydesk-freebsd Configured with: FreeBSD/mips system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-EB" "-EB" "-melf32btsmip_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_9d218390_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_9d218390_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_9d218390_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_9d218390_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_9d218390_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_9d218390=none ARCH=mips OPSYS=FreeBSD _OSRELEASE=11.1-RELEASE-p13 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--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 131072 stack size (kbytes, -s) 8192 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 [111mips-quarterly-job-03] Installing pkg-1.10.5_1... [111mips-quarterly-job-03] 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. => 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. /bin/mv -n /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib-temp/* /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib /bin/mv -n /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib-temp/* /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for freebayes-1.2.0 ===> Applying FreeBSD patches for freebayes-1.2.0 =========================================================================== =================================================== ===> freebayes-1.2.0 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz [111mips-quarterly-job-03] Installing gmake-4.2.1_2... [111mips-quarterly-job-03] `-- Installing gettext-runtime-0.19.8.1_1... [111mips-quarterly-job-03] | `-- Installing indexinfo-0.3.1... [111mips-quarterly-job-03] | `-- Extracting indexinfo-0.3.1: .... done [111mips-quarterly-job-03] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [111mips-quarterly-job-03] Extracting gmake-4.2.1_2: .......... done ===> freebayes-1.2.0 depends on executable: gmake - found ===> Returning to build of freebayes-1.2.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for freebayes-1.2.0 =========================================================================== =================================================== ===> Building for freebayes-1.2.0 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0' cd src && gmake autoversion gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src' DETECTED_VERSION = v1.0.0 CURRENT_VERSION = Updating version file. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src' touch src/version_git.h # wget -q http://hypervolu.me/freebayes/build/v1.0.0 & cd src && gmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src' DETECTED_VERSION = v1.0.0 CURRENT_VERSION = v1.0.0 cd ../SeqLib/htslib && /usr/local/bin/gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o kfunc.o kfunc.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o knetfile.o knetfile.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o kstring.o kstring.c kstring.c: In function 'kputd': kstring.c:64: warning: integer constant is too large for 'long' type kstring.c:91: warning: integer constant is too large for 'long' type /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bgzf.o bgzf.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o errmod.o errmod.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o faidx.o faidx.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hfile.o hfile.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.5"' > version.h /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hts.o hts.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o md5.o md5.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o multipart.o multipart.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o probaln.o probaln.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o realn.o realn.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o regidx.o regidx.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o sam.o sam.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcf_sweep.o vcf_sweep.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o tbx.o tbx.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o textutils.o textutils.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o thread_pool.o thread_pool.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcf.o vcf.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcfutils.o vcfutils.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_decode.o cram/cram_decode.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_encode.o cram/cram_encode.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_external.o cram/cram_external.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_index.o cram/cram_index.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_io.o cram/cram_io.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_stats.o cram/cram_stats.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/files.o cram/files.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/mFILE.o cram/mFILE.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/rANS_static.o cram/rANS_static.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/sam_header.o cram/sam_header.c /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bgzip.o bgzip.c /nxb-bin/usr/bin/cc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o htsfile.o htsfile.c /nxb-bin/usr/bin/cc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o tabix.o tabix.c /nxb-bin/usr/bin/cc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/hts_endian.o test/hts_endian.c test/hts_endian.c:105: warning: integer constant is too large for 'long' type test/hts_endian.c:105: warning: integer constant is too large for 'long' type /nxb-bin/usr/bin/cc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/fieldarith.o test/fieldarith.c /nxb-bin/usr/bin/cc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/hfile.o test/hfile.c /nxb-bin/usr/bin/cc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/sam.o test/sam.c /nxb-bin/usr/bin/cc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test_bgzf.o test/test_bgzf.c /nxb-bin/usr/bin/cc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-regidx.o test/test-regidx.c /nxb-bin/usr/bin/cc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test_view.o test/test_view.c /nxb-bin/usr/bin/cc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c /nxb-bin/usr/bin/cc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c /nxb-bin/usr/bin/cc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread /nxb-bin/usr/bin/cc -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c /nxb-bin/usr/bin/cc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/htslib' cd ../vcflib/tabixpp/ && /usr/local/bin/gmake && cp tabix.hpp ../../src/ gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' /nxb-bin/usr/bin/c++ -O2 -pipe -G0 -fno-strict-aliasing --std=c++11 -c tabix.cpp -Ihtslib cc1plus: error: unrecognized command line option "-std=c++11" gmake[4]: *** [Makefile:35: tabix.o] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' gmake[3]: *** [Makefile:22: all-recur] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' gmake[2]: *** [Makefile:202: ../vcflib/tabixpp/tabix.o] 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