From owner-freebsd-pkg-fallout@freebsd.org Tue Sep 11 01:23:49 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 E13F010A28DB for ; Tue, 11 Sep 2018 01:23:48 +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 718D67E25D for ; Tue, 11 Sep 2018 01:23:48 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 3643910A28D3; Tue, 11 Sep 2018 01:23:48 +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 1448410A28D1 for ; Tue, 11 Sep 2018 01:23:48 +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 BFFC47E25C for ; Tue, 11 Sep 2018 01:23:47 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy16.nyi.freebsd.org (beefy16.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e3]) (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 BB00A10D39 for ; Tue, 11 Sep 2018 01:23:47 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy16.nyi.freebsd.org (localhost [127.0.0.1]) by beefy16.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id w8B1NlmL014011 for ; Tue, 11 Sep 2018 01:23:47 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy16.nyi.freebsd.org (8.15.2/8.15.2/Submit) id w8B1NlbI014007; Tue, 11 Sep 2018 01:23:47 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 11 Sep 2018 01:23:47 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201809110123.w8B1NlbI014007@beefy16.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 111mips64-quarterly][biology/bedtools] Failed for bedtools-2.27.1_1 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, 11 Sep 2018 01:23:49 -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: branches/2018Q3/biology/bedtools/Makefile 472560 2018-06-16 17:55:01Z jwb $ Log URL: http://beefy16.nyi.freebsd.org/data/111mips64-quarterly/479495/logs/bedtools-2.27.1_1.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=111mips64-quarterly&build=479495 Log: =>> Building biology/bedtools build started at Tue Sep 11 01:23:28 UTC 2018 port directory: /usr/ports/biology/bedtools package name: bedtools-2.27.1_1 building for: FreeBSD 111mips64-quarterly-job-11 11.1-RELEASE-p13 FreeBSD 11.1-RELEASE-p13 1101001 mips maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2018Q3/biology/bedtools/Makefile 472560 2018-06-16 17:55:01Z jwb $ Poudriere version: 3.2.7-6-g819c79a1 Host OSVERSION: 1200069 Jail OSVERSION: 1101001 Job Id: 11 ---Begin Environment--- POUDRIEREPATH=/usr/local/bin/poudriere SCRIPTPATH=/usr/local/share/poudriere/bulk.sh OLDPWD=/usr/local/poudriere/data/.m/111mips64-quarterly/ref/.p SCRIPTPREFIX=/usr/local/share/poudriere MASTERNAME=111mips64-quarterly P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/111mips64-quarterly/ref/.p/pool SAVED_TERM= PACKAGE_BUILDING=yes POUDRIERE_BUILD_TYPE=bulk MASTERMNT=/usr/local/poudriere/data/.m/111mips64-quarterly/ref POUDRIERE_VERSION=3.2.7-6-g819c79a1 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=mips64 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 PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/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/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/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 " 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="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd11 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bedtools" EXAMPLESDIR="share/examples/bedtools" DATADIR="share/bedtools" WWWDIR="www/bedtools" ETCDIR="etc/bedtools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bedtools DOCSDIR=/usr/local/share/doc/bedtools EXAMPLESDIR=/usr/local/share/examples/bedtools WWWDIR=/usr/local/www/bedtools ETCDIR=/usr/local/etc/bedtools --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=mips64 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: mips64-undermydesk-freebsd Configured with: FreeBSD/mips64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-EB" "-EB" "-melf64btsmip_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=mips64 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 GPLv2 accepted by the user =========================================================================== =================================================== ===> bedtools-2.27.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [111mips64-quarterly-job-11] Installing pkg-1.10.5_1... [111mips64-quarterly-job-11] Extracting pkg-1.10.5_1: .......... done ===> bedtools-2.27.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bedtools-2.27.1_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.27.1_1 for building =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.27.1_1 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.27.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.27.1_1 for building ===> Extracting for bedtools-2.27.1_1 => SHA256 Checksum OK for arq5x-bedtools2-v2.27.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bedtools-2.27.1_1 ===> Applying FreeBSD patches for bedtools-2.27.1_1 =========================================================================== =================================================== ===> bedtools-2.27.1_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz [111mips64-quarterly-job-11] Installing gmake-4.2.1_2... [111mips64-quarterly-job-11] `-- Installing gettext-runtime-0.19.8.1_1... [111mips64-quarterly-job-11] | `-- Installing indexinfo-0.3.1... [111mips64-quarterly-job-11] | `-- Extracting indexinfo-0.3.1: .... done [111mips64-quarterly-job-11] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [111mips64-quarterly-job-11] Extracting gmake-4.2.1_2: .......... done ===> bedtools-2.27.1_1 depends on executable: gmake - found ===> Returning to build of bedtools-2.27.1_1 ===> bedtools-2.27.1_1 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.15.txz [111mips64-quarterly-job-11] Installing python27-2.7.15... [111mips64-quarterly-job-11] `-- Installing libffi-3.2.1_2... [111mips64-quarterly-job-11] `-- Extracting libffi-3.2.1_2: .......... done [111mips64-quarterly-job-11] `-- Installing readline-7.0.3_1... [111mips64-quarterly-job-11] `-- Extracting readline-7.0.3_1: .......... done [111mips64-quarterly-job-11] Extracting python27-2.7.15: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> bedtools-2.27.1_1 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of bedtools-2.27.1_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bedtools-2.27.1_1 =========================================================================== =================================================== ===> Building for bedtools-2.27.1_1 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.27.1' $CXXFLAGS is [-O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: ========================================================= DETECTED_VERSION = v2.27.1 CURRENT_VERSION = Updating version file. * Creating BamTools API - Building in src/utils/FileRecordTools * compiling FileRecordMgr.cpp /nxb-bin/usr/bin/c++ -c -o ../../../obj//FileRecordMgr.o FileRecordMgr.cpp -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFi le/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ cc1plus: error: unrecognized command line option "-std=c++11" gmake[2]: *** [Makefile:37: ../../../obj//FileRecordMgr.o] Error 1 gmake[1]: *** [Makefile:187: src/utils/FileRecordTools] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.27.1' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bedtools