Date: Sat, 20 Apr 2019 02:40:32 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120powerpc64-quarterly][biology/vcflib] Failed for vcflib-1.0.0.r1.130 in build Message-ID: <201904200240.x3K2eW16026648@pylon.nyi.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: jwb@FreeBSD.org Last committer: linimon@FreeBSD.org Ident: $FreeBSD: branches/2019Q2/biology/vcflib/Makefile 473010 2018-06-22 00:03:08Z linimon $ Log URL: http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/499422/logs/vcflib-1.0.0.r1.130.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=499422 Log: =>> Building biology/vcflib build started at Sat Apr 20 02:39:40 UTC 2019 port directory: /usr/ports/biology/vcflib package name: vcflib-1.0.0.r1.130 building for: FreeBSD 120powerpc64-quarterly-job-14 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q2/biology/vcflib/Makefile 473010 2018-06-22 00:03:08Z linimon $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300012 Jail OSVERSION: 1200086 Job Id: 14 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p3 1200086 UNAME_r=12.0-RELEASE-p3 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=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/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/vcflib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcflib/work HOME=/wrkdirs/usr/ports/biology/vcflib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcflib/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/vcflib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcflib/work HOME=/wrkdirs/usr/ports/biology/vcflib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcflib/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 -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='\"1.0.0.r1.130\"' " 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-- OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vcflib" EXAMPLESDIR="share/examples/vcflib" DATADIR="share/vcflib" WWWDIR="www/vcflib" ETCDIR="etc/vcflib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcflib DOCSDIR=/usr/local/share/doc/vcflib EXAMPLESDIR=/usr/local/share/examples/vcflib WWWDIR=/usr/local/www/vcflib ETCDIR=/usr/local/etc/vcflib --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 # 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_921dbbb2=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_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_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/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=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_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p3 OSREL=12.0 OSVERSION=1200086 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) 33554432 stack size (kbytes, -s) 524288 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-- =======================<phase: check-sanity >============================ ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> vcflib-1.0.0.r1.130 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120powerpc64-quarterly-job-14] Installing pkg-1.10.5_5... [120powerpc64-quarterly-job-14] Extracting pkg-1.10.5_5: .......... done ===> vcflib-1.0.0.r1.130 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcflib-1.0.0.r1.130 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by vcflib-1.0.0.r1.130 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by vcflib-1.0.0.r1.130 for building => SHA256 Checksum OK for ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by vcflib-1.0.0.r1.130 for building ===> Extracting for vcflib-1.0.0.r1.130 => SHA256 Checksum OK for ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for vcflib-1.0.0.r1.130 ===> Applying FreeBSD patches for vcflib-1.0.0.r1.130 =========================================================================== =======================<phase: build-depends >============================ ===> vcflib-1.0.0.r1.130 depends on executable: fastahack - not found ===> Installing existing package /packages/All/fastahack-g20160702.txz [120powerpc64-quarterly-job-14] Installing fastahack-g20160702... [120powerpc64-quarterly-job-14] Extracting fastahack-g20160702: .......... done ===> vcflib-1.0.0.r1.130 depends on executable: fastahack - found ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on executable: filevercmp - not found ===> Installing existing package /packages/All/filevercmp-g20151117.txz [120powerpc64-quarterly-job-14] Installing filevercmp-g20151117... [120powerpc64-quarterly-job-14] Extracting filevercmp-g20151117: ...... done ===> vcflib-1.0.0.r1.130 depends on executable: filevercmp - found ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on executable: fsom - not found ===> Installing existing package /packages/All/fsom-g20151117_1.txz [120powerpc64-quarterly-job-14] Installing fsom-g20151117_1... [120powerpc64-quarterly-job-14] `-- Installing gcc8-8.3.0_1... [120powerpc64-quarterly-job-14] | `-- Installing binutils-2.32,1... [120powerpc64-quarterly-job-14] | | `-- Installing gettext-runtime-0.19.8.1_2... [120powerpc64-quarterly-job-14] | | `-- Installing indexinfo-0.3.1... [120powerpc64-quarterly-job-14] | | `-- Extracting indexinfo-0.3.1: .... done [120powerpc64-quarterly-job-14] | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [120powerpc64-quarterly-job-14] | `-- Extracting binutils-2.32,1: .......... done [120powerpc64-quarterly-job-14] | `-- Installing gmp-6.1.2_1... [120powerpc64-quarterly-job-14] | `-- Extracting gmp-6.1.2_1: .......... done [120powerpc64-quarterly-job-14] | `-- Installing mpc-1.1.0_2... [120powerpc64-quarterly-job-14] | | `-- Installing mpfr-4.0.2... [120powerpc64-quarterly-job-14] | | `-- Extracting mpfr-4.0.2: .......... done [120powerpc64-quarterly-job-14] | `-- Extracting mpc-1.1.0_2: ......... done [120powerpc64-quarterly-job-14] `-- Extracting gcc8-8.3.0_1: .......... done [120powerpc64-quarterly-job-14] Extracting fsom-g20151117_1: ........ done Message from gcc8-8.3.0_1: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> vcflib-1.0.0.r1.130 depends on executable: fsom - found ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on package: multichoose>=1.0.3 - not found ===> Installing existing package /packages/All/multichoose-1.0.3.2.txz [120powerpc64-quarterly-job-14] Installing multichoose-1.0.3.2... [120powerpc64-quarterly-job-14] `-- Installing python27-2.7.16... [120powerpc64-quarterly-job-14] | `-- Installing libffi-3.2.1_3... [120powerpc64-quarterly-job-14] | `-- Extracting libffi-3.2.1_3: .......... done [120powerpc64-quarterly-job-14] | `-- Installing readline-7.0.5... [120powerpc64-quarterly-job-14] | `-- Extracting readline-7.0.5: .......... done [120powerpc64-quarterly-job-14] `-- Extracting python27-2.7.16: .......... done [120powerpc64-quarterly-job-14] Extracting multichoose-1.0.3.2: .......... done Message from python27-2.7.16: =========================================================================== 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 =========================================================================== ===> vcflib-1.0.0.r1.130 depends on package: multichoose>=1.0.3 - found ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on executable: interval_tree_test - not found ===> Installing existing package /packages/All/intervaltree-g20151213_1.txz [120powerpc64-quarterly-job-14] Installing intervaltree-g20151213_1... [120powerpc64-quarterly-job-14] Extracting intervaltree-g20151213_1: ..... done ===> vcflib-1.0.0.r1.130 depends on executable: interval_tree_test - found ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [120powerpc64-quarterly-job-14] Installing gmake-4.2.1_3... [120powerpc64-quarterly-job-14] Extracting gmake-4.2.1_3: .......... done ===> vcflib-1.0.0.r1.130 depends on executable: gmake - found ===> Returning to build of vcflib-1.0.0.r1.130 =========================================================================== =======================<phase: lib-depends >============================ ===> vcflib-1.0.0.r1.130 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.9.txz [120powerpc64-quarterly-job-14] Installing htslib-1.9... [120powerpc64-quarterly-job-14] `-- Installing curl-7.64.1_1... [120powerpc64-quarterly-job-14] | `-- Installing ca_root_nss-3.43... [120powerpc64-quarterly-job-14] | `-- Extracting ca_root_nss-3.43: ........ done [120powerpc64-quarterly-job-14] | `-- Installing libnghttp2-1.37.0... [120powerpc64-quarterly-job-14] | `-- Extracting libnghttp2-1.37.0: .......... done [120powerpc64-quarterly-job-14] `-- Extracting curl-7.64.1_1: .......... done [120powerpc64-quarterly-job-14] Extracting htslib-1.9: .......... done Message from ca_root_nss-3.43: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> vcflib-1.0.0.r1.130 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on shared library: libtabix.so - not found ===> Installing existing package /packages/All/tabixpp-1.0.0.10.txz [120powerpc64-quarterly-job-14] Installing tabixpp-1.0.0.10... [120powerpc64-quarterly-job-14] Extracting tabixpp-1.0.0.10: ........ done ===> vcflib-1.0.0.r1.130 depends on shared library: libtabix.so - found (/usr/local/lib/libtabix.so) ===> Returning to build of vcflib-1.0.0.r1.130 ===> vcflib-1.0.0.r1.130 depends on shared library: libsw.so - not found ===> Installing existing package /packages/All/smithwaterman-g20160702.txz [120powerpc64-quarterly-job-14] Installing smithwaterman-g20160702... [120powerpc64-quarterly-job-14] Extracting smithwaterman-g20160702: .......... done ===> vcflib-1.0.0.r1.130 depends on shared library: libsw.so - found (/usr/local/lib/libsw.so) ===> Returning to build of vcflib-1.0.0.r1.130 =========================================================================== =======================<phase: configure >============================ ===> Configuring for vcflib-1.0.0.r1.130 =========================================================================== =======================<phase: build >============================ ===> Building for vcflib-1.0.0.r1.130 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.0-rc1-130-g7e3d806' c++ -c -o src/Variant.o src/Variant.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 cc1plus: error: unrecognized command line option "-std=c++11" gmake[1]: *** [/usr/ports/biology/vcflib/files/Makefile.external-libs:170: src/Variant.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.0-rc1-130-g7e3d806' *** Error code 1 Stop. make: stopped in /usr/ports/biology/vcflib
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