[package - 120powerpc64-quarterly][biology/vcflib] Failed for vcflib-1.0.0.r1.130 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue May 14 11:25:40 UTC 2019
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 at FreeBSD.org
Last committer: linimon at 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/501608/logs/vcflib-1.0.0.r1.130.log
Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=501608
Log:
=>> Building biology/vcflib
build started at Tue May 14 11:24:46 UTC 2019
port directory: /usr/ports/biology/vcflib
package name: vcflib-1.0.0.r1.130
building for: FreeBSD 120powerpc64-quarterly-job-06 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 powerpc
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q2/biology/vcflib/Makefile 473010 2018-06-22 00:03:08Z linimon $
Poudriere version: 3.2.8-4-g701d8fe1
Host OSVERSION: 1300012
Jail OSVERSION: 1200086
Job Id: 06
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---End OPTIONS List---
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jwb at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
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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
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USE_PACKAGE_DEPENDS=yes
BATCH=yes
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PACKAGES=/packages
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PACKAGE_BUILDING=yes
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#### /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
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#### /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.
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ARCH=powerpc64
OPSYS=FreeBSD
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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-06] Installing pkg-1.10.5_5...
[120powerpc64-quarterly-job-06] 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-06] Installing fastahack-g20160702...
[120powerpc64-quarterly-job-06] 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-06] Installing filevercmp-g20151117...
[120powerpc64-quarterly-job-06] 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-06] Installing fsom-g20151117_1...
[120powerpc64-quarterly-job-06] `-- Installing gcc8-8.3.0_2...
[120powerpc64-quarterly-job-06] | `-- Installing binutils-2.32,1...
[120powerpc64-quarterly-job-06] | | `-- Installing gettext-runtime-0.19.8.1_2...
[120powerpc64-quarterly-job-06] | | `-- Installing indexinfo-0.3.1...
[120powerpc64-quarterly-job-06] | | `-- Extracting indexinfo-0.3.1: .... done
[120powerpc64-quarterly-job-06] | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120powerpc64-quarterly-job-06] | `-- Extracting binutils-2.32,1: .......... done
[120powerpc64-quarterly-job-06] | `-- Installing gmp-6.1.2_1...
[120powerpc64-quarterly-job-06] | `-- Extracting gmp-6.1.2_1: .......... done
[120powerpc64-quarterly-job-06] | `-- Installing mpc-1.1.0_2...
[120powerpc64-quarterly-job-06] | | `-- Installing mpfr-4.0.2...
[120powerpc64-quarterly-job-06] | | `-- Extracting mpfr-4.0.2: .......... done
[120powerpc64-quarterly-job-06] | `-- Extracting mpc-1.1.0_2: ......... done
[120powerpc64-quarterly-job-06] `-- Extracting gcc8-8.3.0_2: .......... done
[120powerpc64-quarterly-job-06] Extracting fsom-g20151117_1: ........ done
Message from gcc8-8.3.0_2:
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-06] Installing multichoose-1.0.3.2...
[120powerpc64-quarterly-job-06] `-- Installing python27-2.7.16...
[120powerpc64-quarterly-job-06] | `-- Installing libffi-3.2.1_3...
[120powerpc64-quarterly-job-06] | `-- Extracting libffi-3.2.1_3: .......... done
[120powerpc64-quarterly-job-06] | `-- Installing readline-7.0.5...
[120powerpc64-quarterly-job-06] | `-- Extracting readline-7.0.5: .......... done
[120powerpc64-quarterly-job-06] `-- Extracting python27-2.7.16: .......... done
[120powerpc64-quarterly-job-06] 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-06] Installing intervaltree-g20151213_1...
[120powerpc64-quarterly-job-06] 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-06] Installing gmake-4.2.1_3...
[120powerpc64-quarterly-job-06] 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-06] Installing htslib-1.9...
[120powerpc64-quarterly-job-06] `-- Installing curl-7.64.1_1...
[120powerpc64-quarterly-job-06] | `-- Installing ca_root_nss-3.44...
[120powerpc64-quarterly-job-06] | `-- Extracting ca_root_nss-3.44: ........ done
[120powerpc64-quarterly-job-06] | `-- Installing libnghttp2-1.37.0...
[120powerpc64-quarterly-job-06] | `-- Extracting libnghttp2-1.37.0: .......... done
[120powerpc64-quarterly-job-06] `-- Extracting curl-7.64.1_1: .......... done
[120powerpc64-quarterly-job-06] Extracting htslib-1.9: .......... done
Message from ca_root_nss-3.44:
********************************* 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-06] Installing tabixpp-1.0.0.10...
[120powerpc64-quarterly-job-06] 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-06] Installing smithwaterman-g20160702...
[120powerpc64-quarterly-job-06] 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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