[package - 111arm64-quarterly][biology/canu] Failed for canu-1.6 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun Mar 4 06:03:38 UTC 2018
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: jwb at FreeBSD.org
Ident: $FreeBSD: branches/2018Q1/biology/canu/Makefile 456982 2017-12-22 14:14:11Z jwb $
Log URL: http://thunderx1.nyi.freebsd.org/data/111arm64-quarterly/463543/logs/canu-1.6.log
Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-quarterly&build=463543
Log:
=>> Building biology/canu
build started at Sun Mar 4 06:01:11 UTC 2018
port directory: /usr/ports/biology/canu
package name: canu-1.6
building for: FreeBSD 111arm64-quarterly-job-21 11.1-RELEASE FreeBSD 11.1-RELEASE arm64
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2018Q1/biology/canu/Makefile 456982 2017-12-22 14:14:11Z jwb $
Poudriere version: 3.2.4-64-g33691b66
Host OSVERSION: 1200052
Jail OSVERSION: 1101001
Job Id: 21
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MAKE_ARGS=
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--MAINTAINER--
jwb at FreeBSD.org
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--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/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--
DESTDIR=/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc6" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing" CPP="cpp6" CPPFLAGS="" LDFLAGS=" -Wl,
-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6" LIBS="" CXX="g++6" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6" 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--
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--End PLIST_SUB--
--SUB_LIST--
JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="1.8+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/canu DOCSDIR=/usr/local/share/doc/canu EXAMPLESDIR=/usr/local/share/examples/canu WWWDIR=/usr/local/www/canu ETCDIR=/usr/local/etc/canu
--End SUB_LIST--
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USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
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PACKAGE_BUILDING_FLAVORS=yes
#### /usr/local/etc/poudriere.d/make.conf ####
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# try the next mirror on checksum failure. It currently retries the same
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#### /usr/ports/Mk/Scripts/ports_env.sh ####
ARCH=aarch64
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.1
OSVERSION=1101001
PYTHONBASE=/usr/local
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core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
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umtx shared locks (-o) unlimited
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=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> canu-1.6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.3_1.txz
[111arm64-quarterly-job-21] Installing pkg-1.10.3_1...
[111arm64-quarterly-job-21] Extracting pkg-1.10.3_1: .......... done
===> canu-1.6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of canu-1.6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.6 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.6 for building
=> SHA256 Checksum OK for marbl-canu-v1.6_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.6 for building
===> Extracting for canu-1.6
=> SHA256 Checksum OK for marbl-canu-v1.6_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for canu-1.6
===> Applying FreeBSD patches for canu-1.6
/usr/bin/sed -i.bak -e 's|-O4||g' -e 's|-funroll-loops||g' -e 's|-fexpensive-optimizations||g' -e 's|amd64|aarch64|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/Makefile
/usr/bin/sed -i.bak -e 's|\\$bin/mhap-|/usr/local/share/java/classes/mhap-|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/pipelines/canu/OverlapMhap.pm
/usr/bin/sed -i.bak -e 's|RealBin/lib|RealBin/../lib/perl5/site_perl/canu|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/pipelines/canu.pl
===========================================================================
=======================<phase: build-depends >============================
===> canu-1.6 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_1.txz
[111arm64-quarterly-job-21] Installing gmake-4.2.1_1...
[111arm64-quarterly-job-21] `-- Installing gettext-runtime-0.19.8.1_1...
[111arm64-quarterly-job-21] | `-- Installing indexinfo-0.3.1...
[111arm64-quarterly-job-21] | `-- Extracting indexinfo-0.3.1: .... done
[111arm64-quarterly-job-21] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[111arm64-quarterly-job-21] Extracting gmake-4.2.1_1: .......... done
===> canu-1.6 depends on executable: gmake - found
===> Returning to build of canu-1.6
===> canu-1.6 depends on executable: gcc6 - not found
===> Installing existing package /packages/All/gcc6-6.4.0_3.txz
[111arm64-quarterly-job-21] Installing gcc6-6.4.0_3...
[111arm64-quarterly-job-21] `-- Installing binutils-2.28,1...
[111arm64-quarterly-job-21] `-- Extracting binutils-2.28,1: .......... done
[111arm64-quarterly-job-21] `-- Installing gmp-6.1.2...
[111arm64-quarterly-job-21] `-- Extracting gmp-6.1.2: .......... done
[111arm64-quarterly-job-21] `-- Installing mpc-1.0.3...
[111arm64-quarterly-job-21] | `-- Installing mpfr-3.1.6...
[111arm64-quarterly-job-21] | `-- Extracting mpfr-3.1.6: .......... done
[111arm64-quarterly-job-21] `-- Extracting mpc-1.0.3: ...... done
[111arm64-quarterly-job-21] Extracting gcc6-6.4.0_3: .......... done
Message from gcc6-6.4.0_3:
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/gcc6
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> canu-1.6 depends on executable: gcc6 - found
===> Returning to build of canu-1.6
===> canu-1.6 depends on file: /usr/local/bin/as - found
===> canu-1.6 depends on package: perl5>=5.24<5.25 - not found
===> Installing existing package /packages/All/perl5-5.24.3.txz
[111arm64-quarterly-job-21] Installing perl5-5.24.3...
[111arm64-quarterly-job-21] Extracting perl5-5.24.3: .......... done
Message from perl5-5.24.3:
The /usr/bin/perl symlink has been removed starting with Perl 5.20.
For shebangs, you should either use:
#!/usr/local/bin/perl
or
#!/usr/bin/env perl
The first one will only work if you have a /usr/local/bin/perl,
the second will work as long as perl is in PATH.
===> canu-1.6 depends on package: perl5>=5.24<5.25 - found
===> Returning to build of canu-1.6
===========================================================================
=======================<phase: lib-depends >============================
===> canu-1.6 depends on shared library: libboost_regex.so - not found
===> Installing existing package /packages/All/boost-libs-1.65.1_1.txz
[111arm64-quarterly-job-21] Installing boost-libs-1.65.1_1...
[111arm64-quarterly-job-21] `-- Installing icu-60.2_1,1...
[111arm64-quarterly-job-21] `-- Extracting icu-60.2_1,1: .......... done
[111arm64-quarterly-job-21] Extracting boost-libs-1.65.1_1: .......... done
Message from boost-libs-1.65.1_1:
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> canu-1.6 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)
===> Returning to build of canu-1.6
===========================================================================
=======================<phase: configure >============================
===> Configuring for canu-1.6
===========================================================================
=======================<phase: build >============================
===> Building for canu-1.6
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src'
Building for 'FreeBSD' '1101001' as 'arm64' into '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm64/{bin,obj}'
CC gcc6 6.4.0
CXX g++6 6.4.0
Building release v1.6
g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm64/obj/libcanu.a/AS_global.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon AS_global.C
AS_global.C: In function 'int AS_configure(int, char**)':
AS_global.C:101:24: error: 'omp_set_num_threads' was not declared in this scope
omp_set_num_threads(1);
^
gmake[1]: *** [Makefile:655: /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm64/obj/libcanu.a/AS_global.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/canu
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