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Date:      Fri, 13 Apr 2018 08:18:45 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 111arm64-default][biology/canu] Failed for canu-1.6_2 in build
Message-ID:  <201804130818.w3D8IjTW044460@thunderx1.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: gerald@FreeBSD.org
Ident:          $FreeBSD: head/biology/canu/Makefile 464084 2018-03-10 17:46:04Z gerald $
Log URL:        http://thunderx1.nyi.freebsd.org/data/111arm64-default/466765/logs/canu-1.6_2.log
Build URL:      http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-default&build=466765
Log:

=>> Building biology/canu
build started at Fri Apr 13 08:17:41 UTC 2018
port directory: /usr/ports/biology/canu
package name: canu-1.6_2
building for: FreeBSD 111arm64-default-job-16 11.1-RELEASE FreeBSD 11.1-RELEASE arm64
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/canu/Makefile 464084 2018-03-10 17:46:04Z gerald $
Poudriere version: 3.2.6-1-ga0ae87a0
Host OSVERSION: 1200060
Jail OSVERSION: 1101001
Job Id: 16

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MAKE_ARGS=
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---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--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--
PORTDOCS="" PORTEXAMPLES="" JAVASHAREDIR="share/java"  JAVAJARDIR="share/java/classes" OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.1  PERL_VER=5.26  PERL5_MAN1=lib/perl5/site_perl/man/man1  PERL5_MAN3=lib/perl5/site_perl/man/man3  SITE_PERL=lib/perl5/site_perl  SITE_ARCH=lib/perl5/site_perl/mach/5.26 DOCSDIR="share/doc/canu"  EXAMPLESDIR="share/examples/canu"  DATADIR="share/canu"  WWWDIR="www/canu"  ETCDIR="etc/canu"
--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--

---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
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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_CXXINTERNAL_acaad9ca=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
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ARCH=aarch64
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GID=0
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--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  1048576
stack size              (kbytes, -s)  1048576
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
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kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   canu-1.6_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5.txz
[111arm64-default-job-16] Installing pkg-1.10.5...
[111arm64-default-job-16] Extracting pkg-1.10.5: .......... done
===>   canu-1.6_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of canu-1.6_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.6_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.6_2 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_2 for building
===>  Extracting for canu-1.6_2
=> SHA256 Checksum OK for marbl-canu-v1.6_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for canu-1.6_2
===>  Applying FreeBSD patches for canu-1.6_2
/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_2 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_2.txz
[111arm64-default-job-16] Installing gmake-4.2.1_2...
[111arm64-default-job-16] `-- Installing gettext-runtime-0.19.8.1_1...
[111arm64-default-job-16] |   `-- Installing indexinfo-0.3.1...
[111arm64-default-job-16] |   `-- Extracting indexinfo-0.3.1: .... done
[111arm64-default-job-16] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[111arm64-default-job-16] Extracting gmake-4.2.1_2: .......... done
===>   canu-1.6_2 depends on executable: gmake - found
===>   Returning to build of canu-1.6_2
===>   canu-1.6_2 depends on executable: gcc6 - not found
===>   Installing existing package /packages/All/gcc6-6.4.0_4.txz
[111arm64-default-job-16] Installing gcc6-6.4.0_4...
[111arm64-default-job-16] `-- Installing binutils-2.30_2,1...
[111arm64-default-job-16] `-- Extracting binutils-2.30_2,1: .......... done
[111arm64-default-job-16] `-- Installing gmp-6.1.2...
[111arm64-default-job-16] `-- Extracting gmp-6.1.2: .......... done
[111arm64-default-job-16] `-- Installing mpc-1.1.0...
[111arm64-default-job-16] |   `-- Installing mpfr-3.1.6...
[111arm64-default-job-16] |   `-- Extracting mpfr-3.1.6: .......... done
[111arm64-default-job-16] `-- Extracting mpc-1.1.0: ...... done
[111arm64-default-job-16] Extracting gcc6-6.4.0_4: .......... done
Message from gcc6-6.4.0_4:

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_2 depends on executable: gcc6 - found
===>   Returning to build of canu-1.6_2
===>   canu-1.6_2 depends on file: /usr/local/bin/as - found
===>   canu-1.6_2 depends on package: perl5>=5.26<5.27 - not found
===>   Installing existing package /packages/All/perl5-5.26.1.txz
[111arm64-default-job-16] Installing perl5-5.26.1...
[111arm64-default-job-16] Extracting perl5-5.26.1: .......... done
Message from perl5-5.26.1:

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_2 depends on package: perl5>=5.26<5.27 - found
===>   Returning to build of canu-1.6_2
===========================================================================
=======================<phase: lib-depends    >============================
===>   canu-1.6_2 depends on shared library: libboost_regex.so - not found
===>   Installing existing package /packages/All/boost-libs-1.66.0_1.txz
[111arm64-default-job-16] Installing boost-libs-1.66.0_1...
[111arm64-default-job-16] `-- Installing icu-61.1,1...
[111arm64-default-job-16] `-- Extracting icu-61.1,1: .......... done
[111arm64-default-job-16] Extracting boost-libs-1.66.0_1: .......... done
Message from boost-libs-1.66.0_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_2 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)
===>   Returning to build of canu-1.6_2
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for canu-1.6_2
===========================================================================
=======================<phase: build          >============================
===>  Building for canu-1.6_2
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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