Skip site navigation (1)Skip section navigation (2)
Date:      Sat, 14 Apr 2018 23:12:48 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-armv6-default][biology/canu] Failed for canu-1.6_2 in build
Message-ID:  <201804142312.w3ENCmP6073328@beefy8.nyi.freebsd.org>

next in thread | raw e-mail | index | archive | help

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://beefy8.nyi.freebsd.org/data/head-armv6-default/p467121_s332419/logs/canu-1.6_2.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p467121_s332419
Log:

=>> Building biology/canu
build started at Sat Apr 14 21:41:55 UTC 2018
port directory: /usr/ports/biology/canu
package name: canu-1.6_2
building for: FreeBSD head-armv6-default-job-11 12.0-CURRENT FreeBSD 12.0-CURRENT 1200061 arm
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: 1200061
Job Id: 11




!!! Jail is newer than host. (Jail: 1200061, Host: 1200060) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1200061
UNAME_v=FreeBSD 12.0-CURRENT 1200061
UNAME_r=12.0-CURRENT
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
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.6-1-ga0ae87a0
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-armv6-default/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 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=12.0 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---
.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=arm
MACHINE_ARCH=armv6
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
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: armv6-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: armv6-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: armv6-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=12.0-CURRENT
OSREL=12.0
OSVERSION=1200061
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)  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 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
[head-armv6-default-job-11] Installing pkg-1.10.5...
[head-armv6-default-job-11] 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>============================
===========================================================================
<snip>
                 from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/multiway_mergesort.h: In function 'void __gnu_parallel::parallel_sort_mwms(_RAIter, _RAIter, _Compare, __gnu_parallel::_ThreadIndex) [with bool __stable = false; bool __exact = true; _RAIter = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     parallel_sort_mwms(_RAIter __begin, _RAIter __end,
     ^~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
In file included from /usr/local/lib/gcc6/include/c++/algorithm:62:0,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const anInput&, const anInput&)>]':
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
In file included from /usr/local/lib/gcc6/include/c++/bits/stl_algo.h:61:0,
                 from /usr/local/lib/gcc6/include/c++/algorithm:62,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _Distance = int; _Tp = anInput; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const anInput&, const anInput&)>]':
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/local/lib/gcc6/include/c++/algorithm:62:0,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const anInput&, const anInput&)>]':
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ^~~
In file included from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37:0,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/algo.h: In function 'void std::__parallel::sort(_RAIter, _RAIter, _Compare, _Parallelism) [with _RAIter = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _Compare = bool (*)(const anInput&, const anInput&); _Parallelism = __gnu_parallel::default_parallel_tag]':
/usr/local/lib/gcc6/include/c++/parallel/algo.h:1754:3: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
   sort(_RAIter __begin, _RAIter __end, _Compare __comp,
   ^~~~
/usr/local/lib/gcc6/include/c++/parallel/algo.h:1754:3: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
In file included from /usr/local/lib/gcc6/include/c++/parallel/algo.h:45:0,
                 from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/sort.h:105:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
       parallel_sort_mwms<__stable, true>
       ^~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc6/include/c++/algorithm:62:0,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ^~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ^~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
    std::__introsort_loop(__first, __last,
    ^~~
In file included from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37:0,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/algo.h: In function 'int main(int, char**)':
/usr/local/lib/gcc6/include/c++/parallel/algo.h:1867:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     sort(__begin, __end, __comp, __gnu_parallel::default_parallel_tag());
     ^~~~
In file included from /usr/local/lib/gcc6/include/c++/bits/stl_algo.h:61:0,
                 from /usr/local/lib/gcc6/include/c++/algorithm:62,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >; _Distance = int; _Tp = std::pair<anInput, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<anInput, int, bool (*)(const anInput&, const anInput&)> >]':
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
     __push_heap(_RandomAccessIterator __first,
     ^~~~~~~~~~~
In file included from /usr/local/lib/gcc6/include/c++/parallel/algo.h:57:0,
                 from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/merge.h: In function '_OutputIterator __gnu_parallel::__merge_advance_movc(_RAIter1&, _RAIter1, _RAIter2&, _RAIter2, _OutputIterator, _DifferenceTp, _Compare) [with _RAIter1 = anInput*; _RAIter2 = anInput*; _OutputIterator = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _DifferenceTp = int; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/parallel/merge.h:105:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     __merge_advance_movc(_RAIter1& __begin1, _RAIter1 __end1,
     ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc6/include/c++/parallel/multiway_mergesort.h:40:0,
                 from /usr/local/lib/gcc6/include/c++/parallel/sort.h:44,
                 from /usr/local/lib/gcc6/include/c++/parallel/algo.h:45,
                 from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_3_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<anInput*, anInput*>*, std::vector<std::pair<anInput*, anInput*>, std::allocator<std::pair<anInput*, anInput*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _DifferenceTp = int; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h:241:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     multiway_merge_3_variant(_RAIterIterator __seqs_begin,
     ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_4_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<anInput*, anInput*>*, std::vector<std::pair<anInput*, anInput*>, std::allocator<std::pair<anInput*, anInput*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _DifferenceTp = int; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h:360:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     multiway_merge_4_variant(_RAIterIterator __seqs_begin,
     ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc6/include/c++/bits/stl_algo.h:61:0,
                 from /usr/local/lib/gcc6/include/c++/algorithm:62,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >; _Distance = int; _Tp = std::pair<anInput, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<anInput, int, bool (*)(const anInput&, const anInput&)> >]':
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >; _Distance = int; _Tp = std::pair<anInput, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<anInput, int, bool (*)(const anInput&, const anInput&)> >]':
/usr/local/lib/gcc6/include/c++/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
In file included from /usr/local/lib/gcc6/include/c++/algorithm:62:0,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<anInput, int, bool (*)(const anInput&, const anInput&)> >]':
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ^~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<anInput, int, bool (*)(const anInput&, const anInput&)> >]':
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<anInput, int, bool (*)(const anInput&, const anInput&)> >]':
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<anInput*, anInput*>*, std::vector<std::pair<anInput*, anInput*>, std::allocator<std::pair<anInput*, anInput*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<anInput**, std::vector<anInput*, std::allocator<anInput*> > >; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
    std::__introsort_loop(__first, __last,
    ^~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ^~~
/usr/local/lib/gcc6/include/c++/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<anInput, int>*, std::vector<std::pair<anInput, int>, std::allocator<std::pair<anInput, int> > > >' will change in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ^~~
In file included from /usr/local/lib/gcc6/include/c++/parallel/multiway_mergesort.h:40:0,
                 from /usr/local/lib/gcc6/include/c++/parallel/sort.h:44,
                 from /usr/local/lib/gcc6/include/c++/parallel/algo.h:45,
                 from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_loser_tree(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with _LT = __gnu_parallel::_LoserTree<false, anInput, bool (*)(const anInput&, const anInput&)>; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<anInput*, anInput*>*, std::vector<std::pair<anInput*, anInput*>, std::allocator<std::pair<anInput*, anInput*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _DifferenceTp = int; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h:491:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     multiway_merge_loser_tree(_RAIterIterator __seqs_begin,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::__sequential_multiway_merge(_RAIterIterator, _RAIterIterator, _RAIter3, const typename std::iterator_traits<typename std::iterator_traits<_OI>::value_type::first_type>::value_type&, _DifferenceTp, _Compare) [with bool __stable = false; bool __sentinels = false; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<anInput*, anInput*>*, std::vector<std::pair<anInput*, anInput*>, std::allocator<std::pair<anInput*, anInput*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >; _DifferenceTp = int; _Compare = bool (*)(const anInput&, const anInput&)]':
/usr/local/lib/gcc6/include/c++/parallel/multiway_merge.h:920:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
     __sequential_multiway_merge(_RAIterIterator __seqs_begin,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc6/include/c++/parallel/algo.h:57:0,
                 from /usr/local/lib/gcc6/include/c++/parallel/algorithm:37,
                 from /usr/local/lib/gcc6/include/c++/algorithm:65,
                 from fastq-utilities/fastqSample.C:45:
/usr/local/lib/gcc6/include/c++/parallel/merge.h:179:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<anInput*, std::vector<anInput> >' will change in GCC 7.1
       __target, __max_length, __comp);
                                     ^
g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/fastqSample -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -L/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/obj/fastqSample/fastq-utilities/fastqSample.o -lcanu
g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/obj/fastqSimulate/fastq-utilities/fastqSimulate.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses -fomit-frame-pointer -g3 -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src -IAS_UTL fastq-utilities/fastqSimulate.C
g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/fastqSimulate -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -L/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/obj/fastqSimulate/fastq-utilities/fastqSimulate.o -lcanu
g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/obj/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses -fomit-frame-pointer -g3 -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src -IAS_UTL fastq-utilities/fastqSimulate-sort.C
fastq-utilities/fastqSimulate-sort.C: In function 'int main(int, char**)':
fastq-utilities/fastqSimulate-sort.C:252:66: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'std::vector<pairedRead>::size_type {aka unsigned int}' [-Wformat=]
   fprintf(stderr, "Loaded " F_U64 " mated reads.\n", reads.size());
                                                                  ^
g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/fastqSimulate-sort -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -L/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/obj/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -lcanu
cp -pf pipelines/canu.pl /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/canu
chmod +x /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/canu
echo > /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/canu.defaults  "# Add site specific options (for setting up Grid or limiting memory/threads) here."
chmod -x /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/canu.defaults
cp -pf pipelines/canu/Consensus.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/CorrectReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Configure.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Defaults.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/ErrorEstimate.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Execution.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Gatekeeper.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid_Cloud.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid_DNANexus.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid_LSF.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid_PBSTorque.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid_SGE.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Grid_Slurm.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/HTML.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Meryl.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Output.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/OverlapBasedTrimming.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/OverlapErrorAdjustment.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/OverlapInCore.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/OverlapMhap.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/OverlapMMap.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/OverlapStore.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Report.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/
cp -pf pipelines/canu/Unitig.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/lib/canu/

Success!
canu installed in /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm/bin/canu
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src'
mv: rename /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-armv6/bin/lib/canu to /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-armv6/lib/perl5/site_perl/canu: No such file or directory
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/canu



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201804142312.w3ENCmP6073328>