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Maintainer: j...@freebsd.org Last committer: j...@freebsd.org Ident: $FreeBSD: head/biology/canu/Makefile 468321 2018-04-26 04:16:15Z jwb $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p472108_s334906/logs/canu-1.7.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p472108_s334906 Log: =>> Building biology/canu build started at Tue Jun 12 19:20:12 UTC 2018 port directory: /usr/ports/biology/canu package name: canu-1.7 building for: FreeBSD head-armv7-default-job-22 12.0-CURRENT FreeBSD 12.0-CURRENT 1200067 arm maintained by: j...@freebsd.org Makefile ident: $FreeBSD: head/biology/canu/Makefile 468321 2018-04-26 04:16:15Z jwb $ Poudriere version: 3.2.7-1-g7087c444 Host OSVERSION: 1200062 Jail OSVERSION: 1200067 Job Id: 22 !!! Jail is newer than host. (Jail: 1200067, Host: 1200062) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200067 UNAME_v=FreeBSD 12.0-CURRENT 1200067 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=3.2.7-1-g7087c444 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-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-- j...@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-1.7/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 CC="gcc6" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing" CPP="cpp6" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/l ib/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=5.26.2 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=armv7 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: armv7-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: armv7-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: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200067 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-1.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [head-armv7-default-job-22] Installing pkg-1.10.5_1... [head-armv7-default-job-22] Extracting pkg-1.10.5_1: .......... done ===> canu-1.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-1.7 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.7 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.7 for building => SHA256 Checksum OK for marbl-canu-v1.7_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== <snip> from /usr/local/lib/gcc6/include/c++/algorithm:65, from fastq-utilities/fastqSample.C:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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:47: /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-1.7/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-1.7/src/usr/local/FreeBSD-arm/lib /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/obj/bin/fastqSample/fastq-utilities/fastqSample.o -lcanu g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/obj/bin/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-1.7/src -IAS_UTL fastq-utilities/fastqSimulate.C g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/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-1.7/src/usr/local/FreeBSD-arm/lib /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/obj/bin/fastqSimulate/fastq-utilities/fastqSimulate.o -lcanu g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/obj/bin/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-1.7/src -IAS_UTL fastq-utilities/fastqSimulate-sort.C g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/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-1.7/src/usr/local/FreeBSD-arm/lib /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -lcanu cp -pf pipelines/canu.pl /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/bin/canu chmod +x /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/bin/canu cp -pf pipelines/trioCanu.pl /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/bin/trioCanu chmod +x /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/bin/trioCanu echo > /wrkdirs/usr/ports/biology/canu/work/canu-1.7/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-1.7/src/usr/local/FreeBSD-arm/bin/canu.defaults cp -pf mhap/mhap-2.1.3.jar /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/share/java/classes/mhap-2.1.3.jar cp -pf pipelines/canu/Consensus.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/CorrectReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/ErrorEstimate.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Gatekeeper.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Cloud.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_PBSTorque.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_SGE.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Slurm.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Meryl.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Output.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMhap.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMMap.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapStore.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/lib/site_perl/canu/ Success! canu installed in /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm/bin/canu gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src' /bin/mkdir -p /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/perl5 /bin/mv /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/site_perl /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/perl5 mv: rename /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/site_perl to /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/perl5/site_perl: No such file or directory *** Error code 1 Stop. make: stopped in /usr/ports/biology/canu _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
