Date: Thu, 5 Dec 2019 05:53:28 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/canu] Failed for canu-1.8_5 in build Message-ID: <201912050553.xB55rSZV021562@beefy13.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: jbeich@FreeBSD.org Ident: $FreeBSD: branches/2019Q4/biology/canu/Makefile 509290 2019-08-19 15:35:27Z jbeich $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/519056/logs/canu-1.8_5.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=519056 Log: =>> Building biology/canu build started at Thu Dec 5 05:42:20 UTC 2019 port directory: /usr/ports/biology/canu package name: canu-1.8_5 building for: FreeBSD 120armv7-quarterly-job-11 12.0-RELEASE-p12 FreeBSD 12.0-RELEASE-p12 1200086 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q4/biology/canu/Makefile 509290 2019-08-19 15:35:27Z jbeich $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300047 Jail OSVERSION: 1200086 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p12 1200086 UNAME_r=12.0-RELEASE-p12 BLOCKSIZE=K 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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. 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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 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) 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_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) 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-RELEASE-p12 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---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-1.8_5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz [120armv7-quarterly-job-11] Installing pkg-1.12.0... [120armv7-quarterly-job-11] Extracting pkg-1.12.0: .......... done ===> canu-1.8_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-1.8_5 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.8_5 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.8_5 for building => SHA256 Checksum OK for marbl-canu-v1.8_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.8_5 for building ===> Extracting for canu-1.8_5 => SHA256 Checksum OK for marbl-canu-v1.8_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ <snip> | ^~~~~~~ utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:252:20: error: expected ';' at end of member declaration 252 | virtual void * get_deleter( detail::sp_typeinfo const & ti ) | ^~~~~~~~~~~ | ; utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:252:52: error: expected ')' before 'const' 252 | virtual void * get_deleter( detail::sp_typeinfo const & ti ) | ~ ^~~~~~ | ) In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28, from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 395 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28, from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:518:12: error: expected ';' at end of member declaration 518 | void * get_deleter( sp_typeinfo const & ti ) const | ^~~~~~~~~~~ | ; utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:518:36: error: expected ')' before 'const' 518 | void * get_deleter( sp_typeinfo const & ti ) const | ~ ^~~~~~ | ) In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 242 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 441 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 454 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 529 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:695:12: error: expected ';' at end of member declaration 695 | void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT | ^~~~~~~~~~~~~~~~~~~~~ | ; utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:695:61: error: expected ')' before 'const' 695 | void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT | ~ ^~~~~~ | ) In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)': utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 531 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/local/lib/gcc9/include/c++/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: /usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:69, from utgcns/libcns/unitigConsensus.C:77: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In function 'D* boost::detail::basic_get_deleter(const boost::shared_ptr<U>&)': utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:887:71: error: expected primary-expression before ')' token 887 | return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) ); | ^ utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:887:54: error: there are no arguments to 'BOOST_SP_TYPEID' that depend on a template parameter, so a declaration of 'BOOST_SP_TYPEID' must be available [-fpermissive] 887 | return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) ); | ^~~~~~~~~~~~~~~ utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:887:54: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) utgcns/libcns/unitigConsensus.C: In member function 'bool unitigConsensus::alignFragment(bool)': utgcns/libcns/unitigConsensus.C:1562:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1562 | oaFull->display("utgCns::alignFragment()--", true); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ utgcns/libcns/unitigConsensus.C:1660:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1660 | oaFull->display("utgCns::alignFragment()-- ", true); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmake[1]: *** [Makefile:705: /wrkdirs/usr/ports/biology/canu/work/canu-1.8/src/usr/local/FreeBSD-armv7/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.8/src' *** Error code 1 Stop. make: stopped in /usr/ports/biology/canu
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