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Maintainer: po...@freebsd.org Last committer: w...@freebsd.org Ident: $FreeBSD: head/biology/libsbml/Makefile 473289 2018-06-25 01:37:52Z wen $ Log URL: http://beefy12.nyi.freebsd.org/data/head-amd64-default/p474481_s336216/logs/libsbml-5.17.0.log Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p474481_s336216 Log: =>> Building biology/libsbml build started at Thu Jul 12 13:24:30 UTC 2018 port directory: /usr/ports/biology/libsbml package name: libsbml-5.17.0 building for: FreeBSD head-amd64-default-job-01 12.0-CURRENT FreeBSD 12.0-CURRENT 1200072 amd64 maintained by: po...@freebsd.org Makefile ident: $FreeBSD: head/biology/libsbml/Makefile 473289 2018-06-25 01:37:52Z wen $ Poudriere version: 3.2.7-1-g7087c444 Host OSVERSION: 1200069 Jail OSVERSION: 1200072 Job Id: 01 !!! Jail is newer than host. (Jail: 1200072, Host: 1200069) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200072 UNAME_v=FreeBSD 12.0-CURRENT 1200072 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 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.7-1-g7087c444 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-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--- ===> The following configuration options are available for libsbml-5.17.0: EXAMPLES=on: Build and/or install examples PYTHON=off: Python bindings or support RUBY=off: Ruby bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- po...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsbml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsbml/work HOME=/wrkdirs/usr/ports/biology/libsbml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/libsbml/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsbml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsbml/work HOME=/wrkdirs/usr/ports/biology/libsbml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/libsbml/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 DESTDIR=/wrkdirs/usr/ports/biology/libsbml/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" -L/usr/lib -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG" 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-- PORTVERSION=5.17.0 PORTDOCS="" PORTEXAMPLES="" EXAMPLES="" NO_EXAMPLES="@comment " PYTHON="@comment " NO_PYTHON="" RUBY="@comment " NO_RUBY="" CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/libsbml" EXAMPLESDIR="share/examples/libsbml" DATADIR="share/libsbml" WWWDIR="www/libsbml" ETCDIR="etc/libsbml" --End PLIST_SUB-- --SUB_LIST-- EXAMPLES="" NO_EXAMPLES="@comment " PYTHON="@comment " NO_PYTHON="" RUBY="@comment " NO_RUBY="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/libsbml DOCSDIR=/usr/local/share/doc/libsbml EXAMPLESDIR=/usr/local/share/examples/libsbml WWWDIR=/usr/local/www/libsbml ETCDIR=/usr/local/etc/libsbml --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. 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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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: x86_64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: x86_64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/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_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: x86_64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200072 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.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 >============================ ===> NOTICE: The libsbml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License LGPL21 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> libsbml-5.17.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [head-amd64-default-job-01] Installing pkg-1.10.5_1... [head-amd64-default-job-01] Extracting pkg-1.10.5_1: .......... done ===> libsbml-5.17.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of libsbml-5.17.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The libsbml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: <snip> -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR) -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Looking for gzopen in /usr/lib/libz.so -- Looking for gzopen in /usr/lib/libz.so - found -- Looking for include file check.h -- Looking for include file check.h - not found -- Looking for include file expat.h -- Looking for include file expat.h - not found -- Looking for include file errno.h -- Looking for include file errno.h - found -- Looking for include file ieeefp.h -- Looking for include file ieeefp.h - found -- Looking for include file math.h -- Looking for include file math.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file float.h -- Looking for include file float.h - found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for sqrt in m -- Looking for sqrt in m - found -- ---------------------------------------------------------------------- libSBML version 5.17.0 ---------------------------------------------------------------------- More information and the latest version are available online at http://sbml.org/Software/libSBML Please report problems using the issue tracker at http://sbml.org/Software/libsbml/issue-tracker To contact the developers directly, email libsbml-t...@googlegroups.com Configured on host 'head-amd64-default-job-01' host type = FreeBSD host operating system = FreeBSD 12.0-CURRENT host CPU architecture = amd64 General build flags: CC = /usr/bin/cc CXX = /usr/bin/c++ CPPFLAGS = -DLINUX CFLAGS = -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC LDFLAGS = -L/usr/lib -fstack-protector XML parser library configuration: XML library = libxml2 CPPFLAGS for XML = -I/usr/local/include/libxml2 LIBS for XML = /usr/local/lib/libxml2.so Other libSBML configuration settings: Installation $prefix = /usr/local -- Value of $LD_LIBRARY_PATH = -- Using SWIG = SWIG_EXECUTABLE-NOTFOUND (Version ) -- Using C++ namespace ('libsbml') = no -- -- Build examples = no -- -- Use Legacy Math = no -- -- Support for SBML Level 3 Packages: -- SBML 'layout' package = OFF -- -- Other potentially important settings: -- Compression support is enabled for .zip and .gz files -- Compression support is enabled for .bz2 files -- ---------------------------------------------------------------------- -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE ICONV_INCLUDE_DIR ICONV_LIBRARIES ICONV_LIBRARY LIBICONV_INCLUDE_DIR LIBICONV_LIBRARIES LIBICONV_LIBRARY 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src/CMakeFiles/sbml-static.dir/sbml/ListOf.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/ListOf.cpp [49/465] /usr/bin/c++ -DLIBSBML_COMPILED_IN_SRC -DLINUX -DUSE_BZ2 -DUSE_LIBXML -DUSE_ZLIB -Isrc/src/sbml -Isrc/src -Isrc -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml -I/usr/local/include/libxml2 -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -MD -MT src/CMakeFiles/sbml-static.dir/sbml/LocalParameter.cpp.o -MF src/CMakeFiles/sbml-static.dir/sbml/LocalParameter.cpp.o.d -o src/CMakeFiles/sbml-static.dir/sbml/LocalParameter.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/LocalParameter.cpp [50/465] /usr/bin/c++ -DLIBSBML_COMPILED_IN_SRC -DLINUX -DUSE_BZ2 -DUSE_LIBXML -DUSE_ZLIB -Isrc/src/sbml -Isrc/src -Isrc -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml -I/usr/local/include/libxml2 -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -MD -MT src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -MF src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o.d -o src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp FAILED: src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o /usr/bin/c++ -DLIBSBML_COMPILED_IN_SRC -DLINUX -DUSE_BZ2 -DUSE_LIBXML -DUSE_ZLIB -Isrc/src/sbml -Isrc/src -Isrc -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src -I/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml -I/usr/local/include/libxml2 -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC -O2 -pipe -I/usr/include -DLIBICONV_PLUG -fstack-protector -fno-strict-aliasing -DLIBICONV_PLUG -MD -MT src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -MF src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o.d -o src/CMakeFiles/sbml-static.dir/sbml/Model.cpp.o -c /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207: /usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted {__nc = __v.__cc; return *this;} ^ /usr/include/c++/v1/__tree:1645:35: note: in instantiation of member function 'std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>::operator=' requested here __cache->__value_ = *__first; ^ /usr/include/c++/v1/__tree:1575:9: note: in instantiation of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::__map_value_compare<std::__1::pair<const std::__1::basic_string<char>, int>, std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::less<std::__1::pair<const std::__1::basic_string<char>, int> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *> > >::__assign_multi<std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::__tree_node<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, void *> *, long> >' requested here __assign_multi(__t.begin(), __t.end()); ^ /usr/include/c++/v1/map:912:21: note: in instantiation of member function 'std::__1::__tree<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::__map_value_compare<std::__1::pair<const std::__1::basic_string<char>, int>, std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>, std::__1::less<std::__1::pair<const std::__1::basic_string<char>, int> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *> > >::operator=' requested here __tree_ = __m.__tree_; ^ /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:243:19: note: in instantiation of member function 'std::__1::map<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *, std::__1::less<std::__1::pair<const std::__1::basic_string<char>, int> >, std::__1::allocator<std::__1::pair<const std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *> > >::operator=' requested here mUnitsDataMap = rhs.mUnitsDataMap; ^ /usr/include/c++/v1/utility:325:5: note: copy assignment operator is implicitly deleted because 'pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' has a user-declared move constructor pair(pair&&) = default; ^ 1 error generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/libsbml _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list 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