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Maintainer: po...@freebsd.org Last committer: amd...@freebsd.org Ident: $FreeBSD: head/biology/lamarc/Makefile 420392 2016-08-18 09:31:58Z amdmi3 $ Log URL: http://beefy11.nyi.freebsd.org/data/head-i386-default/p469985_s333618/logs/lamarc-2.1.8_1,1.log Build URL: http://beefy11.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p469985_s333618 Log: =>> Building biology/lamarc build started at Wed May 16 02:53:30 UTC 2018 port directory: /usr/ports/biology/lamarc package name: lamarc-2.1.8_1,1 building for: FreeBSD head-i386-default-job-07 12.0-CURRENT FreeBSD 12.0-CURRENT 1200063 i386 maintained by: po...@freebsd.org Makefile ident: $FreeBSD: head/biology/lamarc/Makefile 420392 2016-08-18 09:31:58Z amdmi3 $ Poudriere version: 3.2.6-3-g832b198d Host OSVERSION: 1200062 Jail OSVERSION: 1200063 Job Id: 07 !!! Jail is newer than host. (Jail: 1200063, 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=i386 UNAME_m=i386 OSVERSION=1200063 UNAME_v=FreeBSD 12.0-CURRENT 1200063 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=3.2.6-3-g832b198d MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-i386-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 lamarc-2.1.8_1,1: DOCS=on: Build and/or install documentation WXGTK=off: wxGTK GUI toolkit support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- po...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-converter --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/lamarc/work HOME=/wrkdirs/usr/ports/biology/lamarc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/lamarc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/lamarc/work HOME=/wrkdirs/usr/ports/biology/lamarc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/lamarc/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing " 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="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/lamarc" EXAMPLESDIR="share/examples/lamarc" DATADIR="share/lamarc" WWWDIR="www/lamarc" ETCDIR="etc/lamarc" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/lamarc DOCSDIR=/usr/local/share/doc/lamarc EXAMPLESDIR=/usr/local/share/examples/lamarc WWWDIR=/usr/local/www/lamarc ETCDIR=/usr/local/etc/lamarc --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 MACHINE=i386 MACHINE_ARCH=i386 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_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-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" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200063 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--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 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 lamarc 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 APACHE20 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> lamarc-2.1.8_1,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [head-i386-default-job-07] Installing pkg-1.10.5_1... [head-i386-default-job-07] Extracting pkg-1.10.5_1: .......... done ===> lamarc-2.1.8_1,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of lamarc-2.1.8_1,1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The lamarc 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 APACHE20 accepted by the user ===> Fetching all distfiles required by lamarc-2.1.8_1,1 for building =========================================================================== <snip> InputStream& extract_uniform_int(InputStream& is, UniformInt& ud, Impl& impl) ^ In file included from src/report/xml_report.cpp:15: In file included from ./src/force/force.h:16: In file included from ./src/postlike/plforces.h:29: ./src/tree/summary.h:33:1: warning: class 'Interval' was previously declared as a struct [-Wmismatched-tags] class Interval; ^ ./src/tree/intervaldata.h:55:8: note: previous use is here struct Interval ^ ./src/tree/summary.h:33:1: note: did you mean struct here? class Interval; ^~~~~ struct ./src/tree/summary.h:195:52: warning: unused parameter 'totals' [-Wunused-parameter] virtual void AdjustSummary(const DoubleVec1d & totals, long region) {}; ^ ./src/tree/summary.h:195:65: warning: unused parameter 'region' [-Wunused-parameter] virtual void AdjustSummary(const DoubleVec1d & totals, long region) {}; ^ In file included from src/report/xml_report.cpp:15: In file included from ./src/force/force.h:16: ./src/postlike/plforces.h:401:45: warning: unused parameter 'param' [-Wunused-parameter] double DlnWait (const vector < double >¶m, ^ ./src/postlike/plforces.h:402:41: warning: unused parameter 'treedata' [-Wunused-parameter] const TreeSummary * treedata, ^ ./src/postlike/plforces.h:403:33: warning: unused parameter 'whichparam' [-Wunused-parameter] const long &whichparam) { assert(false); return 0;}; ^ ./src/postlike/plforces.h:405:46: warning: unused parameter 'param' [-Wunused-parameter] double DlnPoint (const vector < double >¶m, ^ ./src/postlike/plforces.h:406:42: warning: unused parameter 'treedata' [-Wunused-parameter] const TreeSummary * treedata, ^ ./src/postlike/plforces.h:407:34: warning: unused parameter 'whichparam' [-Wunused-parameter] const long &whichparam) { assert(false); return 0;}; ^ ./src/postlike/plforces.h:468:44: warning: unused parameter 'param' [-Wunused-parameter] double lnWait (const vector < double >¶m, ^ ./src/postlike/plforces.h:469:40: warning: unused parameter 'treedata' [-Wunused-parameter] const TreeSummary * treedata) { return 1.0; }; ^ ./src/postlike/plforces.h:471:45: warning: unused parameter 'param' [-Wunused-parameter] double lnPoint (const vector < double >¶m, ^ ./src/postlike/plforces.h:472:45: warning: unused parameter 'lparam' [-Wunused-parameter] const vector < double >&lparam, ^ ./src/postlike/plforces.h:473:41: warning: unused parameter 'treedata' [-Wunused-parameter] const TreeSummary * treedata) { return 1.0; }; ^ ./src/postlike/plforces.h:475:45: warning: unused parameter 'param' [-Wunused-parameter] double DlnWait (const vector < double >¶m, ^ ./src/postlike/plforces.h:476:41: warning: unused parameter 'treedata' [-Wunused-parameter] const TreeSummary * treedata, ^ ./src/postlike/plforces.h:477:33: warning: unused parameter 'whichparam' [-Wunused-parameter] const long &whichparam) { return 1.0; }; ^ ./src/postlike/plforces.h:479:46: warning: unused parameter 'param' [-Wunused-parameter] double DlnPoint (const vector < double >¶m, ^ ./src/postlike/plforces.h:480:42: warning: unused parameter 'treedata' [-Wunused-parameter] const TreeSummary * treedata, ^ ./src/postlike/plforces.h:481:34: warning: unused parameter 'whichparam' [-Wunused-parameter] const long &whichparam) { return 1.0; }; ^ In file included from src/report/xml_report.cpp:15: ./src/force/force.h:256:61: warning: unused parameter 'fs' [-Wunused-parameter] virtual void ModifyEvents(const ForceSummary& fs, ^ ./src/force/force.h:549:61: warning: unused parameter 'mystatus' [-Wunused-parameter] virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); }; ^ ./src/force/force.h:583:61: warning: unused parameter 'mystatus' [-Wunused-parameter] virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); }; ^ In file included from src/report/xml_report.cpp:18: In file included from ./src/datalike/region.h:38: ./src/tree/newick.h:46:37: warning: unused parameter 'stump' [-Wunused-parameter] virtual void ToLamarcTree(Tree& stump) { assert(false); }; // instantiating NULL tree ^ In file included from src/report/xml_report.cpp:19: ./src/report/reportpage.h:29:1: warning: class 'PlotStruct' was previously declared as a struct [-Wmismatched-tags] class PlotStruct; ^ ./src/postlike/plotstat.h:26:8: note: previous use is here struct PlotStruct ^ ./src/report/reportpage.h:29:1: note: did you mean struct here? class PlotStruct; ^~~~~ struct ./src/report/reportpage.h:212:10: warning: 'ProfPage::PrintTable' hides overloaded virtual function [-Woverloaded-virtual] void PrintTable(StringVec3d& wrappedtable); ^ ./src/report/reportpage.h:106:18: note: hidden overloaded virtual function 'ReportPage::PrintTable' declared here: different number of parameters (4 vs 1) virtual void PrintTable(vector<string> &colhdr, StringVec2d &rowhdr, ^ src/report/xml_report.cpp:39:36: warning: unused parameter 'tag' [-Wunused-parameter] force_type tag, ^ In file included from src/report/xml_report.cpp:13: In file included from ./src/control/chainmanager.h:30: In file included from ./src/control/chainpack.h:18: In file included from ./src/control/chainout.h:31: In file included from /usr/include/c++/v1/map:442: /usr/include/c++/v1/__tree:1819:22: warning: the specified comparator type does not provide a const call operator [-Wuser-defined-warnings] __trigger_diagnostics()), ""); ^ /usr/include/c++/v1/set:400:28: note: in instantiation of member function 'std::__1::__tree<std::__1::pair<long, long>, rangecmp, std::__1::allocator<std::__1::pair<long, long> > >::~__tree' requested here class _LIBCPP_TEMPLATE_VIS set ^ /usr/include/c++/v1/__tree:970:7: note: from 'diagnose_if' attribute on '__trigger_diagnostics': _LIBCPP_DIAGNOSE_WARNING(!__invokable<_Compare const&, _Tp const&, _Tp const&>::value, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__config:1130:20: note: expanded from macro '_LIBCPP_DIAGNOSE_WARNING' __attribute__((diagnose_if(__VA_ARGS__, "warning"))) ^ ~~~~~~~~~~~ 77 warnings generated. mv -f .deps/lamarc-xml_report.Tpo .deps/lamarc-xml_report.Po c++ -DHAVE_CONFIG_H -I. -I./config -DLAMARC_COMPILE_LINUX -DNDEBUG -Wall -Wextra -Wno-unused -I ./config -I ./config -I ./src/bayeslike -I ./src/control -I ./src/conversion -I ./src/convErr -I ./src/convModel -I ./src/convParse -I ./src/convStrings -I ./src/convUtil -I ./src/datalike -I ./src/force -I ./src/guiconv -I ./src/guiutil -I ./src/lamarcmenus -I ./src/menu -I ./src/postlike -I ./src/report -I ./src/tools -I ./src/tree -I ./src/ui_interface -I ./src/ui_util -I ./src/ui_vars -I ./src/xml -I ./boost -I ./resources -I ./tinyxml -DTIXML_USE_STL -O2 -pipe -fstack-protector -fno-strict-aliasing -MT lamarc-mathx.o -MD -MP -MF .deps/lamarc-mathx.Tpo -c -o lamarc-mathx.o `test -f 'src/tools/mathx.cpp' || echo './'`src/tools/mathx.cpp In file included from src/tools/mathx.cpp:21: In file included from ./src/control/registry.h:22: In file included from ./src/tools/random.h:15: In file included from ./boost/random.hpp:42: In file included from ./boost/random/ranlux.hpp:21: ./boost/random/discard_block.hpp:68:38: warning: unused parameter 'x' [-Wunused-parameter] static bool validation(result_type x) { return true; } // dummy ^ In file included from src/tools/mathx.cpp:21: In file included from ./src/control/registry.h:22: In file included from ./src/tools/random.h:15: In file included from ./boost/random.hpp:53: In file included from ./boost/random/random_number_generator.hpp:22: In file included from ./boost/random/uniform_int.hpp:26: ./boost/random/uniform_smallint.hpp:39:63: warning: unused parameter 'ud' [-Wunused-parameter] InputStream& extract_uniform_int(InputStream& is, UniformInt& ud, Impl& impl) ^ In file included from src/tools/mathx.cpp:21: In file included from ./src/control/registry.h:24: In file included from ./src/control/regiongammainfo.h:16: ./src/force/paramstat.h:99:59: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; ^ ./src/force/paramstat.h:100:54: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_identical); }; ^ ./src/force/paramstat.h:121:59: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_constant); }; ^ ./src/force/paramstat.h:122:54: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; ^ ./src/force/paramstat.h:163:59: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; ^ ./src/force/paramstat.h:164:54: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; ^ ./src/force/paramstat.h:181:59: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; ^ ./src/force/paramstat.h:182:54: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; ^ ./src/force/paramstat.h:201:59: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; ^ ./src/force/paramstat.h:202:54: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; ^ ./src/force/paramstat.h:219:59: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; ^ ./src/force/paramstat.h:220:54: warning: unused parameter 'ftype' [-Wunused-parameter] virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; ^ src/tools/mathx.cpp:781:12: error: no matching function for call to 'make_pair' return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/utility:639:1: note: candidate function not viable: no known conversion from 'DoubleVec1d' (aka 'vector<double>') to 'std::__1::vector<double, std::__1::allocator<double> > &&' for 1st argument make_pair(_T1&& __t1, _T2&& __t2) ^ 14 warnings and 1 error generated. *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8 *** Error code 1 Stop. make: stopped in /usr/ports/biology/lamarc _______________________________________________ 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"
