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Maintainer: po...@freebsd.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/pabcd5eaf5ec8_s3df987c99d1/logs/lamarc-2.1.8_1,1.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pabcd5eaf5ec8_s3df987c99d1 Log: =>> Building biology/lamarc build started at Wed Sep 11 20:31:45 UTC 2024 port directory: /usr/ports/biology/lamarc package name: lamarc-2.1.8_1,1 building for: FreeBSD main-amd64-default-job-05 15.0-CURRENT FreeBSD 15.0-CURRENT 1500023 amd64 maintained by: po...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 878 Aug 20 2023 /usr/ports/biology/lamarc/Makefile Ports top last git commit: abcd5eaf5ec Ports top unclean checkout: no Port dir last git commit: bb82d0e6e11 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1500023 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500023 UNAME_v=FreeBSD 15.0-CURRENT 1500023 UNAME_r=15.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-amd64-default/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= 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 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/lamarc/work/.cache 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/lamarc/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/lamarc/work/.cache 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/lamarc/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++98 " 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="" OSREL=15.0 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--- # 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 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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) 8192 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 >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License APACHE20 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> lamarc-2.1.8_1,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [main-amd64-default-job-05] Installing pkg-1.21.3... [main-amd64-default-job-05] Extracting pkg-1.21.3: .......... 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 >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by lamarc-2.1.8_1,1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by lamarc-2.1.8_1,1 for building => SHA256 Checksum OK for lamarc-2.1.8-src.tar.gz. <snip> In file included from ./src/postlike/plforces.h:29: In file included from ./src/tree/summary.h:30: 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] 39 | 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; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 33 | class Interval; | ^ ./src/tree/intervaldata.h:55:8: note: previous use is here 55 | struct Interval | ^ ./src/tree/summary.h:33:1: note: did you mean struct here? 33 | class Interval; | ^~~~~ | struct ./src/tree/summary.h:195:52: warning: unused parameter 'totals' [-Wunused-parameter] 195 | virtual void AdjustSummary(const DoubleVec1d & totals, long region) {}; | ^ ./src/tree/summary.h:195:65: warning: unused parameter 'region' [-Wunused-parameter] 195 | 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] 401 | double DlnWait (const vector < double >¶m, | ^ ./src/postlike/plforces.h:402:41: warning: unused parameter 'treedata' [-Wunused-parameter] 402 | const TreeSummary * treedata, | ^ ./src/postlike/plforces.h:403:33: warning: unused parameter 'whichparam' [-Wunused-parameter] 403 | const long &whichparam) { assert(false); return 0;}; | ^ ./src/postlike/plforces.h:405:46: warning: unused parameter 'param' [-Wunused-parameter] 405 | double DlnPoint (const vector < double >¶m, | ^ ./src/postlike/plforces.h:406:42: warning: unused parameter 'treedata' [-Wunused-parameter] 406 | const TreeSummary * treedata, | ^ ./src/postlike/plforces.h:407:34: warning: unused parameter 'whichparam' [-Wunused-parameter] 407 | const long &whichparam) { assert(false); return 0;}; | ^ ./src/postlike/plforces.h:468:44: warning: unused parameter 'param' [-Wunused-parameter] 468 | double lnWait (const vector < double >¶m, | ^ ./src/postlike/plforces.h:469:40: warning: unused parameter 'treedata' [-Wunused-parameter] 469 | const TreeSummary * treedata) { return 1.0; }; | ^ ./src/postlike/plforces.h:471:45: warning: unused parameter 'param' [-Wunused-parameter] 471 | double lnPoint (const vector < double >¶m, | ^ ./src/postlike/plforces.h:472:45: warning: unused parameter 'lparam' [-Wunused-parameter] 472 | const vector < double >&lparam, | ^ ./src/postlike/plforces.h:473:41: warning: unused parameter 'treedata' [-Wunused-parameter] 473 | const TreeSummary * treedata) { return 1.0; }; | ^ ./src/postlike/plforces.h:475:45: warning: unused parameter 'param' [-Wunused-parameter] 475 | double DlnWait (const vector < double >¶m, | ^ ./src/postlike/plforces.h:476:41: warning: unused parameter 'treedata' [-Wunused-parameter] 476 | const TreeSummary * treedata, | ^ ./src/postlike/plforces.h:477:33: warning: unused parameter 'whichparam' [-Wunused-parameter] 477 | const long &whichparam) { return 1.0; }; | ^ ./src/postlike/plforces.h:479:46: warning: unused parameter 'param' [-Wunused-parameter] 479 | double DlnPoint (const vector < double >¶m, | ^ ./src/postlike/plforces.h:480:42: warning: unused parameter 'treedata' [-Wunused-parameter] 480 | const TreeSummary * treedata, | ^ ./src/postlike/plforces.h:481:34: warning: unused parameter 'whichparam' [-Wunused-parameter] 481 | 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] 256 | virtual void ModifyEvents(const ForceSummary& fs, | ^ ./src/force/force.h:549:61: warning: unused parameter 'mystatus' [-Wunused-parameter] 549 | virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); }; | ^ ./src/force/force.h:583:61: warning: unused parameter 'mystatus' [-Wunused-parameter] 583 | 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] 46 | 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; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 29 | class PlotStruct; | ^ ./src/postlike/plotstat.h:26:8: note: previous use is here 26 | struct PlotStruct | ^ src/report/reportpage.h:29:1: note: did you mean struct here? 29 | class PlotStruct; | ^~~~~ | struct src/report/reportpage.h:212:10: warning: 'ProfPage::PrintTable' hides overloaded virtual function [-Woverloaded-virtual] 212 | 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) 106 | virtual void PrintTable(vector<string> &colhdr, StringVec2d &rowhdr, | ^ src/report/xml_report.cpp:39:36: warning: unused parameter 'tag' [-Wunused-parameter] 39 | force_type tag, | ^ --- lamarc-mathx.o --- 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] 68 | 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] 39 | 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] 99 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; | ^ ./src/force/paramstat.h:100:54: warning: unused parameter 'ftype' [-Wunused-parameter] 100 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_identical); }; | ^ ./src/force/paramstat.h:121:59: warning: unused parameter 'ftype' [-Wunused-parameter] 121 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_constant); }; | ^ ./src/force/paramstat.h:122:54: warning: unused parameter 'ftype' [-Wunused-parameter] 122 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; | ^ ./src/force/paramstat.h:163:59: warning: unused parameter 'ftype' [-Wunused-parameter] 163 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; | ^ ./src/force/paramstat.h:164:54: warning: unused parameter 'ftype' [-Wunused-parameter] 164 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; | ^ ./src/force/paramstat.h:181:59: warning: unused parameter 'ftype' [-Wunused-parameter] 181 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; | ^ ./src/force/paramstat.h:182:54: warning: unused parameter 'ftype' [-Wunused-parameter] 182 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; | ^ ./src/force/paramstat.h:201:59: warning: unused parameter 'ftype' [-Wunused-parameter] 201 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; | ^ ./src/force/paramstat.h:202:54: warning: unused parameter 'ftype' [-Wunused-parameter] 202 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); }; | ^ ./src/force/paramstat.h:219:59: warning: unused parameter 'ftype' [-Wunused-parameter] 219 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); }; | ^ ./src/force/paramstat.h:220:54: warning: unused parameter 'ftype' [-Wunused-parameter] 220 | 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' 781 | return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__utility/pair.h:599:5: note: candidate function template not viable: expects an rvalue for 1st argument 599 | make_pair(_T1&& __t1, _T2&& __t2) { | ^ ~~~~~~~~~~ 14 warnings and 1 error generated. *** [lamarc-mathx.o] Error code 1 make: stopped making "all" in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8 --- lamarc-xml_report.o --- 76 warnings generated. mv -f .deps/lamarc-xml_report.Tpo .deps/lamarc-xml_report.Po --- lamarc-reportpage.o --- 72 warnings generated. mv -f .deps/lamarc-reportpage.Tpo .deps/lamarc-reportpage.Po make: 1 error make: stopped making "all" in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8 ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/lamarc