Date: Sun, 30 Aug 2020 14:00:30 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/grappa] Failed for grappa-2.0 in build Message-ID: <202008301400.07UE0UOH091080@beefy18.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: ports@FreeBSD.org Last committer: rm@FreeBSD.org Ident: $FreeBSD: head/biology/grappa/Makefile 397864 2015-09-25 18:55:08Z rm $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p546860_s364942/logs/grappa-2.0.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p546860_s364942 Log: =>> Building biology/grappa build started at Sun Aug 30 14:00:22 UTC 2020 port directory: /usr/ports/biology/grappa package name: grappa-2.0 building for: FreeBSD head-amd64-default-job-13 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 amd64 maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: head/biology/grappa/Makefile 397864 2015-09-25 18:55:08Z rm $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300113 Job Id: 13 !!! Jail is newer than host. (Jail: 1300113, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300113 UNAME_v=FreeBSD 13.0-CURRENT 1300113 UNAME_r=13.0-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=3.2.8-5-gc81843e5 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--- ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/grappa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/grappa/work HOME=/wrkdirs/usr/ports/biology/grappa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/grappa/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/grappa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/grappa/work HOME=/wrkdirs/usr/ports/biology/grappa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/grappa/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-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/grappa" EXAMPLESDIR="share/examples/grappa" DATADIR="share/grappa" WWWDIR="www/grappa" ETCDIR="etc/grappa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/grappa DOCSDIR=/usr/local/share/doc/grappa EXAMPLESDIR=/usr/local/share/examples/grappa WWWDIR=/usr/local/www/grappa ETCDIR=/usr/local/etc/grappa --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. 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 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 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 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300113 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 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 grappa 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 GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> grappa-2.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-13] Installing pkg-1.14.7... [head-amd64-default-job-13] Extracting pkg-1.14.7: .......... done ===> grappa-2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of grappa-2.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The grappa 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 GPLv2 accepted by the user ===> Fetching all distfiles required by grappa-2.0 for building =========================================================================== =======================<phase: checksum >============================ ===> NOTICE: The grappa 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: <snip> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1345:16: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] next = ( int ) list_get ( &adj_list[v], 0 ) == prev ? ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1346:13: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] ( int ) list_get ( &adj_list[v], 1 ) : ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1347:13: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] ( int ) list_get ( &adj_list[v], 0 ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1687:17: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] label = ( int ) list_get ( V, i ); ^~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1791:49: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast] push ( &mem->comp_grey_edges[comp], ( void * ) mem->upi_cpy[i] ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1860:36: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] ( int ) list_get ( &c1->cyclelist, i )]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1863:36: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] ( int ) list_get ( &c2->cyclelist, j )]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1868:33: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] a = ( int ) list_get ( edges1, k ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1869:33: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] b = ( int ) list_get ( edges2, k2 ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1892:28: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] edges = &cyclelist[( int ) list_get ( &cc->cyclelist, j )]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1897:21: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] a = ( int ) list_get ( edges, k ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1898:21: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] b = ( int ) list_get ( edges, k2 ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1940:12: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] ( int ) list_get ( &conn_comp[h1].double_superhurdle_partners, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:1943:18: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] && ( int ) list_get ( &conn_comp[h1]. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:2219:24: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] comp = ( int ) pop_stack ( &tmpl ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:2222:40: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast] push ( &separated_ocs, ( void * ) comp ); ^~~~~~~~~~~~~~~ all_sorting_reversals.c:2223:45: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast] push ( &separating_hurdles, ( void * ) currenth ); ^~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:2248:25: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] int c = ( int ) pop_stack ( &tmpl ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:2324:27: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast] push ( &tmpl, ( void * ) comp ); ^~~~~~~~~~~~~~~ all_sorting_reversals.c:2347:18: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] oc = ( int ) list_get ( &separated_ocs, i ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:2349:17: warning: cast to smaller integer type 'int' from 'void *' [-Wvoid-pointer-to-int-cast] h = ( int ) list_get ( &separating_hurdles, i ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ all_sorting_reversals.c:2357:34: warning: cast to 'void *' from smaller integer type 'int' [-Wint-to-void-pointer-cast] push ( &( *ocs )[j], ( void * ) oc ); ^~~~~~~~~~~~~ 90 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DFreeBSD -DINIT -o grappa convert.o labeltree.o main.o binencode.o gen_tree.o inittree.o circ_order.o lk_main.o bbtsp.o condense.o const_tree.o greedy_median.o invdist.o uf.o neighborj.o condense3.o getopt3.o randomBSD.o cheaptsp.o specialtsp.o specialinit.o read_input.o circular_ordering.o correction.o inversion_median.o inversion_median_alberto.o priority_stack.o hashtable.o med_util.o simpleio.o vertex_factory.o growTree.o bitvector.o lists.o sorting_reversal_median.o mythread_rwlock.o all_sorting_reversals.o -lm -pthread ld: error: duplicate symbol: MAXEDG >>> defined at labeltree.c >>> labeltree.o:(MAXEDG) >>> defined at main.c >>> main.o:(.bss+0x24) ld: error: duplicate symbol: MAXM >>> defined at labeltree.c >>> labeltree.o:(MAXM) >>> defined at main.c >>> main.o:(.bss+0x20) ld: error: duplicate symbol: MAXNOD >>> defined at labeltree.c >>> labeltree.o:(MAXNOD) >>> defined at main.c >>> main.o:(.bss+0x1C) ld: error: duplicate symbol: Num_Genes >>> defined at labeltree.c >>> labeltree.o:(Num_Genes) >>> defined at main.c >>> main.o:(.bss+0x18) ld: error: duplicate symbol: UB >>> defined at labeltree.c >>> labeltree.o:(UB) >>> defined at main.c >>> main.o:(.bss+0xF8) ld: error: duplicate symbol: at_root >>> defined at labeltree.c >>> labeltree.o:(at_root) >>> defined at main.c >>> main.o:(.bss+0xBC) ld: error: duplicate symbol: bcyceq >>> defined at labeltree.c >>> labeltree.o:(bcyceq) >>> defined at main.c >>> main.o:(.bss+0xB0) ld: error: duplicate symbol: bcycvar >>> defined at labeltree.c >>> labeltree.o:(bcycvar) >>> defined at main.c >>> main.o:(.bss+0xA0) ld: error: duplicate symbol: bdegree >>> defined at labeltree.c >>> labeltree.o:(bdegree) >>> defined at main.c >>> main.o:(.bss+0xA8) ld: error: duplicate symbol: bedge >>> defined at labeltree.c >>> labeltree.o:(bedge) >>> defined at main.c >>> main.o:(.bss+0x94) ld: error: duplicate symbol: best_now >>> defined at labeltree.c >>> labeltree.o:(best_now) >>> defined at main.c >>> main.o:(.bss+0xFC) ld: error: duplicate symbol: bestsol >>> defined at labeltree.c >>> labeltree.o:(bestsol) >>> defined at main.c >>> main.o:(.bss+0xC8) ld: error: duplicate symbol: bestub >>> defined at labeltree.c >>> labeltree.o:(bestub) >>> defined at main.c >>> main.o:(.bss+0xC0) ld: error: duplicate symbol: bsec >>> defined at labeltree.c >>> labeltree.o:(bsec) >>> defined at main.c >>> main.o:(.bss+0xB8) ld: error: duplicate symbol: cycvar >>> defined at labeltree.c >>> labeltree.o:(cycvar) >>> defined at main.c >>> main.o:(.bss+0xF0) ld: error: duplicate symbol: e_ind >>> defined at labeltree.c >>> labeltree.o:(e_ind) >>> defined at main.c >>> main.o:(.bss+0x40) ld: error: duplicate symbol: ec >>> defined at labeltree.c >>> labeltree.o:(ec) >>> defined at main.c >>> main.o:(.bss+0x38) ld: error: duplicate symbol: fid >>> defined at labeltree.c >>> labeltree.o:(fid) >>> defined at main.c >>> main.o:(.bss+0xD8) ld: error: duplicate symbol: fout >>> defined at labeltree.c >>> labeltree.o:(fout) >>> defined at main.c >>> main.o:(.bss+0xE0) ld: error: duplicate symbol: gen >>> defined at labeltree.c >>> labeltree.o:(gen) >>> defined at main.c >>> main.o:(.bss+0x170) ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors) cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[1]: *** [Makefile:129: grappa] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/grappa/work/GRAPPA20' ===> 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 in /usr/ports/biology/grappa
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