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Maintainer: [email protected] Last committer: [email protected] Ident: $FreeBSD: head/biology/bwa/Makefile 460452 2018-01-31 01:07:07Z jwb $ Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p545479_s364329/logs/bwa-0.7.17.log Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p545479_s364329 Log: =>> Building biology/bwa build started at Thu Aug 20 05:15:05 UTC 2020 port directory: /usr/ports/biology/bwa package name: bwa-0.7.17 building for: FreeBSD head-i386-default-job-08 13.0-CURRENT FreeBSD 13.0-CURRENT 1300109 i386 maintained by: [email protected] Makefile ident: $FreeBSD: head/biology/bwa/Makefile 460452 2018-01-31 01:07:07Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300109 Job Id: 08 !!! Jail is newer than host. (Jail: 1300109, Host: 1300100) !!! !!! 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=1300109 UNAME_v=FreeBSD 13.0-CURRENT 1300109 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-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--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bwa/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-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bwa/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 -msse2 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -msse2 -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 PERL_VERSION=5.32.0 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/bwa" EXAMPLESDIR="share/examples/bwa" DATADIR="share/bwa" WWWDIR="www/bwa" ETCDIR="etc/bwa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bwa DOCSDIR=/usr/local/share/doc/bwa EXAMPLESDIR=/usr/local/share/examples/bwa WWWDIR=/usr/local/www/bwa ETCDIR=/usr/local/etc/bwa --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 11.0.0 ([email protected]:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 ([email protected]:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-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" "-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_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 ([email protected]:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300109 PYTHONBASE=/usr/local 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) 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 >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-i386-default-job-08] Installing pkg-1.14.7... [head-i386-default-job-08] Extracting pkg-1.14.7: .......... done ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.17 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building ===> Extracting for bwa-0.7.17 => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bwa-0.7.17 ===> Applying FreeBSD patches for bwa-0.7.17 from /usr/ports/biology/bwa/files =========================================================================== =======================<phase: build-depends >============================ ===> bwa-0.7.17 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [head-i386-default-job-08] Installing gmake-4.3_2... [head-i386-default-job-08] `-- Installing gettext-runtime-0.21... [head-i386-default-job-08] | `-- Installing indexinfo-0.3.1... [head-i386-default-job-08] | `-- Extracting indexinfo-0.3.1: .... done [head-i386-default-job-08] `-- Extracting gettext-runtime-0.21: .......... done [head-i386-default-job-08] Extracting gmake-4.3_2: .......... done ===> bwa-0.7.17 depends on package: gmake>=4.3 - found ===> Returning to build of bwa-0.7.17 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for bwa-0.7.17 =========================================================================== =======================<phase: build >============================ ===> Building for bwa-0.7.17 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.17' cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o bwamem.c:1075:72: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] err_printf("* %ld chains remain after removing duplicated chains\n", regs.n); ~~~ ^~~~~~ %zu cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o bwamem_pair.c:65:131: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); ~~~ ^~~~~~~~~~ %zu bwamem_pair.c:65:143: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); ~~~ ^~~~~~~~~~ %zu bwamem_pair.c:65:155: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); ~~~ ^~~~~~~~~~ %zu bwamem_pair.c:65:167: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); ~~~ ^~~~~~~~~~ %zu 4 warnings generated. cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o 1 warning generated. cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o fastmap.c:413:42: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l); ~~~ ^~~~~~~~~~ %zu cc -c -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o 1 warning generated. ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o cc -O2 -pipe -msse2 -fstack-protector-strong -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread ld: error: duplicate symbol: rle_auxtab >>> defined at bwtindex.c >>> bwtindex.o:(rle_auxtab) in archive ./libbwa.a >>> defined at rope.c >>> rope.o:(.rodata+0x0) in archive ./libbwa.a ld: error: duplicate symbol: rle_auxtab >>> defined at bwtindex.c >>> bwtindex.o:(rle_auxtab) in archive ./libbwa.a >>> defined at rle.c >>> rle.o:(.rodata+0x0) in archive ./libbwa.a cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[1]: *** [Makefile:30: bwa] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.17' ===> 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/bwa _______________________________________________ [email protected] mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "[email protected]"
