Date: Tue, 25 Aug 2020 14:37:42 GMT From: pkg-fallout@FreeBSD.org To: jwb@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/freebayes] Failed for freebayes-1.2.0_2 in build Message-ID: <202008251437.07PEbg7V042114@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: jwb@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/biology/freebayes/Makefile 507372 2019-07-26 20:46:53Z gerald $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p546132_s364744/logs/freebayes-1.2.0_2.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p546132_s364744 Log: =>> Building biology/freebayes build started at Tue Aug 25 14:34:26 UTC 2020 port directory: /usr/ports/biology/freebayes package name: freebayes-1.2.0_2 building for: FreeBSD head-amd64-default-job-02 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 amd64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/freebayes/Makefile 507372 2019-07-26 20:46:53Z gerald $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300111 Job Id: 02 !!! Jail is newer than host. (Jail: 1300111, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300111 UNAME_v=FreeBSD 13.0-CURRENT 1300111 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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/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/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/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 --std=c++11 " 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/freebayes" EXAMPLESDIR="share/examples/freebayes" DATADIR="share/freebayes" WWWDIR="www/freebayes" ETCDIR="etc/freebayes" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/freebayes DOCSDIR=/usr/local/share/doc/freebayes EXAMPLESDIR=/usr/local/share/examples/freebayes WWWDIR=/usr/local/www/freebayes ETCDIR=/usr/local/etc/freebayes --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=1300111 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 >============================ ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> freebayes-1.2.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-02] Installing pkg-1.14.7... [head-amd64-default-job-02] Extracting pkg-1.14.7: .......... done ===> freebayes-1.2.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of freebayes-1.2.0_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_2 for building => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz. => SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz. => SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_2 for building ===> Extracting for freebayes-1.2.0_2 => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. <snip> c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Genotype.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c DataLikelihood.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Multinomial.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Ewens.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c ResultData.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Dirichlet.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Marginals.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c split.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c LeftAlign.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c IndelAllele.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Bias.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -c -o Contamination.o Contamination.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c NonCall.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c SegfaultHandler.cpp cd ../vcflib/smithwaterman && gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/smithwaterman' c++ -O3 -c -o disorder.o disorder.cpp -I. c++ -O3 -c -o smithwaterman.o smithwaterman.cpp -I. c++ -O3 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I. c++ -O3 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I. c++ -O3 -c -o LeftAlign.o LeftAlign.cpp -I. c++ -O3 -c -o Repeats.o Repeats.cpp -I. c++ -O3 -c -o IndelAllele.o IndelAllele.cpp -I. c++ -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman ld -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L. #c++ -O3 -c -o smithwaterman.cpp disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -I. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/smithwaterman' c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c ../vcflib/src/Variant.cpp ./vcflib/src/Variant.cpp:212:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ ./vcflib/src/Variant.cpp:334:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ ./vcflib/src/Variant.cpp:368:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ ./vcflib/src/Variant.cpp:406:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 4 warnings generated. cd ../SeqLib && ./configure && gmake checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/missing: Unknown `--is-lightweight' option Try `/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... nawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... none required checking for library containing lzma_code... none required checking for library containing BZ2_bzBuffToBuffDecompress... none required checking for library containing clock_gettime... none required checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/seqtools/Makefile config.status: creating config.h config.status: executing depfiles commands gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' gmake all-recursive gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' Making all in bwa gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/bwa' cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o bwa.c:147:18: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] w = (max_gap + abs(rlen - l_query) + 1) >> 1; ^ bwa.c:147:18: note: use function 'labs' instead w = (max_gap + abs(rlen - l_query) + 1) >> 1; ^~~ labs bwa.c:149:11: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] min_w = abs(rlen - l_query) + 3; ^ bwa.c:149:11: note: use function 'labs' instead min_w = abs(rlen - l_query) + 3; ^~~ labs 2 warnings generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o ar -csru libbwa.a utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o is.o bwtindex.o rope.o rle.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o bwase.c:181:57: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^ bwase.c:181:57: note: use function 'labs' instead ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^~~ labs bwase.c:181:88: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^ bwase.c:181:88: note: use function 'labs' instead ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^~~ labs 2 warnings generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o bwtsw2_pair.c:239:13: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.); ^ bwtsw2_pair.c:239:13: note: use function 'abs' instead diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.); ^~~~ abs 1 warning generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -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[5]: *** [Makefile:31: bwa] Error 1 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/bwa' gmake[4]: *** [Makefile:358: all-recursive] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' gmake[3]: *** [Makefile:299: all] Error 2 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib' gmake[2]: *** [Makefile:53: ../SeqLib/src/libseqlib.a] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src' gmake[1]: *** [Makefile:2: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/freebayes
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