Date: Sat, 5 Sep 2020 06:41:02 GMT From: pkg-fallout@FreeBSD.org To: jwb@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/subread] Failed for subread-2.0.1 in build Message-ID: <202009050641.0856f20L009154@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: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/subread/Makefile 537982 2020-06-05 01:55:49Z jwb $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p547580_s365355/logs/subread-2.0.1.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p547580_s365355 Log: =>> Building biology/subread build started at Sat Sep 5 06:40:51 UTC 2020 port directory: /usr/ports/biology/subread package name: subread-2.0.1 building for: FreeBSD head-amd64-default-job-01 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 amd64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/subread/Makefile 537982 2020-06-05 01:55:49Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300113 Job Id: 01 !!! 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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/subread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/subread/work HOME=/wrkdirs/usr/ports/biology/subread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/subread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/subread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/subread/work HOME=/wrkdirs/usr/ports/biology/subread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/subread/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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/subread" EXAMPLESDIR="share/examples/subread" DATADIR="share/subread" WWWDIR="www/subread" ETCDIR="etc/subread" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/subread DOCSDIR=/usr/local/share/doc/subread EXAMPLESDIR=/usr/local/share/examples/subread WWWDIR=/usr/local/www/subread ETCDIR=/usr/local/etc/subread --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 >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-01] Installing pkg-1.14.7... [head-amd64-default-job-01] Extracting pkg-1.14.7: .......... done ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of subread-2.0.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by subread-2.0.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by subread-2.0.1 for building => SHA256 Checksum OK for subread-2.0.1-source.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by subread-2.0.1 for building ===> Extracting for subread-2.0.1 => SHA256 Checksum OK for subread-2.0.1-source.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for subread-2.0.1 ===> Applying FreeBSD patches for subread-2.0.1 from /usr/ports/biology/subread/files =========================================================================== =======================<phase: build-depends >============================ ===> subread-2.0.1 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [head-amd64-default-job-01] Installing gmake-4.3_2... [head-amd64-default-job-01] `-- Installing gettext-runtime-0.21... [head-amd64-default-job-01] | `-- Installing indexinfo-0.3.1... [head-amd64-default-job-01] | `-- Extracting indexinfo-0.3.1: .... done [head-amd64-default-job-01] `-- Extracting gettext-runtime-0.21: .......... done [head-amd64-default-job-01] Extracting gmake-4.3_2: .......... done ===> subread-2.0.1 depends on package: gmake>=4.3 - found ===> Returning to build of subread-2.0.1 <snip> cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sambam-file.o sambam-file.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sublog.o sublog.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-algorithms.o gene-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o hashtable.o hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-files.o input-files.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sorted-hashtable.o sorted-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-value-index.o gene-value-index.c gene-value-index.c:457:53: warning: adding 'unsigned long' to a string does not append to the string [-Wstring-plus-int] if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET +strlen(TEST_TARGET) -1 - 30, 30)==0) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ gene-value-index.c:457:53: note: use array indexing to silence this warning if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET +strlen(TEST_TARGET) -1 - 30, 30)==0) ^ & [ ] gene-value-index.c:509:53: warning: adding 'unsigned long' to a string does not append to the string [-Wstring-plus-int] if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET + strlen(TEST_TARGET) - 31, 30)==0) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ gene-value-index.c:509:53: note: use array indexing to silence this warning if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET + strlen(TEST_TARGET) - 31, 30)==0) ^ & [ ] 2 warnings generated. cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o exon-algorithms.o exon-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o HelperFunctions.o HelperFunctions.c HelperFunctions.c:1542:75: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] SUBREADprintf("\t'%s'\t%016llX\t%llu\t%.9f\n", s, randv, randv, randv*1./0xffffffffffffffffllu); ~^~~~~~~~~~~~~~~~~~~~~ ./subread.h:132:44: note: expanded from macro 'SUBREADprintf' #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) ^~~~~~~~~~~ cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o interval_merge.o interval_merge.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o long-hashtable.o long-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-bigtable.o core-bigtable.c 1 warning generated. cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o seek-zlib.o seek-zlib.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-blc.o input-blc.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -fstack-protector-strong -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -fstack-protector-strong -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm gen_rand_reads.c:208:68: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] double rand_01 = plain_txt_to_long_rand(grc->random_seeds, 16)*1./0xffffffffffffffffllu; ~^~~~~~~~~~~~~~~~~~~~~ gen_rand_reads.c:216:62: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] rand_01 = plain_txt_to_long_rand(grc->random_seeds, 16)*1./0xffffffffffffffffllu; ~^~~~~~~~~~~~~~~~~~~~~ ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at core.c >>> core.o:(.bss+0x28) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at core-junction.c >>> core-junction.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at core-indel.c >>> core-indel.o:(.bss+0x18) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at sambam-file.c >>> sambam-file.o:(.bss+0x8) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at gene-algorithms.c >>> gene-algorithms.o:(.bss+0x10) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at input-files.c >>> input-files.o:(.bss+0x28) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at sorted-hashtable.c >>> sorted-hashtable.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at gene-value-index.c >>> gene-value-index.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at HelperFunctions.c >>> HelperFunctions.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at core-bigtable.c >>> core-bigtable.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at seek-zlib.c >>> seek-zlib.o:(.bss+0x8) ld: error: duplicate symbol: replica_index >>> defined at detection-calls.c >>> /tmp/detection-calls-61a52a.o:(replica_index) >>> defined at input-blc.c >>> input-blc.o:(.bss+0x0) cc: error: linker command failed with exit code 1 (use -v to see invocation) 2 warnings generated. gmake[1]: *** [/usr/ports/biology/subread/files/Makefile.pkg:44: detectionCall] Error 1 gmake[1]: *** Waiting for unfinished jobs.... ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at core.c >>> core.o:(.bss+0x28) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at core-junction.c >>> core-junction.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at core-indel.c >>> core-indel.o:(.bss+0x18) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at sambam-file.c >>> sambam-file.o:(.bss+0x8) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at gene-algorithms.c >>> gene-algorithms.o:(.bss+0x10) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at input-files.c >>> input-files.o:(.bss+0x28) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at sorted-hashtable.c >>> sorted-hashtable.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at gene-value-index.c >>> gene-value-index.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at HelperFunctions.c >>> HelperFunctions.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at core-bigtable.c >>> core-bigtable.o:(.bss+0x0) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at seek-zlib.c >>> seek-zlib.o:(.bss+0x8) ld: error: duplicate symbol: replica_index >>> defined at gen_rand_reads.c >>> /tmp/gen_rand_reads-b6471a.o:(replica_index) >>> defined at input-blc.c >>> input-blc.o:(.bss+0x0) cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[1]: *** [/usr/ports/biology/subread/files/Makefile.pkg:38: genRandomReads] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/subread/work/subread-2.0.1-source/src' ===> 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/subread
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