Date: Thu, 6 May 2021 19:20:26 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 122powerpc64-quarterly][biology/cufflinks] Failed for cufflinks-2.2.1.89_2 in build Message-ID: <202105061920.146JKQJc081127@pylon.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: yuri@FreeBSD.org Log URL: http://pylon.nyi.freebsd.org/data/122powerpc64-quarterly/61257645fee1/logs/cufflinks-2.2.1.89_2.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=122powerpc64-quarterly&build=61257645fee1 Log: =>> Building biology/cufflinks build started at Thu May 6 19:17:19 UTC 2021 port directory: /usr/ports/biology/cufflinks package name: cufflinks-2.2.1.89_2 building for: FreeBSD 122powerpc64-quarterly-job-02 12.2-RELEASE FreeBSD 12.2-RELEASE powerpc maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1400003 Jail OSVERSION: 1202000 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1202000 UNAME_v=FreeBSD 12.2-RELEASE UNAME_r=12.2-RELEASE 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=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=122powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/122powerpc64-quarterly/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-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" 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/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc10" CFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -fno-strict-aliasing " CPP="cpp10" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong - Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 " LIBS="" CXX="g++10" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -I/usr/local/include/eigen3 -Wl,-rpath=/usr/local/lib/gcc10 " 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-- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=12.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks --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=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 PPC_ABI=ELFv1 OPSYS=FreeBSD _OSRELEASE=12.2-RELEASE OSREL=12.2 OSVERSION=1202000 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) 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 BSL accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> cufflinks-2.2.1.89_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.3.txz [122powerpc64-quarterly-job-02] Installing pkg-1.16.3... [122powerpc64-quarterly-job-02] Extracting pkg-1.16.3: .......... done ===> cufflinks-2.2.1.89_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.89_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building ===> Extracting for cufflinks-2.2.1.89_2 => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for cufflinks-2.2.1.89_2 ===> Applying distribution patches for cufflinks-2.2.1.89_2 ===> Applying FreeBSD patches for cufflinks-2.2.1.89_2 from /usr/ports/biology/cufflinks/files =========================================================================== =======================<phase: build-depends >============================ ===> cufflinks-2.2.1.89_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.9.txz [122powerpc64-quarterly-job-02] Installing eigen-3.3.9... [122powerpc64-quarterly-job-02] `-- Installing adol-c-2.7.2... [122powerpc64-quarterly-job-02] | `-- Installing boost-libs-1.72.0_4... [122powerpc64-quarterly-job-02] | | `-- Installing gcc10-10.2.0_1... [122powerpc64-quarterly-job-02] | | `-- Installing binutils-2.33.1_4,1... [122powerpc64-quarterly-job-02] | | | `-- Installing gettext-runtime-0.21... [122powerpc64-quarterly-job-02] | | | `-- Installing indexinfo-0.3.1... [122powerpc64-quarterly-job-02] | | | `-- Extracting indexinfo-0.3.1: .... done [122powerpc64-quarterly-job-02] | | | `-- Extracting gettext-runtime-0.21: .......... done [122powerpc64-quarterly-job-02] | | `-- Extracting binutils-2.33.1_4,1: .......... done [122powerpc64-quarterly-job-02] | | `-- Installing gcc9-9.3.0_3... [122powerpc64-quarterly-job-02] | | | `-- Installing gmp-6.2.1... [122powerpc64-quarterly-job-02] | | | `-- Extracting gmp-6.2.1: .......... done [122powerpc64-quarterly-job-02] | | | `-- Installing mpc-1.2.0... [122powerpc64-quarterly-job-02] | | | `-- Installing mpfr-4.1.0... <snip> 903 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:48: required from 'void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gtf_tracking.h:188:7: note: 'class GISeg' declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gtf_tracking.h:359:7: note: 'class GXSeg' declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GBase.h:286:7: note: 'class GSeg' declared here 286 | class GSeg { | ^~~~ In file included from cufflinks.cpp:28: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] 224 | const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ cufflinks.cpp: In function 'bool scaffolds_for_bundle(const HitBundle&, std::vector<boost::shared_ptr<Scaffold> >&, std::vector<boost::shared_ptr<Scaffold> >*, BundleStats*)': cufflinks.cpp:690:30: warning: comparison of integer expressions of different signedness: 'std::vector<MateHit>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 690 | if (bundle.hits().size() >= max_frags_per_bundle) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:690:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 690 | if (bundle.hits().size() >= max_frags_per_bundle) | ^~ cufflinks.cpp:693:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 693 | bool ref_guided = (ref_scaffs != NULL); | ^~~~ cufflinks.cpp: In function 'void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector<Gene>&, bool)': cufflinks.cpp:980:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 980 | for (size_t j = 0; j < N; ++j) | ~~^~~ cufflinks.cpp:988:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 988 | for (size_t j = 0; j < N; ++j) | ~~^~~ cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, boost::shared_ptr<ReadGroupProperties>, boost::shared_ptr<BiasLearner>, FILE*, FILE*, FILE*, FILE*)': cufflinks.cpp:1264:55: warning: comparison of integer expressions of different signedness: 'std::vector<MateHit>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1264 | bool bundle_too_large = bundle_ptr->hits().size() >= max_frags_per_bundle; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:1275:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1275 | if (allow_junk_filtering) | ^~ cufflinks.cpp:1279:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1279 | if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned | ^~ cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable] 1176 | long double map_mass = rg_props->normalized_map_mass(); | ^~~~~~~~ cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, boost::shared_ptr<BiasLearner>)': cufflinks.cpp:1491:38: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1491 | if (bundle.right() - bundle.left() > max_gene_length) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:48: required from 'void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gtf_tracking.h:188:7: note: 'class GISeg' declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gtf_tracking.h:359:7: note: 'class GXSeg' declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GBase.h:286:7: note: 'class GSeg' declared here 286 | class GSeg { | ^~~~ gmake[3]: *** [Makefile:1674: clustering.o] Error 1 gmake[3]: *** Waiting for unfinished jobs.... gmake[3]: *** [Makefile:1674: cufflinks.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' gmake[2]: *** [Makefile:404: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[1]: *** [Makefile:345: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' ===> 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/cufflinks
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