------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/libgff XDG_CONFIG_HOME=/construction/biology/libgff XDG_CACHE_HOME=/construction/biology/libgff/.cache HOME=/construction/biology/libgff TMPDIR="/tmp" PATH=/construction/biology/libgff/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/libgff/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/libgff XDG_CONFIG_HOME=/construction/biology/libgff XDG_CACHE_HOME=/construction/biology/libgff/.cache HOME=/construction/biology/libgff TMPDIR="/tmp" PATH=/construction/biology/libgff/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/libgff/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/libgff/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- CMAKE_BUILD_TYPE="release" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/libgff" EXAMPLESDIR="share/examples/libgff" DATADIR="share/libgff" WWWDIR="www/libgff" ETCDIR="etc/libgff" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/libgff DOCSDIR=/usr/local/share/doc/libgff EXAMPLESDIR=/usr/local/share/examples/libgff WWWDIR=/usr/local/www/libgff ETCDIR=/usr/local/etc/libgff SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/libuv-1.46.0.pkg Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/rhash-1.4.3.pkg Installing /packages/All/pkg-1.19.2.pkg Installing /packages/All/liblz4-1.9.4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/zstd-1.5.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libarchive-3.6.2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ncurses-6.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/cmake-core-3.26.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ccache-3.7.12_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> libgff-2.0.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> libgff-2.0.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by libgff-2.0.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> libgff-2.0.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by libgff-2.0.0 for building => SHA256 Checksum OK for COMBINE-lab-libgff-v2.0.0_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> libgff-2.0.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by libgff-2.0.0 for building ===> Extracting for libgff-2.0.0 => SHA256 Checksum OK for COMBINE-lab-libgff-v2.0.0_GH0.tar.gz. Extracted Memory Use: 0.43M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for libgff-2.0.0 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> libgff-2.0.0 depends on file: /usr/local/bin/cmake - found ===> libgff-2.0.0 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> libgff-2.0.0 depends on file: /usr/local/bin/cmake - found ===> libgff-2.0.0 depends on file: /usr/local/bin/ccache - found ===> Configuring for libgff-2.0.0 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/libgff/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Install prefix : /usr/local version: 2.0.0 -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_NO_BUILTIN_CHRPATH CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/biology/libgff/.build SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for libgff-2.0.0 /usr/local/bin/cmake -S/construction/biology/libgff/libgff-2.0.0 -B/construction/biology/libgff/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/libgff/.build/CMakeFiles /construction/biology/libgff/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/gff.dir/all --- /usr/bin/make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/depend --- CMakeFiles/gff.dir/depend --- cd /construction/biology/libgff/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/.build /construction/biology/libgff/.build /construction/biology/libgff/.build/CMakeFiles/gff.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/build --- CMakeFiles/gff.dir/src/codons.cpp.o --- --- CMakeFiles/gff.dir/src/GArgs.cpp.o --- --- CMakeFiles/gff.dir/src/GBase.cpp.o --- --- CMakeFiles/gff.dir/src/gdna.cpp.o --- --- CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o --- --- CMakeFiles/gff.dir/src/GFastaIndex.cpp.o --- --- CMakeFiles/gff.dir/src/gff.cpp.o --- --- CMakeFiles/gff.dir/src/GStr.cpp.o --- --- CMakeFiles/gff.dir/src/gdna.cpp.o --- [ 9%] Building CXX object CMakeFiles/gff.dir/src/gdna.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/gdna.cpp.o -MF CMakeFiles/gff.dir/src/gdna.cpp.o.d -o CMakeFiles/gff.dir/src/gdna.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/gdna.cpp --- CMakeFiles/gff.dir/src/GBase.cpp.o --- [ 18%] Building CXX object CMakeFiles/gff.dir/src/GBase.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/GBase.cpp.o -MF CMakeFiles/gff.dir/src/GBase.cpp.o.d -o CMakeFiles/gff.dir/src/GBase.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/GBase.cpp --- CMakeFiles/gff.dir/src/codons.cpp.o --- [ 27%] Building CXX object CMakeFiles/gff.dir/src/codons.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/codons.cpp.o -MF CMakeFiles/gff.dir/src/codons.cpp.o.d -o CMakeFiles/gff.dir/src/codons.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/codons.cpp --- CMakeFiles/gff.dir/src/GStr.cpp.o --- [ 45%] Building CXX object CMakeFiles/gff.dir/src/GStr.cpp.o --- CMakeFiles/gff.dir/src/GFastaIndex.cpp.o --- [ 45%] Building CXX object CMakeFiles/gff.dir/src/GFastaIndex.cpp.o --- CMakeFiles/gff.dir/src/GStr.cpp.o --- /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/GStr.cpp.o -MF CMakeFiles/gff.dir/src/GStr.cpp.o.d -o CMakeFiles/gff.dir/src/GStr.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/GStr.cpp --- CMakeFiles/gff.dir/src/GFastaIndex.cpp.o --- /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/GFastaIndex.cpp.o -MF CMakeFiles/gff.dir/src/GFastaIndex.cpp.o.d -o CMakeFiles/gff.dir/src/GFastaIndex.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/GFastaIndex.cpp --- CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o --- [ 54%] Building CXX object CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o -MF CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o.d -o CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/GFaSeqGet.cpp --- CMakeFiles/gff.dir/src/GArgs.cpp.o --- [ 63%] Building CXX object CMakeFiles/gff.dir/src/GArgs.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/GArgs.cpp.o -MF CMakeFiles/gff.dir/src/GArgs.cpp.o.d -o CMakeFiles/gff.dir/src/GArgs.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/GArgs.cpp --- CMakeFiles/gff.dir/src/gff.cpp.o --- [ 72%] Building CXX object CMakeFiles/gff.dir/src/gff.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/gff.dir/src/gff.cpp.o -MF CMakeFiles/gff.dir/src/gff.cpp.o.d -o CMakeFiles/gff.dir/src/gff.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/gff.cpp In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GMapSeg]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GMapSeg]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:126:50: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GMapSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/gff.h:69:7: note: 'class GMapSeg' declared here class GMapSeg:public GSeg { ^~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GSeg]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GSeg]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:310:92: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/gff.h:6, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GBase.h:308:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GeneCDS]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GeneCDS]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:1349:31: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GeneCDS'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/gff.h:1338:7: note: 'class GeneCDS' declared here class GeneCDS: public GSeg { ^~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GffExon]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GffExon]' /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:2315:16: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GffExon'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/gff.h:627:7: note: 'class GffExon' declared here class GffExon : public GSeg { ^~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GSegMatch]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GList.hh:191:76: required from 'GArray::GArray(int (*)(pointer, pointer)) [with OBJ = GSegMatch; GCompareProc = int(void*, void*); pointer = void*]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:1349:31: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers ^~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSegMatch]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:437:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:69:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GList.hh:234:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:1362:22: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:358:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/gff.cpp:1: /construction/biology/libgff/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers ^~~~~~~~~ --- libgff.a --- [ 81%] Linking CXX static library libgff.a /usr/local/bin/cmake -P CMakeFiles/gff.dir/cmake_clean_target.cmake /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gff.dir/link.txt --verbose=1 /usr/bin/ar qc libgff.a CMakeFiles/gff.dir/src/codons.cpp.o CMakeFiles/gff.dir/src/GArgs.cpp.o CMakeFiles/gff.dir/src/GBase.cpp.o CMakeFiles/gff.dir/src/gdna.cpp.o CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o CMakeFiles/gff.dir/src/GFastaIndex.cpp.o CMakeFiles/gff.dir/src/gff.cpp.o CMakeFiles/gff.dir/src/GStr.cpp.o /usr/bin/ranlib libgff.a [ 81%] Built target gff --- CMakeFiles/TestGFFParse.dir/all --- /usr/bin/make -f CMakeFiles/TestGFFParse.dir/build.make CMakeFiles/TestGFFParse.dir/depend --- CMakeFiles/TestGFFParse.dir/depend --- cd /construction/biology/libgff/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/.build /construction/biology/libgff/.build /construction/biology/libgff/.build/CMakeFiles/TestGFFParse.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/TestGFFParse.dir/build.make CMakeFiles/TestGFFParse.dir/build --- CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o --- [ 90%] Building CXX object CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o /usr/local/libexec/ccache/c++ -I/construction/biology/libgff/libgff-2.0.0/include -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG -std=c++14 -MD -MT CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o -MF CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o.d -o CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o -c /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp: In function 'int main(int, char**)': /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:25:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j=0; j < f->attrs->Count(); ++j) { ~~^~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GMapSeg]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GMapSeg]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:126:50: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GMapSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/gff.h:69:7: note: 'class GMapSeg' declared here class GMapSeg:public GSeg { ^~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GSeg]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GSeg]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:310:92: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/gff.h:6, from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/GBase.h:308:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GeneCDS]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GeneCDS]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:1349:31: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GeneCDS'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/gff.h:1338:7: note: 'class GeneCDS' declared here class GeneCDS: public GSeg { ^~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::setCapacity(int) [with OBJ = GSegMatch]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec::GVec(int) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GList.hh:191:76: required from 'GArray::GArray(int (*)(pointer, pointer)) [with OBJ = GSegMatch; GCompareProc = int(void*, void*); pointer = void*]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:1349:31: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess] memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers ^~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/include/GList.hh:8, from /construction/biology/libgff/libgff-2.0.0/include/GFastaIndex.h:12, from /construction/biology/libgff/libgff-2.0.0/include/GFaSeqGet.h:3, from /construction/biology/libgff/libgff-2.0.0/include/gff.h:9, from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSegMatch]': /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:437:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:69:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GList.hh:234:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSegMatch]' /construction/biology/libgff/libgff-2.0.0/include/gff.h:1362:22: required from here /construction/biology/libgff/libgff-2.0.0/include/GVec.hh:358:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/libgff/libgff-2.0.0/src/TestGFFParse.cpp:5: /construction/biology/libgff/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers ^~~~~~~~~ --- TestGFFParse --- [100%] Linking CXX executable TestGFFParse /usr/local/bin/cmake -E cmake_link_script CMakeFiles/TestGFFParse.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -O3 -Wall -D_FILE_OFFSET_BITS=64 -pipe -O2 -fno-strict-aliasing -DNDEBUG CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o -o TestGFFParse libgff.a [100%] Built target TestGFFParse /usr/local/bin/cmake -E cmake_progress_start /construction/biology/libgff/.build/CMakeFiles 0 SUCCEEDED 00:00:21 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for libgff-2.0.0 ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/biology/libgff/libgff-2.0.0 -B/construction/biology/libgff/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/libgff/.build/CMakeFiles /construction/biology/libgff/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/depend cd /construction/biology/libgff/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/.build /construction/biology/libgff/.build /construction/biology/libgff/.build/CMakeFiles/gff.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/build [ 81%] Built target gff /usr/bin/make -f CMakeFiles/TestGFFParse.dir/build.make CMakeFiles/TestGFFParse.dir/depend cd /construction/biology/libgff/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/libgff-2.0.0 /construction/biology/libgff/.build /construction/biology/libgff/.build /construction/biology/libgff/.build/CMakeFiles/TestGFFParse.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/TestGFFParse.dir/build.make CMakeFiles/TestGFFParse.dir/build [100%] Built target TestGFFParse /usr/local/bin/cmake -E cmake_progress_start /construction/biology/libgff/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/biology/libgff/stage/usr/local/lib/libgff/cmake/libgffConfig.cmake -- Installing: /construction/biology/libgff/stage/usr/local/lib/libgff/cmake/libgffConfigVersion.cmake -- Installing: /construction/biology/libgff/stage/usr/local/lib/libgff.a -- Up-to-date: /construction/biology/libgff/stage/usr/local/include -- Installing: /construction/biology/libgff/stage/usr/local/include/GArgs.h -- Installing: /construction/biology/libgff/stage/usr/local/include/GBase.h -- Installing: /construction/biology/libgff/stage/usr/local/include/GFaSeqGet.h -- Installing: /construction/biology/libgff/stage/usr/local/include/GFastaIndex.h -- Installing: /construction/biology/libgff/stage/usr/local/include/GHash.hh -- Installing: /construction/biology/libgff/stage/usr/local/include/GList.hh -- Installing: /construction/biology/libgff/stage/usr/local/include/GStr.h -- Installing: /construction/biology/libgff/stage/usr/local/include/GVec.hh -- Installing: /construction/biology/libgff/stage/usr/local/include/codons.h -- Installing: /construction/biology/libgff/stage/usr/local/include/gdna.h -- Installing: /construction/biology/libgff/stage/usr/local/include/gff.h ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for libgff-2.0.0 file sizes/checksums [14]: 0% file sizes/checksums [14]: 100% Service unavailablepacking files [14]: 0% packing files [14]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:34