------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 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 ------------------------------------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/construction/biology/hisat2 XDG_CONFIG_HOME=/construction/biology/hisat2 HOME=/construction/biology/hisat2 TMPDIR="/tmp" PATH=/construction/biology/hisat2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/hisat2 XDG_CONFIG_HOME=/construction/biology/hisat2 HOME=/construction/biology/hisat2 TMPDIR="/tmp" PATH=/construction/biology/hisat2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes 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/hisat2/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 PROFILE="@comment " DOCSDIR="share/doc/hisat2" EXAMPLESDIR="share/examples/hisat2" DATADIR="share/hisat2" WWWDIR="www/hisat2" ETCDIR="etc/hisat2" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hisat2 DOCSDIR=/usr/local/share/doc/hisat2 EXAMPLESDIR=/usr/local/share/examples/hisat2 WWWDIR=/usr/local/www/hisat2 ETCDIR=/usr/local/etc/hisat2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.4.1.txz Installing /packages/All/mpdecimal-2.5.1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < hisat2-2.1.0.23 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hisat2-2.1.0.23 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hisat2-2.1.0.23 for building => SHA256 Checksum OK for infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hisat2-2.1.0.23 for building ===> Extracting for hisat2-2.1.0.23 => SHA256 Checksum OK for infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz. Extracted Memory Use: 14.48M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for hisat2-2.1.0.23 ===> Applying ports patches for hisat2-2.1.0.23 from /xports/biology/hisat2/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on package: gmake>=4.3 - found ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.8 - found ===> hisat2-2.1.0.23 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on package: gmake>=4.3 - found ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.8 - found ===> hisat2-2.1.0.23 depends on package: perl5>=5.32.r0<5.33 - found ===> Configuring for hisat2-2.1.0.23 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for hisat2-2.1.0.23 gmake[1]: Entering directory '/construction/biology/hisat2/hisat2-2.1.0-23-g20f333e' c++ -pipe -O2 -fno-strict-aliasing -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG \ -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG \ -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG \ -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing \ -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT2_INSPECT_MAIN \ -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing \ -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \ -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from hisat2_build.cpp:35: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1753:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3068:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3069:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3085:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const string&, const string&)': hisat2.cpp:3826:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1753:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3068:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3069:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3085:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const string&, const string&)': hisat2.cpp:3826:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ gmake[1]: Leaving directory '/construction/biology/hisat2/hisat2-2.1.0-23-g20f333e' SUCCEEDED 00:03:29 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.8 - found ===> hisat2-2.1.0.23 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for hisat2-2.1.0.23 ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.8 - found ===> hisat2-2.1.0.23 depends on package: perl5>=5.32.r0<5.33 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/hisat2/hisat2-2.1.0-23-g20f333e' mkdir -p /construction/biology/hisat2/stage/usr/local/bin install -c -s hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l /construction/biology/hisat2/stage/usr/local/bin install -c hisat2 hisat2-build hisat2-inspect \ /construction/biology/hisat2/stage/usr/local/bin mkdir -p /construction/biology/hisat2/stage/usr/local/libexec/hisat2 install -c scripts/*.sh scripts/*.pl *.py \ hisatgenotype_modules/hisat*.py \ hisatgenotype_scripts/*.py hisatgenotype_scripts/*.sh \ /construction/biology/hisat2/stage/usr/local/libexec/hisat2 gmake[1]: Leaving directory '/construction/biology/hisat2/hisat2-2.1.0-23-g20f333e' ====> 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 00:00:02 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for hisat2-2.1.0.23 file sizes/checksums [81]: 0% file sizes/checksums [81]: 100% packing files [81]: 0% packing files [81]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:03:56