=> Building biology/hisat2 Started : Sunday, 7 JUL 2019 at 04:14:42 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- 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/python3.6" 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 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/hisat2/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 PROFILE="@comment " DOCSDIR="share/doc/hisat2" EXAMPLESDIR="share/examples/hisat2" DATADIR="share/hisat2" WWWDIR="www/hisat2" ETCDIR="etc/hisat2" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> hisat2-2.1.0.23 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hisat2-2.1.0.23 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hisat2-2.1.0.23 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> 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. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for hisat2-2.1.0.23 ===> Applying ports patches for hisat2-2.1.0.23 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> hisat2-2.1.0.23 depends on executable: gmake - found ===> Returning to build of hisat2-2.1.0.23 ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.6 - not found ===> Installing existing package /packages/All/python36-3.6.8_2.txz Installing python36-3.6.8_2... `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing libressl-2.9.2... `-- Extracting libressl-2.9.2: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing readline-8.0.0... `-- Extracting readline-8.0.0: .......... done Extracting python36-3.6.8_2: .......... done Message from python36-3.6.8_2: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.6 - found ===> Returning to build of hisat2-2.1.0.23 ===> hisat2-2.1.0.23 depends on package: perl5>=5.28.r1<5.29 - not found ===> Installing existing package /packages/All/perl5-5.28.2.txz Installing perl5-5.28.2... Extracting perl5-5.28.2: .......... done Message from perl5-5.28.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> hisat2-2.1.0.23 depends on package: perl5>=5.28.r1<5.29 - found ===> Returning to build of hisat2-2.1.0.23 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for hisat2-2.1.0.23 -------------------------------------------------------------------------------- -- 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 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 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 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; ^~~~~~~~ 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 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; ^~~~~~~~ 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 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; ^~~~~~~~ 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 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 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 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_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_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 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_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_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 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 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 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 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_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_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 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 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' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> hisat2-2.1.0.23 depends on file: /usr/local/bin/python3.6 - found ===> hisat2-2.1.0.23 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for hisat2-2.1.0.23 ===> 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) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for hisat2-2.1.0.23 file sizes/checksums [84]: . done packing files [84]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:17:57 UTC Duration: 00:03:15