=> Building biology/jellyfish Started : Wednesday, 24 JUL 2019 at 17:02:46 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=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-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 -------------------------------------------------- ===> The following configuration options are available for Jellyfish-2.2.10_5: NLS=on: Native Language Support ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/biology/jellyfish XDG_CONFIG_HOME=/construction/biology/jellyfish HOME=/construction/biology/jellyfish TMPDIR="/tmp" PATH=/construction/biology/jellyfish/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --enable-nls --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/jellyfish XDG_CONFIG_HOME=/construction/biology/jellyfish HOME=/construction/biology/jellyfish TMPDIR="/tmp" PATH=/construction/biology/jellyfish/.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 -faligned-new " 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/jellyfish/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- VER=2.2.10 NLS="" NO_NLS="@comment " OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/Jellyfish" EXAMPLESDIR="share/examples/Jellyfish" DATADIR="share/Jellyfish" WWWDIR="www/Jellyfish" ETCDIR="etc/Jellyfish" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- NLS="" NO_NLS="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Jellyfish DOCSDIR=/usr/local/share/doc/Jellyfish EXAMPLESDIR=/usr/local/share/examples/Jellyfish WWWDIR=/usr/local/www/Jellyfish ETCDIR=/usr/local/etc/Jellyfish -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 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 LICENSES_ACCEPTED= NONE 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=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_5 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 ===> Jellyfish-2.2.10_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of Jellyfish-2.2.10_5 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by Jellyfish-2.2.10_5 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by Jellyfish-2.2.10_5 for building => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.10_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by Jellyfish-2.2.10_5 for building ===> Extracting for Jellyfish-2.2.10_5 ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by Jellyfish-2.2.10_5 for building => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.10_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for Jellyfish-2.2.10_5 ===> Applying ports patches for Jellyfish-2.2.10_5 /usr/bin/sed -i.bak -e 's@Werror@Wno-deprecated-declarations@g' /construction/biology/jellyfish/Jellyfish-2.2.10/development.mk -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_5 depends on executable: yaggo - not found ===> Installing existing package /packages/All/yaggo-1.5.9.txz Installing yaggo-1.5.9... `-- Installing ruby-2.5.5_2,1... | `-- Installing libedit-3.1.20190324,1... | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | `-- Extracting libedit-3.1.20190324,1: .......... done | `-- Installing libffi-3.2.1_3... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done | `-- Installing libyaml-0.2.2... | `-- Extracting libyaml-0.2.2: ......... done `-- Extracting ruby-2.5.5_2,1: .......... done Extracting yaggo-1.5.9: ...... done Message from ruby-2.5.5_2,1: ==== Some of the standard commands are provided as separate ports for ease of upgrading: devel/ruby-gems: gem - RubyGems package manager devel/rubygem-rake: rake - Ruby Make And some of the standard libraries are provided as separate ports since they require extra dependencies: databases/rubygem-dbm: DBM module databases/rubygem-gdbm: GDBM module Install them as occasion demands. ==== ===> Jellyfish-2.2.10_5 depends on executable: yaggo - found ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz Installing autoconf-2.69_2... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing m4-1.4.18_1,1... `-- Extracting m4-1.4.18_1,1: .......... done `-- Installing perl5-5.28.2... `-- Extracting perl5-5.28.2: .......... done Extracting autoconf-2.69_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. ===> Jellyfish-2.2.10_5 depends on package: autoconf>=2.69 - found ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1_1.txz Installing automake-1.16.1_1... Extracting automake-1.16.1_1: .......... done ===> Jellyfish-2.2.10_5 depends on package: automake>=1.16.1 - found ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6_1.txz Installing libtool-2.4.6_1... Extracting libtool-2.4.6_1: .......... done ===> Jellyfish-2.2.10_5 depends on executable: libtoolize - found ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 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... `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> Jellyfish-2.2.10_5 depends on executable: gmake - found ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.6.1,1.txz Installing pkgconf-1.6.1,1... Extracting pkgconf-1.6.1,1: .......... done ===> Jellyfish-2.2.10_5 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 depends on executable: msgfmt - not found ===> Installing existing package /packages/All/gettext-tools-0.20.1.txz Installing gettext-tools-0.20.1... `-- Installing libtextstyle-0.20.1... `-- Extracting libtextstyle-0.20.1: .......... done Extracting gettext-tools-0.20.1: .......... done ===> Jellyfish-2.2.10_5 depends on executable: msgfmt - found ===> Returning to build of Jellyfish-2.2.10_5 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_5 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.9.txz Installing htslib-1.9... `-- Installing curl-7.65.1_1... | `-- Installing ca_root_nss-3.45... | `-- Extracting ca_root_nss-3.45: ........ done | `-- Installing libnghttp2-1.39.1... | `-- Extracting libnghttp2-1.39.1: .......... done `-- Extracting curl-7.65.1_1: .......... done Extracting htslib-1.9: .......... done Message from ca_root_nss-3.45: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> Jellyfish-2.2.10_5 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of Jellyfish-2.2.10_5 ===> Jellyfish-2.2.10_5 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for Jellyfish-2.2.10_5 libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' configure: WARNING: unrecognized options: --enable-nls configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.6 checking host system type... x86_64-portbld-dragonfly5.6 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking whether gmake supports nested variables... (cached) yes checking how to print strings... printf checking whether gmake supports the include directive... yes (GNU style) checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking how to convert x86_64-portbld-dragonfly5.6 file names to x86_64-portbld-dragonfly5.6 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.6 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly5.6 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking pkg-config is at least version 0.9.0... yes checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly5.6 ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for the common suffixes of directories in the library search path... lib,lib checking for HTSLIB... no checking for samtools... no checking for md5sum... no checking for md5... md5 -r checking for yaggo... /usr/local/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 306c3:1100800:7ffafbff:bfebfbff checking for x86 cpuid 0x00000007 output... 0:2fbb:0:0 checking for x86 cpuid 0x80000001 output... 0:0:21:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... no checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... no checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --enable-nls -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for Jellyfish-2.2.10_5 gmake[2]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' /usr/local/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo gmake all-am gmake[3]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' depbase=`echo sub_commands/jellyfish.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/jellyfish.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/count_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/count_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/count_main.o sub_commands/count_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/info_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/info_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/info_main.o sub_commands/info_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/dump_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/dump_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/dump_main.o sub_commands/dump_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/histo_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include 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/construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[3]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake install-am gmake[4]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[5]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c -s libjellyfish-2.0.la '/construction/biology/jellyfish/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.so.2.0.0 libtool: install: strip --strip-unneeded /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /construction/biology/jellyfish/stage/usr/local/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /construction/biology/jellyfish/stage/usr/local/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: strip --strip-debug /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: chmod 644 /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: ranlib /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s bin/jellyfish '/construction/biology/jellyfish/stage/usr/local/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s bin/.libs/jellyfish /construction/biology/jellyfish/stage/usr/local/bin/jellyfish /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/include/jellyfish-2.2.10/jellyfish' install -m 0644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/construction/biology/jellyfish/stage/usr/local/include/jellyfish-2.2.10/jellyfish' install -m 0644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/construction/biology/jellyfish/stage/usr/local/include/jellyfish-2.2.10/jellyfish' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/man/man1' install -m 0644 'doc/jellyfish.man' '/construction/biology/jellyfish/stage/usr/local/man/man1/jellyfish.1' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/libdata/pkgconfig' install -m 0644 jellyfish-2.0.pc '/construction/biology/jellyfish/stage/usr/local/libdata/pkgconfig' gmake[5]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[4]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[3]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[2]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for Jellyfish-2.2.10_5 file sizes/checksums [60]: . done packing files [60]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 17:04:04 UTC Duration: 00:01:18