=> Building biology/vsearch Started : Sunday, 7 JUL 2019 at 04:56:13 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 -------------------------------------------------- ===> The following configuration options are available for vsearch-2.13.4: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/vsearch XDG_CONFIG_HOME=/construction/biology/vsearch HOME=/construction/biology/vsearch TMPDIR="/tmp" PATH=/construction/biology/vsearch/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/vsearch XDG_CONFIG_HOME=/construction/biology/vsearch HOME=/construction/biology/vsearch TMPDIR="/tmp" PATH=/construction/biology/vsearch/.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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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/vsearch/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" DOCS="" NO_DOCS="@comment " OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/vsearch" EXAMPLESDIR="share/examples/vsearch" DATADIR="share/vsearch" WWWDIR="www/vsearch" ETCDIR="etc/vsearch" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- DOCS="" NO_DOCS="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vsearch DOCSDIR=/usr/local/share/doc/vsearch EXAMPLESDIR=/usr/local/share/examples/vsearch WWWDIR=/usr/local/www/vsearch ETCDIR=/usr/local/etc/vsearch -------------------------------------------------- -- /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 -------------------------------------------------------------------------------- ===> vsearch-2.13.4 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 ===> vsearch-2.13.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vsearch-2.13.4 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by vsearch-2.13.4 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by vsearch-2.13.4 for building => SHA256 Checksum OK for torognes-vsearch-v2.13.4_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by vsearch-2.13.4 for building ===> Extracting for vsearch-2.13.4 => SHA256 Checksum OK for torognes-vsearch-v2.13.4_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for vsearch-2.13.4 ===> Applying ports patches for vsearch-2.13.4 ===> Applying dragonfly patches for vsearch-2.13.4 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> vsearch-2.13.4 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 indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... 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. ===> vsearch-2.13.4 depends on package: autoconf>=2.69 - found ===> Returning to build of vsearch-2.13.4 ===> vsearch-2.13.4 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 ===> vsearch-2.13.4 depends on package: automake>=1.16.1 - found ===> Returning to build of vsearch-2.13.4 ===> vsearch-2.13.4 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 ===> vsearch-2.13.4 depends on executable: gmake - found ===> Returning to build of vsearch-2.13.4 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> vsearch-2.13.4 depends on shared library: libsysinfo.so - not found ===> Installing existing package /packages/All/libsysinfo-0.0.3_2.txz Installing libsysinfo-0.0.3_2... Extracting libsysinfo-0.0.3_2: ......... done ===> vsearch-2.13.4 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) ===> Returning to build of vsearch-2.13.4 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for vsearch-2.13.4 configure.ac:98: installing './compile' configure.ac:6: installing './config.guess' configure.ac:6: installing './config.sub' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' src/Makefile.am: installing './depcomp' configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.4 checking host system type... x86_64-portbld-dragonfly5.4 checking target system type... x86_64-portbld-dragonfly5.4 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 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 c++ accepts -g... yes checking whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for ranlib... ranlib checking for pthread_create in -lpthread... yes checking for dlopen in -ldl... yes checking for GetProcessMemoryInfo in -lpsapi... no checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep 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 getopt.h... (cached) yes checking for fcntl.h... (cached) yes checking for float.h... (cached) yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for ctype.h... (cached) yes checking for locale.h... (cached) yes checking for limits.h... (cached) yes checking for string.h... (cached) yes checking for sys/time.h... (cached) yes checking for dlfcn.h... (cached) yes checking for inline... inline checking for size_t... (cached) yes checking for uint32_t... (cached) yes checking for int64_t... (cached) yes checking for uint64_t... (cached) yes checking for uint8_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for working strtod... (cached) yes checking for working alloca.h... no checking for alloca... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for memmove... (cached) yes checking for memcpy... (cached) yes checking for posix_memalign... yes checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for memchr... (cached) yes checking for memset... (cached) yes checking for pow... yes checking for regcomp... yes checking for strcasecmp... (cached) yes checking for strchr... (cached) yes checking for strcspn... (cached) yes checking for sysinfo... no checking for library containing pthread_create... none required checking for ps2pdf... no configure: WARNING: *** ps2pdf is required to build a PDF version of the manual checking for pthread.h... (cached) yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for zlib.h... (cached) yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for gcc... cc 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 that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for vsearch-2.13.4 gmake[1]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4' gmake all-recursive gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4' Making all in src gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4/src' depbase=`echo align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT align.o -MD -MP -MF $depbase.Tpo -c -o align.o align.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo align_simd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT align_simd.o -MD -MP -MF $depbase.Tpo -c -o align_simd.o align_simd.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo allpairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT allpairs.o -MD -MP -MF $depbase.Tpo -c -o allpairs.o allpairs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo arch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT arch.o -MD -MP -MF $depbase.Tpo -c -o arch.o arch.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo attributes.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT attributes.o -MD -MP -MF $depbase.Tpo -c -o attributes.o attributes.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo bitmap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT bitmap.o -MD -MP -MF $depbase.Tpo -c -o bitmap.o bitmap.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo chimera.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT chimera.o -MD -MP -MF $depbase.Tpo -c -o chimera.o chimera.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cluster.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cluster.o -MD -MP -MF $depbase.Tpo -c -o cluster.o cluster.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo db.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT db.o -MD -MP -MF $depbase.Tpo -c -o db.o db.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo dbhash.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT dbhash.o -MD -MP -MF $depbase.Tpo -c -o dbhash.o dbhash.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo dbindex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT dbindex.o -MD -MP -MF $depbase.Tpo -c -o dbindex.o dbindex.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo derep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT derep.o -MD -MP -MF $depbase.Tpo -c -o derep.o derep.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo dynlibs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT dynlibs.o -MD -MP -MF $depbase.Tpo -c -o dynlibs.o dynlibs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo eestats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT eestats.o -MD -MP -MF $depbase.Tpo -c -o eestats.o eestats.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fasta.o -MD -MP -MF $depbase.Tpo -c -o fasta.o fasta.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastq.o -MD -MP -MF $depbase.Tpo -c -o fastq.o fastq.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastqjoin.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastqjoin.o -MD -MP -MF $depbase.Tpo -c -o fastqjoin.o fastqjoin.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo fastqops.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fastqops.o -MD -MP -MF $depbase.Tpo -c -o 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$depbase.Tpo $depbase.Po depbase=`echo kmerhash.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT kmerhash.o -MD -MP -MF $depbase.Tpo -c -o kmerhash.o kmerhash.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo linmemalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT linmemalign.o -MD -MP -MF $depbase.Tpo -c -o linmemalign.o linmemalign.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo maps.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT maps.o -MD -MP -MF $depbase.Tpo -c -o maps.o maps.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo mask.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT mask.o -MD -MP -MF $depbase.Tpo -c -o mask.o mask.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo mergepairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT mergepairs.o -MD -MP -MF $depbase.Tpo -c -o mergepairs.o mergepairs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo minheap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minheap.o -MD -MP -MF $depbase.Tpo -c -o minheap.o minheap.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo msa.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT msa.o -MD -MP -MF $depbase.Tpo -c -o msa.o msa.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo otutable.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT otutable.o -MD -MP -MF $depbase.Tpo -c -o otutable.o otutable.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rerep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rerep.o -MD -MP -MF $depbase.Tpo -c -o rerep.o rerep.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo results.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT results.o -MD -MP -MF $depbase.Tpo -c -o results.o results.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo search.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT search.o -MD -MP -MF $depbase.Tpo -c -o search.o search.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo searchcore.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT searchcore.o -MD -MP -MF $depbase.Tpo -c -o searchcore.o searchcore.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo searchexact.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT searchexact.o -MD -MP -MF $depbase.Tpo -c -o searchexact.o searchexact.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sffconvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sffconvert.o -MD -MP -MF $depbase.Tpo -c -o sffconvert.o sffconvert.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sha1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT sha1.o -MD -MP -MF $depbase.Tpo -c -o sha1.o sha1.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo showalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT showalign.o -MD -MP -MF $depbase.Tpo -c -o showalign.o showalign.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo shuffle.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT shuffle.o -MD -MP -MF $depbase.Tpo -c -o shuffle.o shuffle.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sintax.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sintax.o -MD -MP -MF $depbase.Tpo -c -o sintax.o sintax.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sortbylength.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sortbylength.o -MD -MP -MF $depbase.Tpo -c -o sortbylength.o sortbylength.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sortbysize.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sortbysize.o -MD -MP -MF $depbase.Tpo -c -o sortbysize.o sortbysize.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo subsample.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT subsample.o -MD -MP -MF $depbase.Tpo -c -o subsample.o subsample.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo udb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT udb.o -MD -MP -MF $depbase.Tpo -c -o udb.o udb.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo unique.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT unique.o -MD -MP -MF $depbase.Tpo -c -o unique.o unique.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo userfields.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT userfields.o -MD -MP -MF $depbase.Tpo -c -o userfields.o userfields.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo util.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT util.o -MD -MP -MF $depbase.Tpo -c -o util.o util.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo vsearch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT vsearch.o -MD -MP -MF $depbase.Tpo -c -o vsearch.o vsearch.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -Wno-sign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcityhash_a-city.o -MD -MP -MF .deps/libcityhash_a-city.Tpo -c -o libcityhash_a-city.o `test -f 'city.cc' || echo './'`city.cc mv -f .deps/libcityhash_a-city.Tpo .deps/libcityhash_a-city.Po c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -mssse3 -DSSSE3 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcpu_ssse3_a-cpu.o -MD -MP -MF .deps/libcpu_ssse3_a-cpu.Tpo -c -o libcpu_ssse3_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wsign-compare -msse2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcpu_sse2_a-cpu.o -MD -MP -MF .deps/libcpu_sse2_a-cpu.Tpo -c -o libcpu_sse2_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc rm -f libcityhash.a ar cru libcityhash.a libcityhash_a-city.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcityhash.a mv -f .deps/libcpu_sse2_a-cpu.Tpo .deps/libcpu_sse2_a-cpu.Po rm -f libcpu_sse2.a ar cru libcpu_sse2.a libcpu_sse2_a-cpu.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcpu_sse2.a mv -f .deps/libcpu_ssse3_a-cpu.Tpo .deps/libcpu_ssse3_a-cpu.Po rm -f libcpu_ssse3.a ar cru libcpu_ssse3.a libcpu_ssse3_a-cpu.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcpu_ssse3.a c++ -Wall -Wsign-compare -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -o ../bin/vsearch align.o align_simd.o allpairs.o arch.o attributes.o bitmap.o chimera.o cluster.o db.o dbhash.o dbindex.o derep.o dynlibs.o eestats.o fasta.o fastq.o fastqjoin.o fastqops.o fastx.o filter.o getseq.o kmerhash.o linmemalign.o maps.o mask.o md5.o mergepairs.o minheap.o msa.o otutable.o rerep.o results.o search.o searchcore.o searchexact.o sffconvert.o sha1.o showalign.o shuffle.o sintax.o sortbylength.o sortbysize.o subsample.o udb.o unique.o userfields.o util.o vsearch.o libcityhash.a libcpu_ssse3.a libcpu_sse2.a -ldl -lpthread -L/usr/local/lib gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4/src' Making all in man gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4/man' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4/man' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[1]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for vsearch-2.13.4 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4' Making install in src gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4/src' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4/src' /bin/mkdir -p '/construction/biology/vsearch/stage/usr/local/bin' install -s -m 555 ../bin/vsearch '/construction/biology/vsearch/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4/src' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4/src' Making install in man gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4/man' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4/man' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/vsearch/stage/usr/local/man/man1' install -m 0644 vsearch.1 '/construction/biology/vsearch/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4/man' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4/man' gmake[2]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[3]: Entering directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[2]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4' gmake[1]: Leaving directory '/construction/biology/vsearch/vsearch-2.13.4' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for vsearch-2.13.4 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:57:12 UTC Duration: 00:00:59