=> Building biology/vcftools build started at Tue Oct 4 15:02:15 PDT 2016 port directory: /usr/ports/biology/vcftools building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../04//usr/ports/biology/vcftools/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=vcftools-0.1.14 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ZLIB_CFLAGS=" " ZLIB_LIBS="-lz" MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/biology/vcftools XDG_CONFIG_HOME=/wrkdirs/biology/vcftools HOME=/wrkdirs/biology/vcftools TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/vcftools XDG_CONFIG_HOME=/wrkdirs/biology/vcftools HOME=/wrkdirs/biology/vcftools TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" 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 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 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/5.20 PROFILE="@comment " DOCSDIR="share/doc/vcftools" EXAMPLESDIR="share/examples/vcftools" DATADIR="share/vcftools" WWWDIR="www/vcftools" ETCDIR="etc/vcftools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcftools DOCSDIR=/usr/local/share/doc/vcftools EXAMPLESDIR=/usr/local/share/examples/vcftools WWWDIR=/usr/local/www/vcftools ETCDIR=/usr/local/etc/vcftools --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License LGPL3 accepted by the user =========================================================================== =================================================== ===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcftools-0.1.14 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.14 for building =========================================================================== =================================================== ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.14 for building => SHA256 Checksum OK for vcftools_0.1.14_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.14 for building ===> Extracting for vcftools-0.1.14 => SHA256 Checksum OK for vcftools_0.1.14_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for vcftools-0.1.14 =========================================================================== =================================================== ===> vcftools-0.1.14 depends on executable: autoconf-2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_1.txz Installing autoconf-2.69_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: ........ done `-- Installing perl5-5.20.3_15... `-- Extracting perl5-5.20.3_15: .......... done `-- Installing m4-1.4.17_1,1... `-- Extracting m4-1.4.17_1,1: .......... done Extracting autoconf-2.69_1: .......... done Message from perl5-5.20.3_15: 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. ===> vcftools-0.1.14 depends on executable: autoconf-2.69 - found ===> Returning to build of vcftools-0.1.14 ===> vcftools-0.1.14 depends on executable: autoheader-2.69 - found ===> vcftools-0.1.14 depends on executable: autoreconf-2.69 - found ===> vcftools-0.1.14 depends on executable: aclocal-1.15 - not found ===> Installing existing package /packages/All/automake-1.15_1.txz Installing automake-1.15_1... `-- Installing automake-wrapper-20131203... `-- Extracting automake-wrapper-20131203: ... done Extracting automake-1.15_1: .......... done ===> vcftools-0.1.14 depends on executable: aclocal-1.15 - found ===> Returning to build of vcftools-0.1.14 ===> vcftools-0.1.14 depends on executable: automake-1.15 - found ===> vcftools-0.1.14 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> vcftools-0.1.14 depends on executable: gmake - found ===> Returning to build of vcftools-0.1.14 ===> vcftools-0.1.14 depends on package: pkgconf>=0.9.10 - not found ===> Installing existing package /packages/All/pkgconf-1.0.1.txz Installing pkgconf-1.0.1... Extracting pkgconf-1.0.1: .......... done ===> vcftools-0.1.14 depends on package: pkgconf>=0.9.10 - found ===> Returning to build of vcftools-0.1.14 ===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for vcftools-0.1.14 configure.ac:16: installing './compile' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site 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 for style of include used by gmake... GNU checking dependency style of c++... gcc3 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 how to run the C preprocessor... cpp checking for perl... (cached) /usr/local/bin/perl checking pkg-config is at least version 0.9.0... yes checking for ZLIB... yes 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 arpa/inet.h... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for netdb.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for inline... inline checking for int16_t... (cached) yes checking for int32_t... (cached) yes checking for int64_t... (cached) yes checking for int8_t... (cached) yes checking for off_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint8_t... (cached) yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for error_at_line... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... (cached) yes checking for memset... (cached) yes checking for pow... no checking for select... (cached) yes checking for socket... yes checking for sqrt... no checking for strchr... yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strstr... yes checking for strtol... (cached) yes 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 src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===> Building for vcftools-0.1.14 gmake[1]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake all-recursive gmake[2]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' Making all in src gmake[3]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' Making all in cpp gmake[4]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/cpp' c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp cc -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po cc -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c knetfile.c: In function 'socket_wait': knetfile.c:70:8: warning: implicit declaration of function 'select' [-Wimplicit-function-declaration] ret = select(fd+1, fdr, fdw, 0, &tv); ^ mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_format_convert.o -MD -MP -MF .deps/vcftools-variant_file_format_convert.Tpo -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_output.o -MD -MP -MF .deps/vcftools-variant_file_output.Tpo -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcf_entry.o -MD -MP -MF .deps/vcftools-vcf_entry.Tpo -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcf_entry_setters.o -MD -MP -MF .deps/vcftools-vcf_entry_setters.Tpo -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcf_file.o -MD -MP -MF .deps/vcftools-vcf_file.Tpo -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcftools.o -MD -MP -MF .deps/vcftools-vcftools.Tpo -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_file.Po mv -f .deps/vcftools-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.Po mv -f .deps/vcftools-vcf_entry.Tpo .deps/vcftools-vcf_entry.Po mv -f .deps/vcftools-variant_file_output.Tpo .deps/vcftools-variant_file_output.Po c++ -pipe -O2 -fno-strict-aliasing -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz gmake[4]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/cpp' Making all in perl gmake[4]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/perl' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/perl' gmake[4]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[3]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[3]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[2]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[1]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' =========================================================================== =================================================== ===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== ===> Staging for vcftools-0.1.14 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' Making install in src gmake[2]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' Making install in cpp gmake[3]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/cpp' gmake[4]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/cpp' /bin/mkdir -p '/wrkdirs/biology/vcftools/stage/usr/local/bin' install -s -m 555 vcftools '/wrkdirs/biology/vcftools/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/biology/vcftools/stage/usr/local/man/man1' install -m 0644 vcftools.1 '/wrkdirs/biology/vcftools/stage/usr/local/man/man1' gmake[4]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/cpp' gmake[3]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/cpp' Making install in perl gmake[3]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/perl' gmake[4]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/perl' /bin/mkdir -p '/wrkdirs/biology/vcftools/stage/usr/local/bin' install -m 555 fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/wrkdirs/biology/vcftools/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/biology/vcftools/stage/usr/local/lib/perl5/site_perl' install -m 0644 FaSlice.pm Vcf.pm VcfStats.pm '/wrkdirs/biology/vcftools/stage/usr/local/lib/perl5/site_perl' gmake[4]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/perl' gmake[3]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src/perl' gmake[3]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[4]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[3]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[2]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14/src' gmake[2]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[3]: Entering directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[2]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' gmake[1]: Leaving directory '/wrkdirs/biology/vcftools/vcftools-0.1.14' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for vcftools-0.1.14 file sizes/checksums [32]: . done packing files [32]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for vcftools-0.1.14 build of biology/vcftools ended at Tue Oct 4 15:04:04 PDT 2016 build time: 00:01:49