=> Building biology/htslib build started at Mon Mar 13 04:51:48 PDT 2017 port directory: /usr/ports/biology/htslib building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.1380.gb4315f-DEVELOPMENT #0: Fri Mar 3 17:20:21 PST 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: cartwright@asu.edu ident warning: no id keywords in /build/boomdata/data/.m/Release48-default/ref/../06//usr/ports/biology/htslib/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400713 Jail OSVERSION: 400713 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release48-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=htslib-1.3.1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release48-default/ref/.p/pool MASTERNAME=Release48-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for htslib-1.3.1: CURL=on: Use libcurl for network file access (HTTPS and S3 support). ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --enable-libcurl --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/htslib XDG_CONFIG_HOME=/wrkdirs/biology/htslib HOME=/wrkdirs/biology/htslib 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-- INSTALL_LIB="install -s -m 444" INSTALL_DATA="install -m 0644" INSTALL_PROGRAM="install -s -m 555" INSTALL_DIR="/bin/mkdir -p" XDG_DATA_HOME=/wrkdirs/biology/htslib XDG_CONFIG_HOME=/wrkdirs/biology/htslib HOME=/wrkdirs/biology/htslib 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="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib" 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-- PORTVERSION="1.3.1" OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.1 PERL_VER=5.24 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/5.24 PROFILE="@comment " DOCSDIR="share/doc/htslib" EXAMPLESDIR="share/examples/htslib" DATADIR="share/htslib" WWWDIR="www/htslib" ETCDIR="etc/htslib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/htslib DOCSDIR=/usr/local/share/doc/htslib EXAMPLESDIR=/usr/local/share/examples/htslib WWWDIR=/usr/local/www/htslib ETCDIR=/usr/local/etc/htslib --End SUB_LIST-- ---Begin make.conf--- 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 BSD3CLAUSE MIT accepted by the user =========================================================================== =================================================== ===> htslib-1.3.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz Installing pkg-1.9.4_1... Extracting pkg-1.9.4_1: .......... done ===> htslib-1.3.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of htslib-1.3.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.3.1 for building =========================================================================== =================================================== ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.3.1 for building => SHA256 Checksum OK for samtools-htslib-1.3.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.3.1 for building ===> Extracting for htslib-1.3.1 => SHA256 Checksum OK for samtools-htslib-1.3.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for htslib-1.3.1 ===> Applying ports patches for htslib-1.3.1 =========================================================================== =================================================== ===> htslib-1.3.1 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-0.2.6... `-- Extracting indexinfo-0.2.6: .... done `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: ........ done `-- Installing perl5-5.24.1... `-- Extracting perl5-5.24.1: .......... done `-- Installing m4-1.4.18,1... `-- Extracting m4-1.4.18,1: .......... done Extracting autoconf-2.69_1: .......... done Message from perl5-5.24.1: 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. ===> htslib-1.3.1 depends on executable: autoconf-2.69 - found ===> Returning to build of htslib-1.3.1 ===> htslib-1.3.1 depends on executable: autoheader-2.69 - found ===> htslib-1.3.1 depends on executable: autoreconf-2.69 - found ===> htslib-1.3.1 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 ===> htslib-1.3.1 depends on executable: aclocal-1.15 - found ===> Returning to build of htslib-1.3.1 ===> htslib-1.3.1 depends on executable: automake-1.15 - found ===> htslib-1.3.1 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_1... `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_1: .......... done ===> htslib-1.3.1 depends on executable: gmake - found ===> Returning to build of htslib-1.3.1 =========================================================================== =================================================== ===> htslib-1.3.1 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-7.52.1_1.txz Installing curl-7.52.1_1... `-- Installing ca_root_nss-3.28.1... `-- Extracting ca_root_nss-3.28.1: ........ done `-- Installing krb5-1.14.4_1... | `-- Installing libressl-2.4.5... | `-- Extracting libressl-2.4.5: .......... done | `-- Installing pkgconf-1.2.1_1... | `-- Extracting pkgconf-1.2.1_1: .......... done `-- Extracting krb5-1.14.4_1: .......... done `-- Installing libnghttp2-1.19.0... `-- Extracting libnghttp2-1.19.0: .......... done Extracting curl-7.52.1_1: .......... done Message from ca_root_nss-3.28.1: ********************************* 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 *************************************************************************** ===> htslib-1.3.1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of htslib-1.3.1 =========================================================================== =================================================== ===> Configuring for htslib-1.3.1 configure: loading site script /usr/ports/Templates/config.site 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 for ranlib... ranlib checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking how to run the C preprocessor... cpp 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 stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getpagesize... (cached) yes checking for working mmap... yes checking for gmtime_r... yes checking for zlib.h... (cached) yes checking for inflate in -lz... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto configure: creating ./config.status config.status: creating config.mk config.status: creating config.h =========================================================================== =================================================== ===> Building for htslib-1.3.1 gmake[1]: Entering directory '/wrkdirs/biology/htslib/htslib-1.3.1' cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o kfunc.o kfunc.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o knetfile.o knetfile.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o kstring.o kstring.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bgzf.o bgzf.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o faidx.o faidx.c knetfile.c: In function 'socket_wait': knetfile.c:72:8: warning: implicit declaration of function 'select' [-Wimplicit-function-declaration] ret = select(fd+1, fdr, fdw, 0, &tv); ^ cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o hfile.o hfile.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.1"' > version.h cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o md5.o md5.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o regidx.o regidx.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o sam.o sam.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o vcf_sweep.o vcf_sweep.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o tbx.o tbx.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o vcf.o vcf.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o vcfutils.o vcfutils.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_external.o cram/cram_external.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_index.o cram/cram_index.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_samtools.o cram/cram_samtools.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/files.o cram/files.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/mFILE.o cram/mFILE.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/rANS_static.o cram/rANS_static.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/sam_header.o cram/sam_header.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/thread_pool.o cram/thread_pool.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/vlen.o cram/vlen.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cram/zfio.o cram/zfio.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o kfunc.pico kfunc.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o knetfile.pico knetfile.c knetfile.c: In function 'socket_wait': knetfile.c:72:8: warning: implicit declaration of function 'select' [-Wimplicit-function-declaration] ret = select(fd+1, fdr, fdw, 0, &tv); ^ cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o kstring.pico kstring.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o bgzf.pico bgzf.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o faidx.pico faidx.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o hfile.pico hfile.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o hfile_net.pico hfile_net.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o hts.pico hts.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o md5.pico md5.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o regidx.pico regidx.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o sam.pico sam.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o vcf_sweep.pico vcf_sweep.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o tbx.pico tbx.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o vcf.pico vcf.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o vcfutils.pico vcfutils.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_encode.pico cram/cram_encode.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_external.pico cram/cram_external.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_index.pico cram/cram_index.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_io.pico cram/cram_io.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/files.pico cram/files.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/mFILE.pico cram/mFILE.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/rANS_static.pico cram/rANS_static.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/sam_header.pico cram/sam_header.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/thread_pool.pico cram/thread_pool.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/vlen.pico cram/vlen.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o cram/zfio.pico cram/zfio.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -fpic -c -o hfile_libcurl.pico hfile_libcurl.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bgzip.o bgzip.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o htsfile.o htsfile.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o tabix.o tabix.c cc -pipe -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o hts.o hts.c cc -shared -Wl,-soname,libhts.so.1 -pthread -L/usr/local/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico hfile_libcurl.pico -lz -lm -lcurl -lcrypto ln -sf libhts.so libhts.so.1 ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o hfile_libcurl.o ranlib libhts.a cc -pthread -L/usr/local/lib -o bgzip bgzip.o libhts.a -lz -lcurl -lcrypto cc -pthread -L/usr/local/lib -o htsfile htsfile.o libhts.a -lz -lcurl -lcrypto cc -pthread -L/usr/local/lib -o tabix tabix.o libhts.a -lz -lcurl -lcrypto gmake[1]: Leaving directory '/wrkdirs/biology/htslib/htslib-1.3.1' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for htslib-1.3.1 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/htslib/htslib-1.3.1' /bin/mkdir -p /wrkdirs/biology/htslib/stage/usr/local/bin /wrkdirs/biology/htslib/stage/usr/local/include /wrkdirs/biology/htslib/stage/usr/local/include/htslib /wrkdirs/biology/htslib/stage/usr/local/lib /wrkdirs/biology/htslib/stage/usr/local/man/man1 /wrkdirs/biology/htslib/stage/usr/local/man/man5 /wrkdirs/biology/htslib/stage/usr/local/libdata/pkgconfig if test -n ""; then /bin/mkdir -p /wrkdirs/biology/htslib/stage; fi install -s -m 444 libhts.so /wrkdirs/biology/htslib/stage/usr/local/lib/libhts.so.1.3.1 ln -sf libhts.so.1.3.1 /wrkdirs/biology/htslib/stage/usr/local/lib/libhts.so ln -sf libhts.so.1.3.1 /wrkdirs/biology/htslib/stage/usr/local/lib/libhts.so.1 sed -e 's#@includedir@#/usr/local/include#g;s#@libdir@#/usr/local/lib#g;s#@PACKAGE_VERSION@#1.3.1#g' htslib.pc.in > /wrkdirs/biology/htslib/stage/usr/local/libdata/pkgconfig/htslib.pc chmod 644 /wrkdirs/biology/htslib/stage/usr/local/libdata/pkgconfig/htslib.pc install -s -m 555 bgzip htsfile tabix /wrkdirs/biology/htslib/stage/usr/local/bin if test -n ""; then install -s -m 555 /wrkdirs/biology/htslib/stage; fi install -m 0644 htslib/*.h /wrkdirs/biology/htslib/stage/usr/local/include/htslib install -m 0644 libhts.a /wrkdirs/biology/htslib/stage/usr/local/lib/libhts.a install -m 0644 htsfile.1 tabix.1 /wrkdirs/biology/htslib/stage/usr/local/man/man1 install -m 0644 faidx.5 sam.5 vcf.5 /wrkdirs/biology/htslib/stage/usr/local/man/man5 gmake[1]: Leaving directory '/wrkdirs/biology/htslib/htslib-1.3.1' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for htslib-1.3.1 file sizes/checksums [39]: . done packing files [39]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for htslib-1.3.1 build of biology/htslib ended at Mon Mar 13 04:52:51 PDT 2017 build time: 00:01:03