------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for htslib-1.13: CURL=on: Use libcurl for network file access (HTTPS and S3 support). ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/htslib XDG_CONFIG_HOME=/construction/biology/htslib HOME=/construction/biology/htslib TMPDIR="/tmp" PATH=/construction/biology/htslib/.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 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --enable-libcurl --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr/local OPENSSLDIR=/usr/local/openssl OPENSSLINC=/usr/local/include OPENSSLLIB=/usr/local/lib OPENSSLRPATH=/usr/local/lib XDG_DATA_HOME=/construction/biology/htslib XDG_CONFIG_HOME=/construction/biology/htslib HOME=/construction/biology/htslib TMPDIR="/tmp" PATH=/construction/biology/htslib/.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=" -Wl,-rpath,/usr/local/lib " 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/htslib/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTVERSION="1.13" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 PROFILE="@comment " DOCSDIR="share/doc/htslib" EXAMPLESDIR="share/examples/htslib" DATADIR="share/htslib" WWWDIR="www/htslib" ETCDIR="etc/htslib" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600105 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=12 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.pkg Installing /packages/All/gmake-4.3_2.pkg Installing /packages/All/openssl-1.1.1l,1.pkg Installing /packages/All/m4-1.4.19,1.pkg Installing /packages/All/autoconf-wrapper-20131203.pkg Installing /packages/All/perl5-5.32.1_1.pkg Installing /packages/All/autoconf-2.69_3.pkg Installing /packages/All/automake-1.16.4.pkg Installing /packages/All/libdeflate-1.8.pkg Installing /packages/All/libnghttp2-1.44.0.pkg Installing /packages/All/libssh2-1.9.0_3,3.pkg Installing /packages/All/ca_root_nss-3.69_1.pkg ===== Message from ca_root_nss-3.69_1: -- 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. 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 Installing /packages/All/curl-7.79.1.pkg SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> htslib-1.13 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> htslib-1.13 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by htslib-1.13 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> htslib-1.13 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by htslib-1.13 for building => SHA256 Checksum OK for htslib-1.13.tar.bz2. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> htslib-1.13 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by htslib-1.13 for building ===> Extracting for htslib-1.13 => SHA256 Checksum OK for htslib-1.13.tar.bz2. Extracted Memory Use: 13.00M SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for htslib-1.13 ===> Applying ports patches for htslib-1.13 from /xports/biology/htslib/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> htslib-1.13 depends on package: gmake>=4.3 - found ===> htslib-1.13 depends on file: /usr/local/lib/libcrypto.so.11 - found ===> htslib-1.13 depends on package: autoconf>=2.69 - found ===> htslib-1.13 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> htslib-1.13 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so) ===> htslib-1.13 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> htslib-1.13 depends on package: gmake>=4.3 - found ===> htslib-1.13 depends on file: /usr/local/lib/libcrypto.so.11 - found ===> htslib-1.13 depends on package: autoconf>=2.69 - found ===> htslib-1.13 depends on package: automake>=1.16.1 - found ===> htslib-1.13 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so) ===> htslib-1.13 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Configuring for htslib-1.13 configure: loading site script /xports/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 grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... cpp 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 fsync... (cached) yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... (cached) yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for htslib-1.13 gmake[1]: Entering directory '/construction/biology/htslib/htslib-1.13' cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o kfunc.o kfunc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o kstring.o kstring.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o bcf_sr_sort.o bcf_sr_sort.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o bgzf.o bgzf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o errmod.o errmod.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o faidx.o faidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o header.o header.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.13"' > version.h echo '#define HTS_CC "cc"' > config_vars.h cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hts_expr.o hts_expr.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hts_os.o hts_os.c echo '#define HTS_CPPFLAGS "-isystem /usr/local/include"' >> config_vars.h cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o md5.o md5.c echo '#define HTS_CFLAGS "-Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-Wl,-rpath,/usr/local/lib -fvisibility=hidden "' >> config_vars.h echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto"' >> config_vars.h cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o multipart.o multipart.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o probaln.o probaln.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o realn.o realn.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o regidx.o regidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o region.o region.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o sam.o sam.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o vcf_sweep.o vcf_sweep.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o tbx.o tbx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o textutils.o textutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o thread_pool.o thread_pool.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o vcf.o vcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o vcfutils.o vcfutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_external.o cram/cram_external.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_index.o cram/cram_index.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_io.o cram/cram_io.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/mFILE.o cram/mFILE.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_gcs.o hfile_gcs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_s3.o hfile_s3.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hfile_s3_write.o hfile_s3_write.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o kfunc.pico kfunc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o kstring.pico kstring.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o bgzf.pico bgzf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o errmod.pico errmod.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o faidx.pico faidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o header.pico header.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile.pico hfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hts.pico hts.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hts_expr.pico hts_expr.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hts_os.pico hts_os.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o md5.pico md5.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o multipart.pico multipart.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o probaln.pico probaln.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o realn.pico realn.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o regidx.pico regidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o region.pico region.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o sam.pico sam.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o vcf_sweep.pico vcf_sweep.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o tbx.pico tbx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o textutils.pico textutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o thread_pool.pico thread_pool.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o vcf.pico vcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o vcfutils.pico vcfutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_encode.pico cram/cram_encode.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_external.pico cram/cram_external.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_index.pico cram/cram_index.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_io.pico cram/cram_io.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/mFILE.pico cram/mFILE.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_libcurl.pico hfile_libcurl.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_gcs.pico hfile_gcs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_s3.pico hfile_s3.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -fpic -c -o hfile_s3_write.pico hfile_s3_write.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o bgzip.o bgzip.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o htsfile.o htsfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o tabix.o tabix.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -I. -isystem /usr/local/include -c -o hts.o hts.c cc -shared -Wl,-soname,libhts.so.3 -Wl,-rpath,/usr/local/lib -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.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_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.3 ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a cc -Wl,-rpath,/usr/local/lib -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread cc -Wl,-rpath,/usr/local/lib -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread cc -Wl,-rpath,/usr/local/lib -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread gmake[1]: Leaving directory '/construction/biology/htslib/htslib-1.13' SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> htslib-1.13 depends on file: /usr/local/lib/libcrypto.so.11 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for htslib-1.13 ===> htslib-1.13 depends on file: /usr/local/lib/libcrypto.so.11 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/htslib/htslib-1.13' mkdir -p /construction/biology/htslib/stage/usr/local/bin /construction/biology/htslib/stage/usr/local/include /construction/biology/htslib/stage/usr/local/include/htslib /construction/biology/htslib/stage/usr/local/lib /construction/biology/htslib/stage/usr/local/man/man1 /construction/biology/htslib/stage/usr/local/man/man5 /construction/biology/htslib/stage/usr/local/man/man7 /construction/biology/htslib/stage/usr/local/libdata/pkgconfig if test -n ""; then mkdir -p /construction/biology/htslib/stage; fi install -s -m 0644 libhts.so /construction/biology/htslib/stage/usr/local/lib/libhts.so.1.13 ln -sf libhts.so.1.13 /construction/biology/htslib/stage/usr/local/lib/libhts.so ln -sf libhts.so.1.13 /construction/biology/htslib/stage/usr/local/lib/libhts.so.3 sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.13#g' htslib.pc.tmp > /construction/biology/htslib/stage/usr/local/libdata/pkgconfig/htslib.pc chmod 644 /construction/biology/htslib/stage/usr/local/libdata/pkgconfig/htslib.pc install -s -m 555 bgzip htsfile tabix /construction/biology/htslib/stage/usr/local/bin if test -n ""; then install -s -m 555 /construction/biology/htslib/stage; fi install -m 0644 htslib/*.h /construction/biology/htslib/stage/usr/local/include/htslib install -m 0644 libhts.a /construction/biology/htslib/stage/usr/local/lib/libhts.a install -m 444 bgzip.1 htsfile.1 tabix.1 /construction/biology/htslib/stage/usr/local/man/man1 install -m 444 faidx.5 sam.5 vcf.5 /construction/biology/htslib/stage/usr/local/man/man5 install -m 444 htslib-s3-plugin.7 /construction/biology/htslib/stage/usr/local/man/man7 gmake[1]: Leaving directory '/construction/biology/htslib/htslib-1.13' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/libhts.so.1.13 is linked to /usr/local/lib/libnghttp2.so.14 from www/libnghttp2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libnghttp2.so:www/libnghttp2 Error: /usr/local/lib/libhts.so.1.13 is linked to /usr/local/lib/libssh2.so.1 from security/libssh2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libssh2.so:security/libssh2 Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for htslib-1.13 file sizes/checksums [43]: 0% file sizes/checksums [43]: 100% packing files [43]: 0% packing files [43]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:00:55