=> Building biology/htslib Started : Saturday, 6 JUL 2019 at 02:15:30 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 htslib-1.9: CURL=on: Use libcurl for network file access (HTTPS and S3 support). ===> Use 'make config' to modify these settings -------------------------------------------------- -- 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 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --enable-libcurl --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/htslib/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTVERSION="1.9" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 PROFILE="@comment " DOCSDIR="share/doc/htslib" EXAMPLESDIR="share/examples/htslib" DATADIR="share/htslib" WWWDIR="www/htslib" ETCDIR="etc/htslib" -------------------------------------------------- -- 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 -------------------------------------------------- -- /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 BSD3CLAUSE MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> htslib-1.9 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 ===> htslib-1.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of htslib-1.9 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.9 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.9 for building => SHA256 Checksum OK for samtools-htslib-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE MIT accepted by the user ===> Fetching all distfiles required by htslib-1.9 for building ===> Extracting for htslib-1.9 => SHA256 Checksum OK for samtools-htslib-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for htslib-1.9 ===> Applying ports patches for htslib-1.9 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> htslib-1.9 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. ===> htslib-1.9 depends on package: autoconf>=2.69 - found ===> Returning to build of htslib-1.9 ===> htslib-1.9 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 ===> htslib-1.9 depends on package: automake>=1.16.1 - found ===> Returning to build of htslib-1.9 ===> htslib-1.9 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 ===> htslib-1.9 depends on executable: gmake - found ===> Returning to build of htslib-1.9 ===> htslib-1.9 depends on file: /usr/local/lib/libcrypto.so.45 - not found ===> Installing existing package /packages/All/libressl-2.9.2.txz Installing libressl-2.9.2... Extracting libressl-2.9.2: .......... done ===> htslib-1.9 depends on file: /usr/local/lib/libcrypto.so.45 - found ===> Returning to build of htslib-1.9 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> htslib-1.9 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-7.65.1.txz Installing curl-7.65.1... `-- Installing ca_root_nss-3.44... `-- Extracting ca_root_nss-3.44: ........ done `-- Installing libnghttp2-1.39.1... `-- Extracting libnghttp2-1.39.1: .......... done Extracting curl-7.65.1: .......... done Message from ca_root_nss-3.44: ********************************* 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-1.9 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of htslib-1.9 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for htslib-1.9 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 special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-DragonFly... plain .so 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 whether fdatasync is declared... no 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 for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for htslib-1.9 gmake[1]: Entering directory '/construction/biology/htslib/htslib-1.9' cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kfunc.o kfunc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o knetfile.o knetfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kstring.o kstring.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -c -o bgzf.o bgzf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o errmod.o errmod.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o faidx.o faidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hfile.o hfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hts_os.o hts_os.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o md5.o md5.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o multipart.o multipart.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o probaln.o probaln.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o realn.o realn.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o regidx.o regidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o sam.o sam.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -c -o vcf_sweep.o vcf_sweep.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tbx.o tbx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o textutils.o textutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o thread_pool.o thread_pool.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcf.o vcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfutils.o vcfutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -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 -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 -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 -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 -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 -I. -isystem /usr/local/include -c -o cram/cram_samtools.o cram/cram_samtools.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -c -o cram/files.o cram/files.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/mFILE.o cram/mFILE.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -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 -I. -isystem /usr/local/include -c -o cram/rANS_static.o cram/rANS_static.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/sam_header.o cram/sam_header.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hfile_gcs.o hfile_gcs.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hfile_s3.o hfile_s3.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o kfunc.pico kfunc.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o knetfile.pico knetfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o kstring.pico kstring.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -fpic -c -o bgzf.pico bgzf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o errmod.pico errmod.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o faidx.pico faidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o hfile.pico hfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o hfile_net.pico hfile_net.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o hts.pico hts.c In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3823:17: cram/cram_io.c:3748:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:3740:9: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -fpic -c -o md5.pico md5.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o multipart.pico multipart.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o probaln.pico probaln.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o realn.pico realn.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o regidx.pico regidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o sam.pico sam.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -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 -I. -isystem /usr/local/include -fpic -c -o tbx.pico tbx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o textutils.pico textutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -fpic -c -o vcf.pico vcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o vcfutils.pico vcfutils.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -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 -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 -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 -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 -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 -I. -isystem /usr/local/include -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -I. -isystem /usr/local/include -fpic -c -o cram/files.pico cram/files.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -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 -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 -I. -isystem /usr/local/include -fpic -c -o cram/rANS_static.pico cram/rANS_static.c In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3823:17: cram/cram_io.c:3748:13: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:3740:9: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fpic -c -o cram/sam_header.pico cram/sam_header.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -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 -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 -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 -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 -I. -isystem /usr/local/include -c -o bgzip.o bgzip.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o htsfile.o htsfile.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tabix.o tabix.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hts.o hts.c cc -shared -Wl,-soname,libhts.so.2 -Wl,-rpath,/usr/local/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.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_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 hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.2 ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.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_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 hfile_libcurl.o hfile_gcs.o hfile_s3.o ranlib libhts.a cc -Wl,-rpath,/usr/local/lib -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread cc -Wl,-rpath,/usr/local/lib -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread cc -Wl,-rpath,/usr/local/lib -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -L/usr/local/lib -lcurl -lcrypto -lpthread gmake[1]: Leaving directory '/construction/biology/htslib/htslib-1.9' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> htslib-1.9 depends on file: /usr/local/lib/libcrypto.so.45 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for htslib-1.9 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/htslib/htslib-1.9' 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/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.1.9 ln -sf libhts.so.1.9 /construction/biology/htslib/stage/usr/local/lib/libhts.so ln -sf libhts.so.1.9 /construction/biology/htslib/stage/usr/local/lib/libhts.so.2 sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9#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 gmake[1]: Leaving directory '/construction/biology/htslib/htslib-1.9' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for htslib-1.9 file sizes/checksums [44]: . done packing files [44]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Saturday, 6 JUL 2019 at 02:16:24 UTC Duration: 00:00:54