=> Building biology/tabixpp Started : Thursday, 30 AUG 2018 at 13:00:13 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/tabixpp XDG_CONFIG_HOME=/construction/biology/tabixpp HOME=/construction/biology/tabixpp TMPDIR="/tmp" PATH=/construction/biology/tabixpp/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CMAKE_PREFIX_PATH="/usr/local" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- HTS_HEADERS='' HTS_LIB='' XDG_DATA_HOME=/construction/biology/tabixpp XDG_CONFIG_HOME=/construction/biology/tabixpp HOME=/construction/biology/tabixpp TMPDIR="/tmp" PATH=/construction/biology/tabixpp/.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=gcc50 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=" -L/usr/local/lib" LIBS="" 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/tabixpp/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/tabixpp" EXAMPLESDIR="share/examples/tabixpp" DATADIR="share/tabixpp" WWWDIR="www/tabixpp" ETCDIR="etc/tabixpp" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/tabixpp DOCSDIR=/usr/local/share/doc/tabixpp EXAMPLESDIR=/usr/local/share/examples/tabixpp WWWDIR=/usr/local/www/tabixpp ETCDIR=/usr/local/etc/tabixpp -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> tabixpp-1.0.0.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> tabixpp-1.0.0.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of tabixpp-1.0.0.10 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by tabixpp-1.0.0.10 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by tabixpp-1.0.0.10 for building => SHA256 Checksum OK for ekg-tabixpp-v1.0.0-10-g6bbe690_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by tabixpp-1.0.0.10 for building ===> Extracting for tabixpp-1.0.0.10 => SHA256 Checksum OK for ekg-tabixpp-v1.0.0-10-g6bbe690_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for tabixpp-1.0.0.10 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> tabixpp-1.0.0.10 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.6.txz Installing htslib-1.6... `-- Installing curl-7.60.0... | `-- Installing ca_root_nss-3.38... | `-- Extracting ca_root_nss-3.38: ........ done | `-- Installing krb5-1.16.1_5... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting krb5-1.16.1_5: .......... done | `-- Installing libnghttp2-1.32.0... | `-- Extracting libnghttp2-1.32.0: .......... done `-- Extracting curl-7.60.0: .......... done Extracting htslib-1.6: .......... done Message from ca_root_nss-3.38: ********************************* 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 *************************************************************************** ===> tabixpp-1.0.0.10 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of tabixpp-1.0.0.10 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for tabixpp-1.0.0.10 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for tabixpp-1.0.0.10 --- tabix.o --- c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -c tabix.cpp -Ihtslib tabix.cpp: In constructor 'Tabix::Tabix(std::__cxx11::string&)': tabix.cpp:15:10: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] if ( bgzf_is_bgzf(cfilename)!=1 ) ^ In file included from tabix.hpp:4:0, from tabix.cpp:1: /usr/local/include/htslib/bgzf.h:242:9: note: declared here int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); ^ tabix.cpp:15:10: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] if ( bgzf_is_bgzf(cfilename)!=1 ) ^ In file included from tabix.hpp:4:0, from tabix.cpp:1: /usr/local/include/htslib/bgzf.h:242:9: note: declared here int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); ^ tabix.cpp:15:32: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] if ( bgzf_is_bgzf(cfilename)!=1 ) ^ In file included from tabix.hpp:4:0, from tabix.cpp:1: /usr/local/include/htslib/bgzf.h:242:9: note: declared here int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); ^ --- libtabix.a --- --- libtabix.so.1 --- --- tabix++ --- --- libtabix.a --- ar rs libtabix.a tabix.o /usr/libexec/binutils227/elf/ar: creating libtabix.a --- libtabix.so.1 --- c++ -shared -Wl,-soname,libtabix.so.1 -o libtabix.so.1 tabix.o --- tabix++ --- c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -o tabix++ main.cpp tabix.o -Ihtslib -L/usr/local/lib -L. -lhts -lpthread -lm -lz -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for tabixpp-1.0.0.10 ===> Generating temporary packing list mkdir -p /construction/biology/tabixpp/stage/usr/local/bin mkdir -p /construction/biology/tabixpp/stage/usr/local/include mkdir -p /construction/biology/tabixpp/stage/usr/local/lib install tabix++ /construction/biology/tabixpp/stage/usr/local/bin install *.hpp /construction/biology/tabixpp/stage/usr/local/include install libtabix.a libtabix.so.1 /construction/biology/tabixpp/stage/usr/local/lib strip /construction/biology/tabixpp/stage/usr/local/bin/tabix++ /construction/biology/tabixpp/stage/usr/local/lib/libtabix.so.1 /bin/sh /xports/Mk/Scripts/relative_link.sh /construction/biology/tabixpp/stage/usr/local/lib/libtabix.so.1 /construction/biology/tabixpp/stage/usr/local/lib/libtabix.so ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for tabixpp-1.0.0.10 file sizes/checksums [8]: . done packing files [8]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:00:26 UTC Duration: 00:00:12