------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 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 ------------------------------------------------------------------------------- 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/barrnap XDG_CONFIG_HOME=/construction/biology/barrnap XDG_CACHE_HOME=/construction/biology/barrnap/.cache HOME=/construction/biology/barrnap TMPDIR="/tmp" PATH=/construction/biology/barrnap/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/barrnap/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/barrnap XDG_CONFIG_HOME=/construction/biology/barrnap XDG_CACHE_HOME=/construction/biology/barrnap/.cache HOME=/construction/biology/barrnap TMPDIR="/tmp" PATH=/construction/biology/barrnap/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/barrnap/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 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/barrnap/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.5 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/barrnap" EXAMPLESDIR="share/examples/barrnap" DATADIR="share/barrnap" WWWDIR="www/barrnap" ETCDIR="etc/barrnap" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/barrnap DOCSDIR=/usr/local/share/doc/barrnap EXAMPLESDIR=/usr/local/share/examples/barrnap WWWDIR=/usr/local/www/barrnap ETCDIR=/usr/local/etc/barrnap SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/gmake-4.3_2.pkg Installing /packages/All/perl5-5.32.1_3.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/bedtools-2.31.0.pkg Installing /packages/All/hmmer-3.3.2.pkg ===== Message from hmmer-3.3.2: -- HMMER reads three optional environment variables: HMMERDB - directory location of HMM databases (e.g. PFAM) BLASTDB - directory location of FASTA-formatted sequence databases BLASTMAT - directory location of PAM scoring matrices The BLASTDB and BLASTMAT variables are shared with versions of BLAST such as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port). If these variables are set, you do not have to specify the full path to your databases on the command line when using HMMER. Please see the documentation for more information. SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by barrnap-0.9 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by barrnap-0.9 for building => SHA256 Checksum OK for tseemann-barrnap-0.9_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by barrnap-0.9 for building ===> Extracting for barrnap-0.9 => SHA256 Checksum OK for tseemann-barrnap-0.9_GH0.tar.gz. Extracted Memory Use: 44.85M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for barrnap-0.9 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on package: gmake>=4.3 - found ===> barrnap-0.9 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on package: gmake>=4.3 - found ===> barrnap-0.9 depends on package: perl5>=5.32.r0<5.33 - found ===> Configuring for barrnap-0.9 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> barrnap-0.9 depends on executable: bedtools - found ===> barrnap-0.9 depends on executable: nhmmer - found ===> barrnap-0.9 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for barrnap-0.9 ===> barrnap-0.9 depends on executable: bedtools - found ===> barrnap-0.9 depends on executable: nhmmer - found ===> barrnap-0.9 depends on package: perl5>=5.32.r0<5.33 - found ===> Generating temporary packing list install -m 555 /construction/biology/barrnap/barrnap-0.9/bin/barrnap /construction/biology/barrnap/stage/usr/local/bin cd /construction/biology/barrnap/barrnap-0.9 && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE db /construction/biology/barrnap/stage/usr/local/share/barrnap /usr/bin/env WRKSRC=/construction/biology/barrnap/barrnap-0.9 REWARNFILE=/construction/biology/barrnap/reinplace_warnings.txt /bin/sh /xports/Mk/Scripts/sed_checked.sh -i '' -e 's|^my $DBDIR = .*|my $DBDIR = "/usr/local/share/barrnap/db";|' /construction/biology/barrnap/stage/usr/local/bin/barrnap ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- 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 barrnap-0.9 file sizes/checksums [5]: 0% file sizes/checksums [5]: 100% Service unavailablepacking files [5]: 0% packing files [5]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:09