=> Building biology/njplot Started : Sunday, 9 DEC 2018 at 13:16:01 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.25.g9bb66-DEVELOPMENT #33: Mon Dec 3 06:33:52 PST 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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 njplot-2.4: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/njplot XDG_CONFIG_HOME=/construction/biology/njplot HOME=/construction/biology/njplot TMPDIR="/tmp" PATH=/construction/biology/njplot/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- MOTIFLIB="-L/usr/local/lib -lXm -lXp" XDG_DATA_HOME=/construction/biology/njplot XDG_CONFIG_HOME=/construction/biology/njplot HOME=/construction/biology/njplot TMPDIR="/tmp" PATH=/construction/biology/njplot/.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 -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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/njplot/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/njplot" EXAMPLESDIR="share/examples/njplot" DATADIR="share/njplot" WWWDIR="www/njplot" ETCDIR="etc/njplot" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/njplot DOCSDIR=/usr/local/share/doc/njplot EXAMPLESDIR=/usr/local/share/examples/njplot WWWDIR=/usr/local/www/njplot ETCDIR=/usr/local/etc/njplot -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE 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 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License NONE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> njplot-2.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> njplot-2.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of njplot-2.4 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License NONE accepted by the user ===> Fetching all distfiles required by njplot-2.4 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License NONE accepted by the user ===> Fetching all distfiles required by njplot-2.4 for building => SHA256 Checksum OK for njplot-2.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License NONE accepted by the user ===> Fetching all distfiles required by njplot-2.4 for building ===> Extracting for njplot-2.4 => SHA256 Checksum OK for njplot-2.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for njplot-2.4 ===> Applying ports patches for njplot-2.4 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> njplot-2.4 depends on executable: cdscan - not found ===> Installing existing package /packages/All/ncbi-toolkit-2017.01.06.txz Installing ncbi-toolkit-2017.01.06... `-- Installing fontconfig-2.12.6,1... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing freetype2-2.9.1... | `-- Extracting freetype2-2.9.1: .......... done `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded `-- Installing gettext-runtime-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... done `-- Installing gmp-6.1.2_1... `-- Extracting gmp-6.1.2_1: .......... done `-- Installing gnutls-3.5.19_1... | `-- Installing ca_root_nss-3.40... | `-- Extracting ca_root_nss-3.40: ........ done | `-- Installing libidn2-2.0.5_1... | | `-- Installing libunistring-0.9.10_1... | | `-- Extracting libunistring-0.9.10_1: .......... done | `-- Extracting libidn2-2.0.5_1: .......... done | `-- Installing libtasn1-4.13_1... | `-- Extracting libtasn1-4.13_1: .......... done | `-- Installing nettle-3.4_1... | `-- Extracting nettle-3.4_1: .......... done | `-- Installing p11-kit-0.23.14... | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | `-- Extracting p11-kit-0.23.14: .......... done | `-- Installing trousers-0.3.14_2... | | `-- Installing libressl-2.8.2... | | `-- Extracting libressl-2.8.2: .......... done | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | `-- Extracting trousers-0.3.14_2: .......... done `-- Extracting gnutls-3.5.19_1: .......... done `-- Installing jpeg-turbo-2.0.0... `-- Extracting jpeg-turbo-2.0.0: .......... done `-- Installing libX11-1.6.6_1,1... | `-- Installing libXau-1.0.8_5... | `-- Extracting libXau-1.0.8_5: .......... done | `-- Installing libXdmcp-1.1.2_2... | | `-- Installing xorgproto-2018.4... | | `-- Extracting xorgproto-2018.4: .......... done | `-- Extracting libXdmcp-1.1.2_2: ......... done | `-- Installing libxcb-1.13.1... | | `-- Installing libpthread-stubs-0.4... | | `-- Extracting libpthread-stubs-0.4: .... done | | `-- Installing libxml2-2.9.7... | | `-- Extracting libxml2-2.9.7: .......... done | `-- Extracting libxcb-1.13.1: .......... done `-- Extracting libX11-1.6.6_1,1: .......... done `-- Installing libXext-1.3.3_3,1... `-- Extracting libXext-1.3.3_3,1: .......... done `-- Installing libXft-2.3.2_3... | `-- Installing libXrender-0.9.10_2... | `-- Extracting libXrender-0.9.10_2: .......... done `-- Extracting libXft-2.3.2_3: .......... done `-- Installing libXmu-1.1.2_5,1... | `-- Installing libXt-1.1.5_2,1... | | `-- Installing libICE-1.0.9_3,1... | | `-- Extracting libICE-1.0.9_3,1: .......... done | | `-- Installing libSM-1.2.3,1... | | `-- Extracting libSM-1.2.3,1: .......... done | `-- Extracting libXt-1.1.5_2,1: .......... done `-- Extracting libXmu-1.1.2_5,1: .......... done `-- Installing libXp-1.0.3_2,1... `-- Extracting libXp-1.0.3_2,1: .......... done `-- Installing libXpm-3.5.12_2... `-- Extracting libXpm-3.5.12_2: .......... done `-- Installing open-motif-2.3.8... | `-- Installing libXaw-1.0.13_2,2... | `-- Extracting libXaw-1.0.13_2,2: .......... done | `-- Installing png-1.6.35... | `-- Extracting png-1.6.35: .......... done | `-- Installing xbitmaps-1.1.2... | `-- Extracting xbitmaps-1.1.2: .......... done `-- Extracting open-motif-2.3.8: .......... done Extracting ncbi-toolkit-2017.01.06: .......... done Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from ca_root_nss-3.40: ********************************* 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 *************************************************************************** Message from trousers-0.3.14_2: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Message from ncbi-toolkit-2017.01.06: ===================================================================== The data files are installed in "/usr/local/share/ncbi-toolkit". To use them you need to create a .ncbirc file in your home directory with the following lines: [NCBI] Data=/usr/local/share/ncbi-toolkit/ ===================================================================== ===> njplot-2.4 depends on executable: cdscan - found ===> Returning to build of njplot-2.4 ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xp.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> njplot-2.4 depends on shared library: libXm.so.4 - found (/usr/local/lib/libXm.so.4) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for njplot-2.4 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for njplot-2.4 --- newicktops --- --- newicktotxt --- --- njplot-vib.o --- --- unrooted-vib.o --- --- preptree.o --- --- newicktops --- cc -DNO_GUI -DNO_PDF -o newicktops njplot-vib.c -lm --- newicktotxt --- cc -DTTY -o newicktotxt njplot-vib.c -lm --- njplot-vib.o --- cc -c -DWIN_MOTIF -Dunix -I/usr/local/include -I/usr/local/include/ncbi -DHELPFILENAME=\"/njplot.help\" -DNO_PDF -Wimplicit-function-declaration njplot-vib.c --- unrooted-vib.o --- cc -c -DWIN_MOTIF -Dunix -I/usr/local/include -I/usr/local/include/ncbi -DHELPFILENAME=\"/njplot.help\" -DNO_PDF -Wimplicit-function-declaration unrooted-vib.c --- preptree.o --- cc -c -DWIN_MOTIF -Dunix -I/usr/local/include -I/usr/local/include/ncbi -DHELPFILENAME=\"/njplot.help\" -DNO_PDF -Wimplicit-function-declaration preptree.c --- unrooted --- cc -o unrooted unrooted-vib.o preptree.o -L/usr/local/lib/ncbi -lvibrant -lncbi -L/usr/local/lib -lXm -lXp -L/usr/local/lib -lXmu -lXt -lX11 -lm unrooted-vib.o:unrooted-vib.c:function paste_tree: warning: warning: tempnam() possibly used unsafely; consider using mkstemp() /usr/local/lib/ncbi/libncbi.a(ncbifile.o):ncbifile.c:function Nlm_TmpNam: warning: warning: tempnam() possibly used unsafely; consider using mkstemp() --- njplot --- cc -o njplot njplot-vib.o -L/usr/local/lib/ncbi -lvibrant -lncbi -L/usr/local/lib -lXm -lXp -L/usr/local/lib -lXmu -lXt -lX11 -lm njplot-vib.o:njplot-vib.c:function paste_tree: warning: warning: tempnam() possibly used unsafely; consider using mkstemp() /usr/local/lib/ncbi/libncbi.a(ncbifile.o):ncbifile.c:function Nlm_TmpNam: warning: warning: tempnam() possibly used unsafely; consider using mkstemp() -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xp.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> njplot-2.4 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for njplot-2.4 ===> Generating temporary packing list install -s -m 555 /construction/biology/njplot/njplot-2.4/newicktops /construction/biology/njplot/njplot-2.4/newicktotxt /construction/biology/njplot/njplot-2.4/njplot /construction/biology/njplot/njplot-2.4/unrooted /construction/biology/njplot/stage/usr/local/bin install -m 444 /construction/biology/njplot/njplot-2.4/*.1 /construction/biology/njplot/stage/usr/local/man/man1 install -m 0644 /construction/biology/njplot/njplot-2.4/njplot.help /construction/biology/njplot/stage/usr/local/share/njplot install -m 0644 /construction/biology/njplot/njplot-2.4/njplot.html /construction/biology/njplot/njplot-2.4/njplot.gif /construction/biology/njplot/stage/usr/local/share/doc/njplot ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for njplot-2.4 file sizes/checksums [12]: . done packing files [12]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 9 DEC 2018 at 13:16:45 UTC Duration: 00:00:44