=>> Building biology/cytoscape build started at Thu May 8 01:26:21 BST 2025 port directory: /usr/ports/biology/cytoscape package name: cytoscape-3.6.1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2612 Jan 27 13:48 /usr/ports/biology/cytoscape/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 0835676e36 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cytoscape/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cytoscape/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/cytoscape/work/.cache HOME=/wrkdirs/usr/ports/biology/cytoscape/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cytoscape/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/cytoscape/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cytoscape/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cytoscape/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/cytoscape/work/.cache HOME=/wrkdirs/usr/ports/biology/cytoscape/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cytoscape/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/cytoscape/work/.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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cytoscape" EXAMPLESDIR="share/examples/cytoscape" DATADIR="share/cytoscape" WWWDIR="www/cytoscape" ETCDIR="etc/cytoscape" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cytoscape DOCSDIR=/usr/local/share/doc/cytoscape EXAMPLESDIR=/usr/local/share/examples/cytoscape WWWDIR=/usr/local/www/cytoscape ETCDIR=/usr/local/etc/cytoscape --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cytoscape-3.6.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> cytoscape-3.6.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cytoscape-3.6.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cytoscape-3.6.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cytoscape-3.6.1 for building => SHA256 Checksum OK for FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-api-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-support-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cytoscape-3.6.1 for building ===> Extracting for cytoscape-3.6.1 => SHA256 Checksum OK for FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-api-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-support-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz. => SHA256 Checksum OK for cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for cytoscape-3.6.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cytoscape-3.6.1 depends on package: maven363>0 - not found ===> Installing existing package /packages/All/maven363-3.6.3.pkg [pkg-builder.dan.net.uk] Installing maven363-3.6.3... [pkg-builder.dan.net.uk] `-- Installing maven-wrapper-2... [pkg-builder.dan.net.uk] `-- Extracting maven-wrapper-2: ... done [pkg-builder.dan.net.uk] `-- Installing openjdk21-21.0.7+6.1... [pkg-builder.dan.net.uk] | `-- Installing alsa-lib-1.2.13... [pkg-builder.dan.net.uk] | `-- Extracting alsa-lib-1.2.13: .......... done [pkg-builder.dan.net.uk] | `-- Installing fontconfig-2.15.0_3,1... [pkg-builder.dan.net.uk] | | `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] | | `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing freetype2-2.13.3... [pkg-builder.dan.net.uk] | | `-- Extracting freetype2-2.13.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing giflib-5.2.2... [pkg-builder.dan.net.uk] | `-- Extracting giflib-5.2.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing harfbuzz-10.3.0... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing glib-2.84.1_2,2... [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libinotify-20240724_1... [pkg-builder.dan.net.uk] | | `-- Extracting libinotify-20240724_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pcre2-10.45_1... [pkg-builder.dan.net.uk] | | | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | | | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pcre2-10.45_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-packaging-24.2... [pkg-builder.dan.net.uk] | | | `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | | | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | | | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting py311-packaging-24.2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting glib-2.84.1_2,2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing graphite2-1.3.14... [pkg-builder.dan.net.uk] | | `-- Extracting graphite2-1.3.14: .......... done [pkg-builder.dan.net.uk] | `-- Extracting harfbuzz-10.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing javavmwrapper-2.7.10... [pkg-builder.dan.net.uk] | `-- Extracting javavmwrapper-2.7.10: .......... done [pkg-builder.dan.net.uk] | `-- Installing jpeg-turbo-3.1.0... [pkg-builder.dan.net.uk] | `-- Extracting jpeg-turbo-3.1.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing lcms2-2.17... [pkg-builder.dan.net.uk] | | `-- Installing tiff-4.7.0... [pkg-builder.dan.net.uk] | | `-- Installing jbigkit-2.1_3... [pkg-builder.dan.net.uk] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing lerc-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting lerc-4.0.0: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] | | `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting tiff-4.7.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting lcms2-2.17: .......... done [pkg-builder.dan.net.uk] | `-- Installing libX11-1.8.12,1... [pkg-builder.dan.net.uk] | | `-- Installing libxcb-1.17.0... [pkg-builder.dan.net.uk] | | `-- Installing libXau-1.0.11... [pkg-builder.dan.net.uk] | | `-- Extracting libXau-1.0.11: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | | `-- Installing xorgproto-2024.1... [pkg-builder.dan.net.uk] | | | `-- Extracting xorgproto-2024.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting libxcb-1.17.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libX11-1.8.12,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] | `-- Extracting libXext-1.3.6,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXi-1.8.1,1... [pkg-builder.dan.net.uk] | | `-- Installing libXfixes-6.0.1... [pkg-builder.dan.net.uk] | | `-- Extracting libXfixes-6.0.1: ....... done [pkg-builder.dan.net.uk] | `-- Extracting libXi-1.8.1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXrandr-1.5.4... [pkg-builder.dan.net.uk] | | `-- Installing libXrender-0.9.12... [pkg-builder.dan.net.uk] | | `-- Extracting libXrender-0.9.12: ....... done [pkg-builder.dan.net.uk] | `-- Extracting libXrandr-1.5.4: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXt-1.3.0,1... [pkg-builder.dan.net.uk] | | `-- Installing libICE-1.1.1,1... [pkg-builder.dan.net.uk] | | `-- Extracting libICE-1.1.1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libSM-1.2.6,1... [pkg-builder.dan.net.uk] | | `-- Extracting libSM-1.2.6,1: ........ done [pkg-builder.dan.net.uk] | `-- Extracting libXt-1.3.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXtst-1.2.4... [pkg-builder.dan.net.uk] | `-- Extracting libXtst-1.2.4: .......... done [pkg-builder.dan.net.uk] | `-- Installing png-1.6.47... [pkg-builder.dan.net.uk] | `-- Extracting png-1.6.47: .......... done [pkg-builder.dan.net.uk] | `-- Installing xorg-fonts-truetype-7.7_1... [pkg-builder.dan.net.uk] | | `-- Installing dejavu-2.37_3... [pkg-builder.dan.net.uk] | | `-- Installing mkfontscale-1.2.3... [pkg-builder.dan.net.uk] | | | `-- Installing libfontenc-1.1.8... [pkg-builder.dan.net.uk] | | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | | `-- Extracting dejavu-2.37_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing encodings-1.1.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting encodings-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing font-bh-ttf-1.0.3_5... [pkg-builder.dan.net.uk] | | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | | `-- Installing font-misc-ethiopic-1.0.4... [pkg-builder.dan.net.uk] | | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg-builder.dan.net.uk] | | `-- Installing font-misc-meltho-1.0.3_5... [pkg-builder.dan.net.uk] | | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg-builder.dan.net.uk] `-- Extracting openjdk21-21.0.7+6.1: .......... done [pkg-builder.dan.net.uk] Extracting maven363-3.6.3: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.13.3: -- 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. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from libinotify-20240724_1: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from dejavu-2.37_3: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===== Message from openjdk21-21.0.7+6.1: -- This OpenJDK implementation may require fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t fdescfs fdesc /dev/fd mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: fdesc /dev/fd fdescfs rw 0 0 proc /proc procfs rw 0 0 ===> cytoscape-3.6.1 depends on package: maven363>0 - found ===> Returning to build of cytoscape-3.6.1 ===> cytoscape-3.6.1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... done ===> cytoscape-3.6.1 depends on executable: bash - found ===> Returning to build of cytoscape-3.6.1 ===> cytoscape-3.6.1 depends on file: /usr/local/openjdk21/bin/java - found ===> cytoscape-3.6.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> cytoscape-3.6.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of cytoscape-3.6.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for cytoscape-3.6.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for cytoscape-3.6.1 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.cytoscape:taglets:jar:3.6.1 [WARNING] 'dependencies.dependency.systemPath' for com.sun:tools:jar refers to a non-existing file /usr/local/openjdk21/../lib/tools.jar. Please verify that you run Maven using a JDK and not just a JRE. @ line 38, column 16 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.cytoscape:app-api:bundle:3.6.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.cytoscape:jobs-api:jar -> duplicate declaration of version ${project.version} @ line 180, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Basic Cytoscape POM Configuration [pom] [INFO] Cytoscape API Parent Project POM [pom] [INFO] Cytoscape Documentation Taglets [jar] [INFO] Cytoscape Event API (event-api) [bundle] [INFO] Cytoscape Model API (model-api) [bundle] [INFO] Cytoscape Service API (service-api) [bundle] [INFO] Cytoscape View Model API (viewmodel-api) [bundle] [INFO] Cytoscape CI API (ci-api) [bundle] [INFO] Cytoscape Work API (work-api) [bundle] [INFO] Cytoscape Presentation API (presentation-api) [bundle] [INFO] Cytoscape Application API (application-api) [bundle] [INFO] Cytoscape Property API (property-api) [bundle] [INFO] Cytoscape VizMap API (vizmap-api) [bundle] [INFO] Cytoscape Session API (session-api) [bundle] [INFO] Cytoscape Filter API (filter-api) [bundle] [INFO] Cytoscape IO API (io-api) [bundle] [INFO] Cytoscape Core Task API (core-task-api) [bundle] [INFO] Cytoscape Equations API (equations-api) [bundle] [INFO] Cytoscape Layout API (layout-api) [bundle] [INFO] Cytoscape Groups API (group-api) [bundle] [INFO] Cytoscape Groups API (jobs-api) [bundle] [INFO] Cytoscape Webservice API (webservice-api) [bundle] [INFO] Cytoscape Data Source API (datasource-api) [bundle] [INFO] Cytoscape Command Executor API (command-executor-api) [bundle] [INFO] Cytoscape App API (app-api) [bundle] [INFO] Cytoscape Work Swing API (work-swing-api) [bundle] [INFO] Cytoscape Swing Application API (swing-application-api) [bundle] [INFO] Cytoscape VizMap GUI API (vizmap-gui-api) [bundle] [INFO] Cytoscape Swing Utility API (swing-util-api) [bundle] [INFO] Cytoscape Webservice Swing API (webservice-swing-api) [bundle] [INFO] Cytoscape Swing App API (swing-app-api) [bundle] [INFO] Cytoscape Util API (util-api) [bundle] [INFO] Cytoscape API (api-bundle) [bundle] [INFO] Cytoscape Implementation Parent Project POM [pom] [INFO] Cytoscape Equations Impl (equations-impl) [bundle] [INFO] Cytoscape Model Impl Parent (model-impl-parent) [pom] [INFO] Cytoscape Model Impl (model-impl) [bundle] [INFO] Cytoscape Command Executor Impl (command-executor-impl) [bundle] [INFO] Cytoscape Ding Impl Parent (ding-impl) [pom] [INFO] Cytoscape Ding View/Presentation Impl (ding-presentation-impl) [bundle] [INFO] Cytoscape View Model Impl Parent (viewmodel-impl-parent) [pom] [INFO] Cytoscape View Model Impl (viewmodel-impl) [bundle] [INFO] Cytoscape Groups Impl (group-impl) [bundle] [INFO] Cytoscape Event Impl Parent (event-impl-parent) [pom] [INFO] Cytoscape Event Impl (event-impl) [bundle] [INFO] Cytoscape Filters Impl (filter-impl) [bundle] [INFO] Cytoscape Filters 2 Impl (filter2-impl) [bundle] [INFO] Cytoscape IO Impl Parent (io-impl-parent) [pom] [INFO] Cytoscape IO Impl (io-impl) [bundle] [INFO] Cytoscape Layout Impl (layout-impl) [bundle] [INFO] Cytoscape Ding View/Presentation Impl Performance (ding-impl-performance-debug) [jar] [INFO] Cytoscape Editor Impl (editor-impl) [bundle] [INFO] Cytoscape Equation Functions Impl (equations-functions-impl) [bundle] [INFO] Cytoscape GraphML Impl (graphml-impl) [bundle] [INFO] Cytoscape IO Impl Performance (io-impl-performance) [jar] [INFO] Cytoscape Jobs Impl (jobs-impl) [bundle] [INFO] Cytoscape Layout Algorithms Impl (layout-cytoscape-impl) [bundle] [INFO] Cytoscape JGraph Layout Impl (layout-jgraph-impl) [bundle] [INFO] Cytoscape Prefuse Layout Impl (layout-prefuse-impl) [bundle] [INFO] Cytoscape Linkout Impl (linkout-impl) [bundle] [INFO] Cytoscape Log Swing Impl (log-swing-impl) [bundle] [INFO] Cytoscape Manual Layout Impl (manual-layout-impl) [bundle] [INFO] Cytoscape Model Impl Performance Debug (model-impl-performance-debug) [jar] [INFO] Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) [jar] [INFO] Cytoscape App Impl (app-impl) [bundle] [INFO] Cytoscape Presentation Impl (presentation-impl) [bundle] [INFO] Cytoscape Property Impl (property-impl) [bundle] [INFO] Cytoscape Search Impl (search-impl) [bundle] [INFO] Cytoscape Session Impl (session-impl) [bundle] [INFO] Cytoscape Swing Utility Impl (swing-util-impl) [bundle] [INFO] Cytoscape Swing Application Impl (swing-application-impl) [bundle] [INFO] Cytoscape Table Browser Impl (table-browser-impl) [bundle] [INFO] Cytoscape Table Import Impl (table-import-impl) [bundle] [INFO] Cytoscape VizMap GUI Core Impl (vizmap-gui-core-impl) [bundle] [INFO] Cytoscape VizMap GUI Impl (vizmap-gui-impl) [bundle] [INFO] Cytoscape VizMap Impl Parent (vizmap-impl-parent) [pom] [INFO] Cytoscape VizMap Impl (vizmap-impl) [bundle] [INFO] Cytoscape Webservice Impl (webservice-impl) [bundle] [INFO] org.cytoscape.work-headless-impl [bundle] [INFO] org.cytoscape.work-impl [bundle] [INFO] Cytoscape Work Swing Impl Parent (work-swing-impl-parent) [pom] [INFO] Cytoscape Work Swing Impl (work-swing-impl) [bundle] [INFO] Cytoscape Application Impl (application-impl) [bundle] [INFO] Cytoscape Datasource Impl (datasource-impl) [bundle] [INFO] Cytoscape Support Parent Project POM [pom] [INFO] Cytoscape Launch Framework [pom] [INFO] CommandLine Provider [bundle] [INFO] Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) [bundle] [INFO] Cytoscape Edge Bundler Impl (edge-bundler-impl) [bundle] [INFO] Cytoscape Scripting Impl (scripting-impl) [bundle] [INFO] Cytoscape Core Task Impl (core-task-impl) [bundle] [INFO] Cytoscape Headless Application Impl (headless-application-impl) [bundle] [INFO] org.cytoscape.cy-commons-cli [bundle] [INFO] Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl) [bundle] [INFO] Cytoscape 3 App Archetypes Parent [pom] [INFO] Cytoscape 3 Archetype - Creates an App providing public API [maven-archetype] [INFO] Cytoscape 3 Archetype - Creates an App with a Task [maven-archetype] [INFO] Cytoscape 3 Archetype - Creates a CyAction (menu item) for desktop application [maven-archetype] [INFO] Cytoscape 3 Archetype - Creates a Meta-App to install multiple related apps [maven-archetype] [INFO] org.cytoscape.integration-test-support [bundle] [INFO] Launcher [jar] [INFO] StartLevel Assembly [jar] [INFO] Tasks for Testing [bundle] [INFO] Cytoscape Desktop Application Distribution [pom] [INFO] Cytoscape Third-Party Dependencies (third-party) [bundle] [INFO] SplashScreen Launcher [jar] [INFO] Cytoscape Launcher [jar] [INFO] Splash Updater [bundle] [INFO] Cytoscape Command Line Provider Implementation [bundle] [INFO] Cytoscape Diagnostics [bundle] [INFO] Cytoscape Branding [bundle] [INFO] Cytoscape Application Implementation Metadata [bundle] [INFO] Cytoscape GUI-Distribution Integration Test (integration-test) [jar] [INFO] Cytoscape Feature Repository [pom] [INFO] Cytoscape Karaf Distribution [pom] [INFO] Distribution [pom] [INFO] Cytoscape Project POM [pom] [INFO] [INFO] ------------------------< org.cytoscape:parent >------------------------ [INFO] Building Basic Cytoscape POM Configuration 3.6.1 [1/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ parent >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ parent <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ parent --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ parent --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/parent/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/parent/3.6.1/parent-3.6.1.pom [INFO] [INFO] ----------------------< org.cytoscape:api-parent >---------------------- [INFO] Building Cytoscape API Parent Project POM 3.6.1 [2/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ api-parent >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ api-parent <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ api-parent --- [INFO] [INFO] >>> maven-source-plugin:2.4:aggregate (aggregate-source) > generate-sources @ api-parent >>> [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking Cytoscape Property API (property-api) 3.6.1 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-jaxb2-plugin:0.8.1:generate (bookmarks) @ property-api --- [INFO] Started execution. [ERROR] Could not find JAXB 2.x API classes. Make sure JAXB 2.x API is on the classpath. [INFO] pluginArtifacts:[org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.8.1:, org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-core:jar:0.8.1:compile, com.sun.org.apache.xml.internal:resolver:jar:20050927:compile, org.apache.maven:maven-plugin-api:jar:2.0.6:compile, org.sonatype.plexus:plexus-build-api:jar:0.0.7:compile, org.apache.maven:maven-project:jar:2.0.6:compile, org.apache.maven:maven-settings:jar:2.0.6:compile, org.apache.maven:maven-profile:jar:2.0.6:compile, org.apache.maven:maven-model:jar:2.0.6:compile, org.apache.maven:maven-artifact-manager:jar:2.0.6:compile, org.apache.maven:maven-repository-metadata:jar:2.0.6:compile, org.apache.maven:maven-plugin-registry:jar:2.0.6:compile, org.apache.maven:maven-artifact:jar:2.0.6:compile, org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-9-stable-1:compile, junit:junit:jar:4.8.1:compile, classworlds:classworlds:jar:1.1-alpha-2:compile, org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1:compile, org.codehaus.plexus:plexus-utils:jar:1.5.15:compile, org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:0.8.1:compile, com.sun.xml.bind:jaxb-impl:jar:2.2.5-b10:compile, com.sun.xml.bind:jaxb-xjc:jar:2.2.5-b10:compile] [INFO] specVersion:2.1 [INFO] encoding:UTF-8 [INFO] schemaLanguage:null [INFO] schemaDirectory:/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd [INFO] schemaIncludes:[bookmarks.xsd, xlinks-2001.xsd] [INFO] schemaExcludes:null [INFO] schemas:[] [INFO] bindingDirectory:/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd [INFO] bindingIncludes:[*.xjb] [INFO] bindingExcludes:null [INFO] bindings:[] [INFO] disableDefaultExcludes:false [INFO] catalog:null [INFO] catalogResolver:null [INFO] generatePackage:org.cytoscape.property.bookmark [INFO] generateDirectory:/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/target/generated-sources/xjc/bookmarks [INFO] readOnly:false [INFO] extension:false [INFO] strict:true [INFO] writeCode:true [INFO] verbose:true [INFO] debug:false [INFO] args:[] [INFO] forceRegenerate:false [INFO] removeOldOutput:false [INFO] produces:[**/*.*, **/*.java, **/bgm.ser, **/jaxb.properties] [INFO] otherDepends:null [INFO] episodeFile:/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/target/generated-sources/xjc/bookmarks/META-INF/sun-jaxb.episode [INFO] episode:true [INFO] classpathElements:[/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/target/classes] [INFO] plugins:null [INFO] episodes:null [INFO] useDependenciesAsEpisodes:false [INFO] xjcPlugins:null [INFO] episodes:null [INFO] schemaFiles (calculated):[/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/xlinks-2001.xsd, /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/bookmarks.xsd] [INFO] bindingFiles (calculated):[] [INFO] xjcPluginArtifacts (resolved):[] [INFO] xjcPluginFiles (resolved):[] [INFO] xjcPluginURLs (resolved):[] [INFO] episodeArtifacts (resolved):[] [INFO] episodeFiles (resolved):[] [INFO] optionsConfiguration:OptionsConfiguration [specVersion=2.1 generateDirectory=/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/target/generated-sources/xjc/bookmarks generatePackage=org.cytoscape.property.bookmark schemaLanguage=null schemas=[file:/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/xlinks-2001.xsd, file:/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/bookmarks.xsd] bindings=[] plugins=[] catalogs=[] catalogResolver=org.jvnet.jaxb2.maven2.resolver.tools.MavenCatalogResolver@7b351446 readOnly=false extension=false strict=true verbose=true debugMode=false arguments=[-episode, /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/target/generated-sources/xjc/bookmarks/META-INF/sun-jaxb.episode]] Using java.util.ServiceLoader [INFO] File [/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/xlinks-2001.xsd] was changed since the last build. [INFO] File [/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/bookmarks.xsd] was changed since the last build. [INFO] File [/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/pom.xml] was changed since the last build. [INFO] Checking up-to-date depends [[/wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/xlinks-2001.xsd, /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/src/main/xsd/bookmarks.xsd, /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/api/property-api/pom.xml]]. [INFO] Checking up-to-date produces [[]]. [INFO] Depends timestamp [1,515,095,338,000], produces timestamp [null]. [INFO] Parsing input schema(s)... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Documentation Taglets [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Event API (event-api) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Model API (model-api) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Service API (service-api) [INFO] This project has been banned from the build due to previous failures. 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[INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape VizMap GUI API (vizmap-gui-api) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Swing Utility API (swing-util-api) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Webservice Swing API (webservice-swing-api) [INFO] This project has been banned from the build due to previous failures. 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[INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Implementation Parent Project POM [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Equations Impl (equations-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Model Impl Parent (model-impl-parent) [INFO] This project has been banned from the build due to previous failures. 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[INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Groups Impl (group-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Event Impl Parent (event-impl-parent) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Event Impl (event-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Filters Impl (filter-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Filters 2 Impl (filter2-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape IO Impl Parent (io-impl-parent) [INFO] This project has been banned from the build due to previous failures. 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[INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Log Swing Impl (log-swing-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Manual Layout Impl (manual-layout-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Model Impl Performance Debug (model-impl-performance-debug) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape App Impl (app-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Presentation Impl (presentation-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Property Impl (property-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Search Impl (search-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Session Impl (session-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Swing Utility Impl (swing-util-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Swing Application Impl (swing-application-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Table Browser Impl (table-browser-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Table Import Impl (table-import-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape VizMap GUI Core Impl (vizmap-gui-core-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape VizMap GUI Impl (vizmap-gui-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape VizMap Impl Parent (vizmap-impl-parent) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape VizMap Impl (vizmap-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Webservice Impl (webservice-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping org.cytoscape.work-headless-impl [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping org.cytoscape.work-impl [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Work Swing Impl Parent (work-swing-impl-parent) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Work Swing Impl (work-swing-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Application Impl (application-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Datasource Impl (datasource-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --------------------< org.cytoscape:support-parent >-------------------- [INFO] Building Cytoscape Support Parent Project POM 3.6.1 [3/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ support-parent >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ support-parent <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ support-parent --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ support-parent --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/support-parent/3.6.1/support-parent-3.6.1.pom [INFO] [INFO] -------------------< org.cytoscape:launch-framework >------------------- [INFO] Building Cytoscape Launch Framework 3.6.1 [4/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ launch-framework >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ launch-framework <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ launch-framework --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ launch-framework --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/launch-framework/3.6.1/launch-framework-3.6.1.pom [INFO] [INFO] -----------------------< org.cytoscape:cmdline >------------------------ [INFO] Building CommandLine Provider 3.6.1 [5/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cmdline --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/cmdline/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ cmdline --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/cmdline/target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cmdline --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ cmdline --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ cmdline --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ cmdline --- [WARNING] Bundle org.cytoscape:cmdline:bundle:3.6.1 : Unused Private-Package instructions, no such package(s) on the class path: [org.cytoscape.cmdline.internal.*] [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ cmdline >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ cmdline <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ cmdline --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/cmdline/target/cmdline-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ cmdline --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/cmdline/target/cmdline-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/cmdline/3.6.1/cmdline-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/cmdline/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/cmdline/3.6.1/cmdline-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/cmdline/target/cmdline-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/cmdline/3.6.1/cmdline-3.6.1-sources.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ cmdline --- [INFO] Installing org/cytoscape/cmdline/3.6.1/cmdline-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Edge Bundler Impl (edge-bundler-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Scripting Impl (scripting-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Core Task Impl (core-task-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Headless Application Impl (headless-application-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --------------------< org.cytoscape:cy-commons-cli >-------------------- [INFO] Building org.cytoscape.cy-commons-cli 3.6.1 [6/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cy-commons-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ cy-commons-cli --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/src/main/java/org/apache/commons/cli/TypeHandler.java:[105,38] newInstance() in java.lang.Class has been deprecated [WARNING] /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/src/main/java/org/apache/commons/cli/TypeHandler.java:[179,32] URL(java.lang.String) in java.net.URL has been deprecated [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cy-commons-cli --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ cy-commons-cli --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ cy-commons-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ cy-commons-cli --- [WARNING] Bundle org.cytoscape:cy-commons-cli:bundle:3.6.1 : Unused Private-Package instructions, no such package(s) on the class path: [org.apache.commons.cli.internal.*] [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ cy-commons-cli >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ cy-commons-cli <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ cy-commons-cli --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/target/cy-commons-cli-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ cy-commons-cli --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/target/cy-commons-cli-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/cy-commons-cli/3.6.1/cy-commons-cli-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/cy-commons-cli/3.6.1/cy-commons-cli-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/cy-commons-cli/target/cy-commons-cli-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/cy-commons-cli/3.6.1/cy-commons-cli-3.6.1-sources.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ cy-commons-cli --- [INFO] Installing org/cytoscape/cy-commons-cli/3.6.1/cy-commons-cli-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------< org.cytoscape:archetypes-parent >------------------- [INFO] Building Cytoscape 3 App Archetypes Parent 3.6.1 [7/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ archetypes-parent >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ archetypes-parent <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ archetypes-parent --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ archetypes-parent --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes-parent/3.6.1/archetypes-parent-3.6.1.pom [INFO] [INFO] -------------< org.cytoscape.archetypes:api-provider-app >-------------- [INFO] Building Cytoscape 3 Archetype - Creates an App providing public API 3.6.1 [8/117] [INFO] --------------------------[ maven-archetype ]--------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ api-provider-app --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ api-provider-app --- [INFO] Not copying test resources [INFO] [INFO] --- maven-archetype-plugin:2.2:jar (default-jar) @ api-provider-app --- [INFO] Building archetype jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/api-provider-app/target/api-provider-app-3.6.1 [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ api-provider-app >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ api-provider-app <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ api-provider-app --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/api-provider-app/target/api-provider-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:integration-test (default-integration-test) @ api-provider-app --- [WARNING] No Archetype IT projects: root 'projects' directory not found. [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ api-provider-app --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/api-provider-app/target/api-provider-app-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/api-provider-app/3.6.1/api-provider-app-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/api-provider-app/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/api-provider-app/3.6.1/api-provider-app-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/api-provider-app/target/api-provider-app-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/api-provider-app/3.6.1/api-provider-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:update-local-catalog (default-update-local-catalog) @ api-provider-app --- [INFO] [INFO] -----------------< org.cytoscape.archetypes:task-app >------------------ [INFO] Building Cytoscape 3 Archetype - Creates an App with a Task 3.6.1 [9/117] [INFO] --------------------------[ maven-archetype ]--------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ task-app --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ task-app --- [INFO] Not copying test resources [INFO] [INFO] --- maven-archetype-plugin:2.2:jar (default-jar) @ task-app --- [INFO] Building archetype jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/task-app/target/task-app-3.6.1 [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ task-app >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ task-app <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ task-app --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/task-app/target/task-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:integration-test (default-integration-test) @ task-app --- [WARNING] No Archetype IT projects: root 'projects' directory not found. [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ task-app --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/task-app/target/task-app-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/task-app/3.6.1/task-app-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/task-app/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/task-app/3.6.1/task-app-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/task-app/target/task-app-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/task-app/3.6.1/task-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:update-local-catalog (default-update-local-catalog) @ task-app --- [INFO] [INFO] ---------------< org.cytoscape.archetypes:cyaction-app >---------------- [INFO] Building Cytoscape 3 Archetype - Creates a CyAction (menu item) for desktop application 3.6.1 [10/117] [INFO] --------------------------[ maven-archetype ]--------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cyaction-app --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 4 resources [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cyaction-app --- [INFO] Not copying test resources [INFO] [INFO] --- maven-archetype-plugin:2.2:jar (default-jar) @ cyaction-app --- [INFO] Building archetype jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/cyaction-app/target/cyaction-app-3.6.1 [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ cyaction-app >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ cyaction-app <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ cyaction-app --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/cyaction-app/target/cyaction-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:integration-test (default-integration-test) @ cyaction-app --- [WARNING] No Archetype IT projects: root 'projects' directory not found. [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ cyaction-app --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/cyaction-app/target/cyaction-app-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/cyaction-app/3.6.1/cyaction-app-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/cyaction-app/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/cyaction-app/3.6.1/cyaction-app-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/cyaction-app/target/cyaction-app-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/cyaction-app/3.6.1/cyaction-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:update-local-catalog (default-update-local-catalog) @ cyaction-app --- [INFO] [INFO] -----------------< org.cytoscape.archetypes:meta-app >------------------ [INFO] Building Cytoscape 3 Archetype - Creates a Meta-App to install multiple related apps 3.6.1 [11/117] [INFO] --------------------------[ maven-archetype ]--------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ meta-app --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ meta-app --- [INFO] Not copying test resources [INFO] [INFO] --- maven-archetype-plugin:2.2:jar (default-jar) @ meta-app --- [INFO] Building archetype jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/meta-app/target/meta-app-3.6.1 [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ meta-app >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ meta-app <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ meta-app --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/meta-app/target/meta-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:integration-test (default-integration-test) @ meta-app --- [WARNING] No Archetype IT projects: root 'projects' directory not found. [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ meta-app --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/meta-app/target/meta-app-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/meta-app/3.6.1/meta-app-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/meta-app/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/meta-app/3.6.1/meta-app-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/archetypes/meta-app/target/meta-app-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/archetypes/meta-app/3.6.1/meta-app-3.6.1-sources.jar [INFO] [INFO] --- maven-archetype-plugin:2.2:update-local-catalog (default-update-local-catalog) @ meta-app --- [INFO] [INFO] ---------------< org.cytoscape:integration-test-support >--------------- [INFO] Building org.cytoscape.integration-test-support 3.6.1 [12/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ integration-test-support --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/integration-test-support/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ integration-test-support --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/integration-test-support/target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ integration-test-support --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ integration-test-support --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ integration-test-support --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ integration-test-support --- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ integration-test-support >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ integration-test-support <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ integration-test-support --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/integration-test-support/target/integration-test-support-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ integration-test-support --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/integration-test-support/target/integration-test-support-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/integration-test-support/3.6.1/integration-test-support-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/integration-test-support/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/integration-test-support/3.6.1/integration-test-support-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/integration-test-support/target/integration-test-support-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/integration-test-support/3.6.1/integration-test-support-3.6.1-sources.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ integration-test-support --- [INFO] Installing org/cytoscape/integration-test-support/3.6.1/integration-test-support-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] -----------------------< org.cytoscape:launcher >----------------------- [INFO] Building Launcher 3.6.1 [13/117] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ launcher --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ launcher --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java:[56,99] newInstance() in java.lang.Class has been deprecated [INFO] /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/src/main/java/org/cytoscape/launcher/internal/Launcher.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ launcher --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ launcher --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ launcher --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/launcher-3.6.1.jar [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ launcher >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ launcher <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/launcher-3.6.1-sources.jar [INFO] [INFO] --- maven-assembly-plugin:2.2-beta-5:single (make-assembly) @ launcher --- [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/maven/ already added, skipping [INFO] org/ already added, skipping [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/launcher-3.6.1-jar-with-dependencies.jar [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/maven/ already added, skipping [INFO] org/ already added, skipping [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ launcher --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/launcher-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/launcher/3.6.1/launcher-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/launcher/3.6.1/launcher-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/launcher-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/launcher/3.6.1/launcher-3.6.1-sources.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/launcher/target/launcher-3.6.1-jar-with-dependencies.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/launcher/3.6.1/launcher-3.6.1-jar-with-dependencies.jar [INFO] [INFO] -----------------< org.cytoscape:startlevel-assembly >------------------ [INFO] Building StartLevel Assembly 3.6.1 [14/117] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ startlevel-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ startlevel-assembly --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ startlevel-assembly --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ startlevel-assembly --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ startlevel-assembly --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ startlevel-assembly --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/startlevel-assembly/target/startlevel-assembly-3.6.1.jar [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ startlevel-assembly >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ startlevel-assembly <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ startlevel-assembly --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/startlevel-assembly/target/startlevel-assembly-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ startlevel-assembly --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/startlevel-assembly/target/startlevel-assembly-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/startlevel-assembly/3.6.1/startlevel-assembly-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/startlevel-assembly/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/startlevel-assembly/3.6.1/startlevel-assembly-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/support/launch-framework/startlevel-assembly/target/startlevel-assembly-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/startlevel-assembly/3.6.1/startlevel-assembly-3.6.1-sources.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Tasks for Testing [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] -----------------< org.cytoscape.distribution:parent >------------------ [INFO] Building Cytoscape Desktop Application Distribution 3.6.1 [15/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ parent >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ parent <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ parent --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ parent --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/parent/3.6.1/parent-3.6.1.pom [INFO] [INFO] ---------------< org.cytoscape.distribution:third-party >--------------- [INFO] Building Cytoscape Third-Party Dependencies (third-party) 3.6.1 [16/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ third-party --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/third-party/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ third-party --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ third-party --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ third-party --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ third-party --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ third-party --- [WARNING] Bundle org.cytoscape.distribution:third-party:bundle:3.6.1 : Invalid package name: 'org.jdesktop.swingx.autocomplete.doc-files' [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ third-party >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ third-party <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ third-party --- [INFO] No sources in project. Archive not created. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default) @ third-party --- [WARNING] Bundle org.cytoscape.distribution:third-party:bundle:3.6.1 : Invalid package name: 'org.jdesktop.swingx.autocomplete.doc-files' [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ third-party --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/third-party/target/third-party-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/third-party/3.6.1/third-party-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/third-party/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/third-party/3.6.1/third-party-3.6.1.pom [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ third-party --- [INFO] Installing org/cytoscape/distribution/third-party/3.6.1/third-party-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] -----------< org.cytoscape.gui-distribution:splash-launcher >----------- [INFO] Building SplashScreen Launcher 3.6.1 [17/117] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ splash-launcher --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ splash-launcher --- [INFO] No sources to compile [INFO] [INFO] --- batik-maven-plugin:1.0-beta-1:rasterize (default) @ splash-launcher --- [INFO] Rasterizing 1 image from SVG to image/png [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ splash-launcher --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ splash-launcher --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ splash-launcher --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ splash-launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1.jar [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ splash-launcher >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ splash-launcher <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ splash-launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1-sources.jar [INFO] [INFO] --- maven-assembly-plugin:2.5.5:single (splash-assembly) @ splash-launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1-jar-with-dependencies.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ splash-launcher --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/gui-distribution/splash-launcher/3.6.1/splash-launcher-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/gui-distribution/splash-launcher/3.6.1/splash-launcher-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/gui-distribution/splash-launcher/3.6.1/splash-launcher-3.6.1-sources.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1-jar-with-dependencies.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/gui-distribution/splash-launcher/3.6.1/splash-launcher-3.6.1-jar-with-dependencies.jar [INFO] [INFO] -------------< org.cytoscape.distribution:karaf-launcher >-------------- [INFO] Building Cytoscape Launcher 3.6.1 [18/117] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ karaf-launcher --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ karaf-launcher --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ karaf-launcher --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ karaf-launcher --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ karaf-launcher --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ karaf-launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/target/karaf-launcher-3.6.1.jar [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ karaf-launcher >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ karaf-launcher <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ karaf-launcher --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/target/karaf-launcher-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ karaf-launcher --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/target/karaf-launcher-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/karaf-launcher/3.6.1/karaf-launcher-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/karaf-launcher/3.6.1/karaf-launcher-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/launcher/target/karaf-launcher-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/karaf-launcher/3.6.1/karaf-launcher-3.6.1-sources.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Splash Updater [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape Command Line Provider Implementation [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ------------< org.cytoscape.distribution:diagnostics-impl >------------- [INFO] Building Cytoscape Diagnostics 3.6.1 [19/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ diagnostics-impl --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ diagnostics-impl --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 15 source files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/src/main/java/org/cytoscape/diagnostics/internal/SystemDetailsImpl.java:[125,65] newInstance() in java.lang.Class has been deprecated [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ diagnostics-impl --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ diagnostics-impl --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ diagnostics-impl --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ diagnostics-impl --- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ diagnostics-impl >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ diagnostics-impl <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ diagnostics-impl --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/target/diagnostics-impl-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ diagnostics-impl --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/target/diagnostics-impl-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/diagnostics-impl/3.6.1/diagnostics-impl-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/diagnostics-impl/3.6.1/diagnostics-impl-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/diagnostics/target/diagnostics-impl-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/diagnostics-impl/3.6.1/diagnostics-impl-3.6.1-sources.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ diagnostics-impl --- [INFO] Installing org/cytoscape/distribution/diagnostics-impl/3.6.1/diagnostics-impl-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] ----------------< org.cytoscape.distribution:branding >----------------- [INFO] Building Cytoscape Branding 3.6.1 [20/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ branding --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/branding/target/dependencies/branding [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ branding --- [INFO] No sources to compile [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (preprocess-logo) @ branding --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ branding --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ branding --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ branding --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (replace-logo) @ branding --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ branding --- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ branding >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ branding <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ branding --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/branding/target/branding-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ branding --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/branding/target/branding-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/branding/3.6.1/branding-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/branding/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/branding/3.6.1/branding-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/branding/target/branding-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/branding/3.6.1/branding-3.6.1-sources.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ branding --- [INFO] Installing org/cytoscape/distribution/branding/3.6.1/branding-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] --------< org.cytoscape.distribution:application-metadata-impl >-------- [INFO] Building Cytoscape Application Implementation Metadata 3.6.1 [21/117] [INFO] -------------------------------[ bundle ]------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ application-metadata-impl --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ application-metadata-impl --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ application-metadata-impl --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ application-metadata-impl --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ application-metadata-impl --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ application-metadata-impl --- [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ application-metadata-impl >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ application-metadata-impl <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ application-metadata-impl --- [INFO] Building jar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/application-metadata-impl/target/application-metadata-impl-3.6.1-sources.jar [INFO] [INFO] --- maven-install-plugin:2.5.2:install (default-install) @ application-metadata-impl --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/application-metadata-impl/target/application-metadata-impl-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/application-metadata-impl/3.6.1/application-metadata-impl-3.6.1.jar [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/application-metadata-impl/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/application-metadata-impl/3.6.1/application-metadata-impl-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/application-metadata-impl/target/application-metadata-impl-3.6.1-sources.jar to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/application-metadata-impl/3.6.1/application-metadata-impl-3.6.1-sources.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ application-metadata-impl --- [INFO] Installing org/cytoscape/distribution/application-metadata-impl/3.6.1/application-metadata-impl-3.6.1.jar [INFO] Writing OBR metadata [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Cytoscape GUI-Distribution Integration Test (integration-test) [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] ----------------< org.cytoscape.distribution:features >----------------- [INFO] Building Cytoscape Feature Repository 3.6.1 [22/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:copy-resources (copy-resources) @ features --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ features >>> [INFO] [INFO] --- maven-resources-plugin:2.6:copy-resources (copy-resources) @ features --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ features <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ features --- [INFO] [INFO] --- build-helper-maven-plugin:1.7:attach-artifact (attach-artifacts) @ features --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ features --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/features/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/features/3.6.1/features-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/features/target/features.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/features/3.6.1/features-3.6.1-features.xml [INFO] [INFO] ----------------< org.cytoscape.distribution:cytoscape >---------------- [INFO] Building Cytoscape Karaf Distribution 3.6.1 [23/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- xml-maven-plugin:1.0:transform (generate-descriptors) @ cytoscape --- [INFO] Transforming file: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/src/main/descriptors/config-windows.xml [INFO] Transforming file: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/src/main/descriptors/config-dev.xml [INFO] Transforming file: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/src/main/descriptors/config-unix.xml [INFO] Transformed 3 file(s). [INFO] [INFO] --- maven-resources-plugin:2.6:resources (filter) @ cytoscape --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 30 resources [INFO] [INFO] >>> karaf-maven-plugin:3.0.3:features-add-to-repository (add-features-to-repo) > compile @ cytoscape >>> [INFO] [INFO] --- xml-maven-plugin:1.0:transform (generate-descriptors) @ cytoscape --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (filter) @ cytoscape --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 30 resources [INFO] [INFO] --- maven-dependency-plugin:2.10:copy (copy-dependencies) @ cytoscape --- [INFO] Configured Artifact: org.cytoscape.distribution:branding:3.6.1:jar [INFO] Configured Artifact: org.cytoscape.distribution:karaf-launcher:3.6.1:jar [INFO] Copying branding-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/branding/branding-3.6.1.jar [INFO] Copying karaf-launcher-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/launcher/karaf-launcher-3.6.1.jar [INFO] [INFO] --- maven-dependency-plugin:2.10:copy-dependencies (copy-dependencies) @ cytoscape --- [INFO] Copying apache-karaf-3.0.3.tar.gz to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/bundles/apache-karaf-3.0.3.tar.gz [INFO] Copying apache-karaf-3.0.3.zip to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/bundles/apache-karaf-3.0.3.zip [INFO] Copying standard-3.0.3-features.xml to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/bundles/standard-3.0.3-features.xml [INFO] [INFO] --- maven-dependency-plugin:2.10:unpack (unpack-dependencies) @ cytoscape --- [INFO] Configured Artifact: org.apache.karaf:apache-karaf:?:tar.gz [INFO] Configured Artifact: org.cytoscape.gui-distribution:splash-launcher:3.6.1:jar [INFO] Unpacking /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/apache/karaf/apache-karaf/3.0.3/apache-karaf-3.0.3.tar.gz to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies with includes "" and excludes "" [INFO] Expanding: /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/apache/karaf/apache-karaf/3.0.3/apache-karaf-3.0.3.tar.gz into /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies [INFO] Unpacking /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/splash-launcher/target/splash-launcher-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/splash-launcher with includes "" and excludes "" [INFO] [INFO] --- maven-dependency-plugin:2.10:copy (copy) @ cytoscape --- [INFO] Configured Artifact: org.cytoscape:core-apps-meta:3.6.0:jar [INFO] Configured Artifact: org.cytoscape:biopax:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:command-dialog:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:json:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:idmapper:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:network-analyzer:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:network-merge:3.3.4:jar [INFO] Configured Artifact: org.cytoscape:psi-mi:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:sbml:3.3.3:jar [INFO] Configured Artifact: org.cytoscape:webservice-biomart-client:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:webservice-psicquic-client:3.4.0:jar [INFO] Configured Artifact: org.cytoscape:cy-rest:3.7.0:jar [INFO] Configured Artifact: org.cytoscape:opencl-cycl:3.5.0:jar [INFO] Configured Artifact: org.cytoscape:opencl-layout:3.5.0:jar [INFO] Configured Artifact: org.cytoscape:welcome:3.5.2:jar [INFO] Configured Artifact: org.cytoscape.diffusion:diffusion:1.5.2:jar [INFO] Configured Artifact: org.cytoscape.copycatLayout:copycatLayout:1.2.3:jar [INFO] Configured Artifact: edu.ucsf.rbvi:cyBrowser:1.0.0:jar [INFO] Configured Artifact: org.cytoscape:cx-support:2.2.2:jar [INFO] Configured Artifact: org.cytoscape:cy-ndex-2:2.2.2:jar [INFO] Copying core-apps-meta-3.6.0.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/core-apps-meta-3.6.0.jar [INFO] Copying biopax-3.3.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/biopax-3.3.2.jar [INFO] Copying command-dialog-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/command-dialog-3.6.1.jar [INFO] Copying json-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/json-3.6.1.jar [INFO] Copying idmapper-3.6.1.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/idmapper-3.6.1.jar [INFO] Copying network-analyzer-3.3.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/network-analyzer-3.3.2.jar [INFO] Copying network-merge-3.3.4.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/network-merge-3.3.4.jar [INFO] Copying psi-mi-3.3.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/psi-mi-3.3.2.jar [INFO] Copying sbml-3.3.3.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/sbml-3.3.3.jar [INFO] Copying webservice-biomart-client-3.3.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/webservice-biomart-client-3.3.2.jar [INFO] Copying webservice-psicquic-client-3.4.0.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/webservice-psicquic-client-3.4.0.jar [INFO] Copying cy-rest-3.7.0.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/cy-rest-3.7.0.jar [INFO] Copying opencl-cycl-3.5.0.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/opencl-cycl-3.5.0.jar [INFO] Copying opencl-layout-3.5.0.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/opencl-layout-3.5.0.jar [INFO] Copying welcome-3.5.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/welcome-3.5.2.jar [INFO] Copying diffusion-1.5.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/diffusion-1.5.2.jar [INFO] Copying copycatLayout-1.2.3.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/copycatLayout-1.2.3.jar [INFO] Copying cyBrowser-1.0.0.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/cyBrowser-1.0.0.jar [INFO] Copying cx-support-2.2.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/cx-support-2.2.2.jar [INFO] Copying cy-ndex-2-2.2.2.jar to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps/cy-ndex-2-2.2.2.jar [INFO] [INFO] --- maven-assembly-plugin:2.5.5:single (directory) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-dev.xml [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /apps [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/etc/ [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/system [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [INFO] Copying files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape [WARNING] Assembly file: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-unix) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-wrap-deployer-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-disable-jmx) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] <<< karaf-maven-plugin:3.0.3:features-add-to-repository (add-features-to-repo) < compile @ cytoscape <<< [INFO] [INFO] [INFO] --- karaf-maven-plugin:3.0.3:features-add-to-repository (add-features-to-repo) @ cytoscape --- [WARNING] The POM for org.eclipse.aether:aether-api:jar:0.9.0.M2 is missing, no dependency information available [INFO] Base repo: file:///wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/ [INFO] Copying artifact: org.cytoscape.distribution:features:xml:features:3.6.1 [INFO] Copying artifact: org.cytoscape.distribution:diagnostics-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape.distribution:splash-updater-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape.distribution:third-party:jar:3.6.1 [INFO] Copying artifact: org.apache.servicemix.bundles:org.apache.servicemix.bundles.xmlbeans:jar:2.4.0_5 [INFO] Copying artifact: commons-io:commons-io:jar:2.1 [INFO] Copying artifact: cytoscape-temp:uk.ac.ebi.enfin.mi.cluster.micluster:jar:1.6 [INFO] Copying artifact: org.apache.servicemix.specs:org.apache.servicemix.specs.jaxb-api-2.1:jar:1.2.0 [INFO] Copying artifact: org.apache.servicemix.bundles:org.apache.servicemix.bundles.jaxb-impl:jar:2.1.6_1 [INFO] Copying artifact: javax.activation:com.springsource.javax.activation:jar:1.1.1 [INFO] Copying artifact: javax.xml.stream:com.springsource.javax.xml.stream:jar:1.0.1 [INFO] Copying artifact: javax.ws.rs:javax.ws.rs-api:jar:2.0 [INFO] Copying artifact: org.cytoscape:cmdline:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:api-bundle:jar:3.6.1 [INFO] Copying artifact: org.cytoscape.distribution:cmdline-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:property-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:event-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:datasource-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:equations-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape.distribution:application-metadata-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:application-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:swing-util-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:model-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:work-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:work-swing-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:work-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:presentation-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:viewmodel-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:vizmap-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:layout-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:group-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:session-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:vizmap-gui-core-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:ding-presentation-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:io-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:core-task-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:command-executor-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:swing-application-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:jobs-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:search-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:table-browser-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:vizmap-gui-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:manual-layout-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:layout-cytoscape-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:webservice-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:editor-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:layout-prefuse-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:linkout-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:table-import-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:filter2-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:graphml-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:edge-bundler-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:app-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:scripting-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:gui-cmdline-parser-impl:jar:3.6.1 [INFO] Copying artifact: org.cytoscape:equations-functions-impl:jar:3.6.1 [INFO] [INFO] >>> karaf-maven-plugin:3.0.3:features-add-to-repository (add-features-to-repo-dev) > compile @ cytoscape >>> [INFO] [INFO] --- xml-maven-plugin:1.0:transform (generate-descriptors) @ cytoscape --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (filter) @ cytoscape --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 30 resources [INFO] [INFO] --- maven-dependency-plugin:2.10:copy (copy-dependencies) @ cytoscape --- [INFO] Configured Artifact: org.cytoscape.distribution:branding:3.6.1:jar [INFO] Configured Artifact: org.cytoscape.distribution:karaf-launcher:3.6.1:jar [INFO] org.cytoscape.distribution:branding:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/branding [INFO] org.cytoscape.distribution:karaf-launcher:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/launcher [INFO] [INFO] --- maven-dependency-plugin:2.10:copy-dependencies (copy-dependencies) @ cytoscape --- [INFO] org.apache.karaf:apache-karaf:tar.gz:3.0.3 already exists in destination. [INFO] org.apache.karaf:apache-karaf:zip:3.0.3 already exists in destination. [INFO] org.apache.karaf.features:standard:xml:features:3.0.3 already exists in destination. [INFO] [INFO] --- maven-dependency-plugin:2.10:unpack (unpack-dependencies) @ cytoscape --- [INFO] Configured Artifact: org.apache.karaf:apache-karaf:?:tar.gz [INFO] Configured Artifact: org.cytoscape.gui-distribution:splash-launcher:3.6.1:jar [INFO] apache-karaf-3.0.3.tar.gz already unpacked. [INFO] splash-launcher-3.6.1.jar already unpacked. [INFO] [INFO] --- maven-dependency-plugin:2.10:copy (copy) @ cytoscape --- [INFO] Configured Artifact: org.cytoscape:core-apps-meta:3.6.0:jar [INFO] Configured Artifact: org.cytoscape:biopax:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:command-dialog:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:json:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:idmapper:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:network-analyzer:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:network-merge:3.3.4:jar [INFO] Configured Artifact: org.cytoscape:psi-mi:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:sbml:3.3.3:jar [INFO] Configured Artifact: org.cytoscape:webservice-biomart-client:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:webservice-psicquic-client:3.4.0:jar [INFO] Configured Artifact: org.cytoscape:cy-rest:3.7.0:jar [INFO] Configured Artifact: org.cytoscape:opencl-cycl:3.5.0:jar [INFO] Configured Artifact: org.cytoscape:opencl-layout:3.5.0:jar [INFO] Configured Artifact: org.cytoscape:welcome:3.5.2:jar [INFO] Configured Artifact: org.cytoscape.diffusion:diffusion:1.5.2:jar [INFO] Configured Artifact: org.cytoscape.copycatLayout:copycatLayout:1.2.3:jar [INFO] Configured Artifact: edu.ucsf.rbvi:cyBrowser:1.0.0:jar [INFO] Configured Artifact: org.cytoscape:cx-support:2.2.2:jar [INFO] Configured Artifact: org.cytoscape:cy-ndex-2:2.2.2:jar [INFO] org.cytoscape:core-apps-meta:3.6.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:biopax:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:command-dialog:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:json:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:idmapper:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:network-analyzer:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:network-merge:3.3.4:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:psi-mi:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:sbml:3.3.3:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:webservice-biomart-client:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:webservice-psicquic-client:3.4.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:cy-rest:3.7.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:opencl-cycl:3.5.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:opencl-layout:3.5.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:welcome:3.5.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape.diffusion:diffusion:1.5.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape.copycatLayout:copycatLayout:1.2.3:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] edu.ucsf.rbvi:cyBrowser:1.0.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:cx-support:2.2.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:cy-ndex-2:2.2.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] [INFO] --- maven-assembly-plugin:2.5.5:single (directory) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-dev.xml [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /apps [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/etc/ [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/system [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [INFO] Copying files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape [WARNING] Assembly file: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-unix) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-wrap-deployer-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-disable-jmx) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] <<< karaf-maven-plugin:3.0.3:features-add-to-repository (add-features-to-repo-dev) < compile @ cytoscape <<< [INFO] [INFO] [INFO] --- karaf-maven-plugin:3.0.3:features-add-to-repository (add-features-to-repo-dev) @ cytoscape --- [INFO] Base repo: file:///wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/ [INFO] Copying artifact: org.cytoscape.distribution:features:xml:features:3.6.1 [INFO] [INFO] --- maven-dependency-plugin:2.10:copy (copy-dependencies) @ cytoscape --- [INFO] Configured Artifact: org.cytoscape.distribution:branding:3.6.1:jar [INFO] Configured Artifact: org.cytoscape.distribution:karaf-launcher:3.6.1:jar [INFO] org.cytoscape.distribution:branding:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/branding [INFO] org.cytoscape.distribution:karaf-launcher:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/launcher [INFO] [INFO] --- maven-dependency-plugin:2.10:copy-dependencies (copy-dependencies) @ cytoscape --- [INFO] org.apache.karaf:apache-karaf:tar.gz:3.0.3 already exists in destination. [INFO] org.apache.karaf:apache-karaf:zip:3.0.3 already exists in destination. [INFO] org.apache.karaf.features:standard:xml:features:3.0.3 already exists in destination. [INFO] [INFO] --- maven-dependency-plugin:2.10:unpack (unpack-dependencies) @ cytoscape --- [INFO] Configured Artifact: org.apache.karaf:apache-karaf:?:tar.gz [INFO] Configured Artifact: org.cytoscape.gui-distribution:splash-launcher:3.6.1:jar [INFO] apache-karaf-3.0.3.tar.gz already unpacked. [INFO] splash-launcher-3.6.1.jar already unpacked. [INFO] [INFO] --- maven-dependency-plugin:2.10:copy (copy) @ cytoscape --- [INFO] Configured Artifact: org.cytoscape:core-apps-meta:3.6.0:jar [INFO] Configured Artifact: org.cytoscape:biopax:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:command-dialog:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:json:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:idmapper:3.6.1:jar [INFO] Configured Artifact: org.cytoscape:network-analyzer:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:network-merge:3.3.4:jar [INFO] Configured Artifact: org.cytoscape:psi-mi:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:sbml:3.3.3:jar [INFO] Configured Artifact: org.cytoscape:webservice-biomart-client:3.3.2:jar [INFO] Configured Artifact: org.cytoscape:webservice-psicquic-client:3.4.0:jar [INFO] Configured Artifact: org.cytoscape:cy-rest:3.7.0:jar [INFO] Configured Artifact: org.cytoscape:opencl-cycl:3.5.0:jar [INFO] Configured Artifact: org.cytoscape:opencl-layout:3.5.0:jar [INFO] Configured Artifact: org.cytoscape:welcome:3.5.2:jar [INFO] Configured Artifact: org.cytoscape.diffusion:diffusion:1.5.2:jar [INFO] Configured Artifact: org.cytoscape.copycatLayout:copycatLayout:1.2.3:jar [INFO] Configured Artifact: edu.ucsf.rbvi:cyBrowser:1.0.0:jar [INFO] Configured Artifact: org.cytoscape:cx-support:2.2.2:jar [INFO] Configured Artifact: org.cytoscape:cy-ndex-2:2.2.2:jar [INFO] org.cytoscape:core-apps-meta:3.6.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:biopax:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:command-dialog:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:json:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:idmapper:3.6.1:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:network-analyzer:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:network-merge:3.3.4:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:psi-mi:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:sbml:3.3.3:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:webservice-biomart-client:3.3.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:webservice-psicquic-client:3.4.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:cy-rest:3.7.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:opencl-cycl:3.5.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:opencl-layout:3.5.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:welcome:3.5.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape.diffusion:diffusion:1.5.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape.copycatLayout:copycatLayout:1.2.3:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] edu.ucsf.rbvi:cyBrowser:1.0.0:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:cx-support:2.2.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] org.cytoscape:cy-ndex-2:2.2.2:jar already exists in /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/dependencies/apps [INFO] [INFO] --- maven-assembly-plugin:2.5.5:single (directory) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-dev.xml [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /apps [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/etc/ [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/system [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [INFO] Copying files to /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape [WARNING] Assembly file: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-unix) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-main-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-wrap-deployer-windows) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] --- maven-replacer-plugin:1.3.9:replace (patch-karaf-disable-jmx) @ cytoscape --- [INFO] Replacement run on 1 file. [INFO] [INFO] >>> maven-source-plugin:2.4:jar (attach-sources) > generate-sources @ cytoscape >>> [INFO] [INFO] <<< maven-source-plugin:2.4:jar (attach-sources) < generate-sources @ cytoscape <<< [INFO] [INFO] [INFO] --- maven-source-plugin:2.4:jar (attach-sources) @ cytoscape --- [INFO] [INFO] --- maven-assembly-plugin:2.5.5:single (unix-bin) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-unix.xml [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /apps [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/etc/ [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/system [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [INFO] Building tar: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape-unix-3.6.1.tar.gz [INFO] [INFO] --- maven-assembly-plugin:2.5.5:single (windows-bin) @ cytoscape --- [INFO] Reading assembly descriptor: target/generated-resources/xml/xslt/config-windows.xml [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible / [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /apps [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/lib [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/etc/ [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /framework/system [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [WARNING] The assembly descriptor contains a filesystem-root relative reference, which is not cross platform compatible /sampleData [INFO] Building zip: /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape-windows-3.6.1.zip [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cytoscape --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/cytoscape/3.6.1/cytoscape-3.6.1.pom [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape-unix-3.6.1.tar.gz to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/cytoscape/3.6.1/cytoscape-3.6.1.tar.gz [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/gui-distribution/assembly/target/cytoscape-windows-3.6.1.zip to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/distribution/cytoscape/3.6.1/cytoscape-3.6.1.zip [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Skipping Distribution [INFO] This project has been banned from the build due to previous failures. [INFO] ------------------------------------------------------------------------ [INFO] [INFO] -----------------------< org.cytoscape:project >------------------------ [INFO] Building Cytoscape Project POM 3.6.1 [24/117] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ project --- [INFO] Installing /wrkdirs/usr/ports/biology/cytoscape/work/cytoscape-3.6.1/pom.xml to /wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/cytoscape/project/3.6.1/project-3.6.1.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Cytoscape Project POM 3.6.1: [INFO] [INFO] Basic Cytoscape POM Configuration .................. SUCCESS [ 0.190 s] [INFO] Cytoscape API Parent Project POM ................... FAILURE [ 0.394 s] [INFO] Cytoscape Documentation Taglets .................... SKIPPED [INFO] Cytoscape Event API (event-api) .................... SKIPPED [INFO] Cytoscape Model API (model-api) .................... SKIPPED [INFO] Cytoscape Service API (service-api) ................ SKIPPED [INFO] Cytoscape View Model API (viewmodel-api) ........... SKIPPED [INFO] Cytoscape CI API (ci-api) .......................... SKIPPED [INFO] Cytoscape Work API (work-api) ...................... SKIPPED [INFO] Cytoscape Presentation API (presentation-api) ...... SKIPPED [INFO] Cytoscape Application API (application-api) ........ SKIPPED [INFO] Cytoscape Property API (property-api) .............. SKIPPED [INFO] Cytoscape VizMap API (vizmap-api) .................. SKIPPED [INFO] Cytoscape Session API (session-api) ................ SKIPPED [INFO] Cytoscape Filter API (filter-api) .................. SKIPPED [INFO] Cytoscape IO API (io-api) .......................... SKIPPED [INFO] Cytoscape Core Task API (core-task-api) ............ SKIPPED [INFO] Cytoscape Equations API (equations-api) ............ SKIPPED [INFO] Cytoscape Layout API (layout-api) .................. SKIPPED [INFO] Cytoscape Groups API (group-api) ................... SKIPPED [INFO] Cytoscape Groups API (jobs-api) .................... SKIPPED [INFO] Cytoscape Webservice API (webservice-api) .......... SKIPPED [INFO] Cytoscape Data Source API (datasource-api) ......... SKIPPED [INFO] Cytoscape Command Executor API (command-executor-api) SKIPPED [INFO] Cytoscape App API (app-api) ........................ SKIPPED [INFO] Cytoscape Work Swing API (work-swing-api) .......... SKIPPED [INFO] Cytoscape Swing Application API (swing-application-api) SKIPPED [INFO] Cytoscape VizMap GUI API (vizmap-gui-api) .......... SKIPPED [INFO] Cytoscape Swing Utility API (swing-util-api) ....... SKIPPED [INFO] Cytoscape Webservice Swing API (webservice-swing-api) SKIPPED [INFO] Cytoscape Swing App API (swing-app-api) ............ SKIPPED [INFO] Cytoscape Util API (util-api) ...................... SKIPPED [INFO] Cytoscape API (api-bundle) ......................... SKIPPED [INFO] Cytoscape Implementation Parent Project POM ........ SKIPPED [INFO] Cytoscape Equations Impl (equations-impl) .......... SKIPPED [INFO] Cytoscape Model Impl Parent (model-impl-parent) .... SKIPPED [INFO] Cytoscape Model Impl (model-impl) .................. SKIPPED [INFO] Cytoscape Command Executor Impl (command-executor-impl) SKIPPED [INFO] Cytoscape Ding Impl Parent (ding-impl) ............. SKIPPED [INFO] Cytoscape Ding View/Presentation Impl (ding-presentation-impl) SKIPPED [INFO] Cytoscape View Model Impl Parent (viewmodel-impl-parent) SKIPPED [INFO] Cytoscape View Model Impl (viewmodel-impl) ......... SKIPPED [INFO] Cytoscape Groups Impl (group-impl) ................. SKIPPED [INFO] Cytoscape Event Impl Parent (event-impl-parent) .... SKIPPED [INFO] Cytoscape Event Impl (event-impl) .................. SKIPPED [INFO] Cytoscape Filters Impl (filter-impl) ............... SKIPPED [INFO] Cytoscape Filters 2 Impl (filter2-impl) ............ SKIPPED [INFO] Cytoscape IO Impl Parent (io-impl-parent) .......... SKIPPED [INFO] Cytoscape IO Impl (io-impl) ........................ SKIPPED [INFO] Cytoscape Layout Impl (layout-impl) ................ SKIPPED [INFO] Cytoscape Ding View/Presentation Impl Performance (ding-impl-performance-debug) SKIPPED [INFO] Cytoscape Editor Impl (editor-impl) ................ SKIPPED [INFO] Cytoscape Equation Functions Impl (equations-functions-impl) SKIPPED [INFO] Cytoscape GraphML Impl (graphml-impl) .............. SKIPPED [INFO] Cytoscape IO Impl Performance (io-impl-performance) SKIPPED [INFO] Cytoscape Jobs Impl (jobs-impl) .................... SKIPPED [INFO] Cytoscape Layout Algorithms Impl (layout-cytoscape-impl) SKIPPED [INFO] Cytoscape JGraph Layout Impl (layout-jgraph-impl) .. SKIPPED [INFO] Cytoscape Prefuse Layout Impl (layout-prefuse-impl) SKIPPED [INFO] Cytoscape Linkout Impl (linkout-impl) .............. SKIPPED [INFO] Cytoscape Log Swing Impl (log-swing-impl) .......... SKIPPED [INFO] Cytoscape Manual Layout Impl (manual-layout-impl) .. SKIPPED [INFO] Cytoscape Model Impl Performance Debug (model-impl-performance-debug) SKIPPED [INFO] Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) SKIPPED [INFO] Cytoscape App Impl (app-impl) ...................... SKIPPED [INFO] Cytoscape Presentation Impl (presentation-impl) .... SKIPPED [INFO] Cytoscape Property Impl (property-impl) ............ SKIPPED [INFO] Cytoscape Search Impl (search-impl) ................ SKIPPED [INFO] Cytoscape Session Impl (session-impl) .............. SKIPPED [INFO] Cytoscape Swing Utility Impl (swing-util-impl) ..... SKIPPED [INFO] Cytoscape Swing Application Impl (swing-application-impl) SKIPPED [INFO] Cytoscape Table Browser Impl (table-browser-impl) .. SKIPPED [INFO] Cytoscape Table Import Impl (table-import-impl) .... SKIPPED [INFO] Cytoscape VizMap GUI Core Impl (vizmap-gui-core-impl) SKIPPED [INFO] Cytoscape VizMap GUI Impl (vizmap-gui-impl) ........ SKIPPED [INFO] Cytoscape VizMap Impl Parent (vizmap-impl-parent) .. SKIPPED [INFO] Cytoscape VizMap Impl (vizmap-impl) ................ SKIPPED [INFO] Cytoscape Webservice Impl (webservice-impl) ........ SKIPPED [INFO] org.cytoscape.work-headless-impl ................... SKIPPED [INFO] org.cytoscape.work-impl ............................ SKIPPED [INFO] Cytoscape Work Swing Impl Parent (work-swing-impl-parent) SKIPPED [INFO] Cytoscape Work Swing Impl (work-swing-impl) ........ SKIPPED [INFO] Cytoscape Application Impl (application-impl) ...... SKIPPED [INFO] Cytoscape Datasource Impl (datasource-impl) ........ SKIPPED [INFO] Cytoscape Support Parent Project POM ............... SUCCESS [ 0.011 s] [INFO] Cytoscape Launch Framework ......................... SUCCESS [ 0.006 s] [INFO] CommandLine Provider ............................... SUCCESS [ 1.393 s] [INFO] Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) SKIPPED [INFO] Cytoscape Edge Bundler Impl (edge-bundler-impl) .... SKIPPED [INFO] Cytoscape Scripting Impl (scripting-impl) .......... SKIPPED [INFO] Cytoscape Core Task Impl (core-task-impl) .......... SKIPPED [INFO] Cytoscape Headless Application Impl (headless-application-impl) SKIPPED [INFO] org.cytoscape.cy-commons-cli ....................... SUCCESS [ 0.850 s] [INFO] Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl) SKIPPED [INFO] Cytoscape 3 App Archetypes Parent .................. SUCCESS [ 0.104 s] [INFO] Cytoscape 3 Archetype - Creates an App providing public API SUCCESS [ 0.226 s] [INFO] Cytoscape 3 Archetype - Creates an App with a Task . SUCCESS [ 0.031 s] [INFO] Cytoscape 3 Archetype - Creates a CyAction (menu item) for desktop application SUCCESS [ 0.027 s] [INFO] Cytoscape 3 Archetype - Creates a Meta-App to install multiple related apps SUCCESS [ 0.027 s] [INFO] org.cytoscape.integration-test-support ............. SUCCESS [ 0.360 s] [INFO] Launcher ........................................... SUCCESS [ 0.795 s] [INFO] StartLevel Assembly ................................ SUCCESS [ 0.032 s] [INFO] Tasks for Testing .................................. SKIPPED [INFO] Cytoscape Desktop Application Distribution ......... SUCCESS [ 0.006 s] [INFO] Cytoscape Third-Party Dependencies (third-party) ... SUCCESS [ 27.902 s] [INFO] SplashScreen Launcher .............................. SUCCESS [ 1.168 s] [INFO] Cytoscape Launcher ................................. SUCCESS [ 0.297 s] [INFO] Splash Updater ..................................... SKIPPED [INFO] Cytoscape Command Line Provider Implementation ..... SKIPPED [INFO] Cytoscape Diagnostics .............................. SUCCESS [ 0.344 s] [INFO] Cytoscape Branding ................................. SUCCESS [ 0.223 s] [INFO] Cytoscape Application Implementation Metadata ...... SUCCESS [ 0.140 s] [INFO] Cytoscape GUI-Distribution Integration Test (integration-test) SKIPPED [INFO] Cytoscape Feature Repository ....................... SUCCESS [ 0.055 s] [INFO] Cytoscape Karaf Distribution ....................... SUCCESS [ 16.892 s] [INFO] Distribution ....................................... SKIPPED [INFO] Cytoscape Project POM .............................. SUCCESS [ 0.025 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 52.959 s [INFO] Finished at: 2025-05-08T00:28:27Z [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.8.1:generate (bookmarks) on project property-api: Execution bookmarks of goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.8.1:generate failed: A required class was missing while executing org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.8.1:generate: javax/xml/bind/JAXBException [ERROR] ----------------------------------------------------- [ERROR] realm = plugin>org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.8.1 [ERROR] strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy [ERROR] urls[0] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/0.8.1/maven-jaxb2-plugin-0.8.1.jar [ERROR] urls[1] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin-core/0.8.1/maven-jaxb2-plugin-core-0.8.1.jar [ERROR] urls[2] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/com/sun/org/apache/xml/internal/resolver/20050927/resolver-20050927.jar [ERROR] urls[3] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar [ERROR] urls[4] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar [ERROR] urls[5] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/jfrog/maven/annomojo/maven-plugin-anno/1.3.1/maven-plugin-anno-1.3.1.jar [ERROR] urls[6] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar [ERROR] urls[7] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb22-plugin/0.8.1/maven-jaxb22-plugin-0.8.1.jar [ERROR] urls[8] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/com/sun/xml/bind/jaxb-impl/2.2.5-b10/jaxb-impl-2.2.5-b10.jar [ERROR] urls[9] = file:/wrkdirs/usr/ports/biology/cytoscape/work/.m2/repository/com/sun/xml/bind/jaxb-xjc/2.2.5-b10/jaxb-xjc-2.2.5-b10.jar [ERROR] Number of foreign imports: 1 [ERROR] import: Entry[import from realm ClassRealm[project>org.cytoscape:event-api:3.6.1, parent: ClassRealm[maven.api, parent: null]]] [ERROR] [ERROR] ----------------------------------------------------- [ERROR] : javax.xml.bind.JAXBException [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginContainerException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :property-api *** Error code 1 Stop. make: stopped in /usr/ports/biology/cytoscape =>> Cleaning up wrkdir ===> Cleaning for cytoscape-3.6.1 build of biology/cytoscape | cytoscape-3.6.1 ended at Thu May 8 01:28:34 BST 2025 build time: 00:02:14 !!! build failure encountered !!!