Date: Tue, 27 Oct 2020 11:02:56 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 114amd64-default][biology/cytoscape] Failed for cytoscape-3.6.1 in build Message-ID: <202010271102.09RB2tCq032874@beefy9.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: jkim@FreeBSD.org Ident: $FreeBSD: head/biology/cytoscape/Makefile 518482 2019-11-26 21:46:12Z jkim $ Log URL: http://beefy9.nyi.freebsd.org/data/114amd64-default/553405/logs/cytoscape-3.6.1.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=553405 Log: =>> Building biology/cytoscape build started at Tue Oct 27 10:56:20 UTC 2020 port directory: /usr/ports/biology/cytoscape package name: cytoscape-3.6.1 building for: FreeBSD 114amd64-default-job-14 11.4-RELEASE-p4 FreeBSD 11.4-RELEASE-p4 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/cytoscape/Makefile 518482 2019-11-26 21:46:12Z jkim $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300121 Jail OSVERSION: 1104001 Job Id: 14 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1104001 UNAME_v=FreeBSD 11.4-RELEASE-p4 UNAME_r=11.4-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/114amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/114amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=114amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/114amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= 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 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 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 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 NO_PIE=yes 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 " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=11.4 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=11.4-RELEASE-p4 OSREL=11.4 OSVERSION=1104001 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1024 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 --End resource limits-- =======================<phase: check-sanity >============================ ===> License LGPL21 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> cytoscape-3.6.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.15.10.txz [114amd64-default-job-14] Installing pkg-1.15.10... [114amd64-default-job-14] Extracting pkg-1.15.10: .......... done ===> cytoscape-3.6.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cytoscape-3.6.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by cytoscape-3.6.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License LGPL21 accepted by the user ===> 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License LGPL21 accepted by the user ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for cytoscape-3.6.1 =========================================================================== =======================<phase: build-depends >============================ ===> cytoscape-3.6.1 depends on executable: mvn - not found ===> Installing existing package /packages/All/maven-3.6.3.txz [114amd64-default-job-14] Installing maven-3.6.3... [114amd64-default-job-14] `-- Installing maven-wrapper-1_2... [114amd64-default-job-14] `-- Extracting maven-wrapper-1_2: .. done [114amd64-default-job-14] `-- Installing openjdk8-8.272.10.1_1... <snip> [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 *** Signal 9 Stop. make: stopped in /usr/ports/biology/cytoscape
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