=>> Building science/cdk build started at Sat Jan 24 08:56:32 EST 2026 port directory: /usr/ports/science/cdk package name: cdk-chemistry-2.7.1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1478 Jan 14 2025 /usr/ports/science/cdk/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 0835676e361b Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 13 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 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/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/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/science/cdk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/cdk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/cdk/work/.cache HOME=/wrkdirs/usr/ports/science/cdk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/cdk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/cdk/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/science/cdk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/cdk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/cdk/work/.cache HOME=/wrkdirs/usr/ports/science/cdk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/cdk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/cdk/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=" " 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=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cdk" EXAMPLESDIR="share/examples/cdk" DATADIR="share/cdk" WWWDIR="www/cdk" ETCDIR="etc/cdk" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cdk DOCSDIR=/usr/local/share/doc/cdk EXAMPLESDIR=/usr/local/share/examples/cdk WWWDIR=/usr/local/www/cdk ETCDIR=/usr/local/etc/cdk --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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 --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 ===> cdk-chemistry-2.7.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> cdk-chemistry-2.7.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cdk-chemistry-2.7.1 =========================================================================== =================================================== ===== 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 cdk-chemistry-2.7.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cdk-chemistry-2.7.1 for building => SHA256 Checksum OK for cdk-2.7.1-deps.tar.gz. => SHA256 Checksum OK for cdk-cdk-cdk-2.7.1_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 cdk-chemistry-2.7.1 for building ===> Extracting for cdk-chemistry-2.7.1 => SHA256 Checksum OK for cdk-2.7.1-deps.tar.gz. => SHA256 Checksum OK for cdk-cdk-cdk-2.7.1_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 cdk-chemistry-2.7.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cdk-chemistry-2.7.1 depends on package: maven>0 - not found ===> Installing existing package /packages/All/maven-3.8.9.pkg [pkg.DaveG.ca] Installing maven-3.8.9... [pkg.DaveG.ca] `-- Installing maven-wrapper-2... [pkg.DaveG.ca] `-- Extracting maven-wrapper-2: ... done [pkg.DaveG.ca] `-- Installing openjdk8-8.472.08.1_1... [pkg.DaveG.ca] | `-- Installing alsa-lib-1.2.14... [pkg.DaveG.ca] | `-- Extracting alsa-lib-1.2.14: .......... done [pkg.DaveG.ca] | `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | | `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | | `-- Installing expat-2.7.3... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | | `-- Installing png-1.6.53... [pkg.DaveG.ca] | | | `-- Extracting png-1.6.53: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | | `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting dejavu-2.37_4: .......... done [pkg.DaveG.ca] | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Installing java-zoneinfo-2021.e... [pkg.DaveG.ca] | `-- Extracting java-zoneinfo-2021.e: .......... done [pkg.DaveG.ca] | `-- Installing javavmwrapper-2.7.10... [pkg.DaveG.ca] | `-- Extracting javavmwrapper-2.7.10: .......... done [pkg.DaveG.ca] | `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] | `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] | `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] | `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] | `-- Installing libXi-1.8.2,1... [pkg.DaveG.ca] | | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] | `-- Extracting libXi-1.8.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] | `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] | `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libXtst-1.2.5... [pkg.DaveG.ca] | `-- Extracting libXtst-1.2.5: .......... done [pkg.DaveG.ca] | `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] `-- Extracting openjdk8-8.472.08.1_1: .......... done [pkg.DaveG.ca] Extracting maven-3.8.9: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. 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_3: -- 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 openjdk8-8.472.08.1_1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> cdk-chemistry-2.7.1 depends on package: maven>0 - found ===> Returning to build of cdk-chemistry-2.7.1 ===> cdk-chemistry-2.7.1 depends on file: /usr/local/openjdk17/bin/java - not found ===> Installing existing package /packages/All/openjdk17-17.0.17+10.1_1.pkg [pkg.DaveG.ca] Installing openjdk17-17.0.17+10.1_1... [pkg.DaveG.ca] `-- Installing harfbuzz-12.3.0... [pkg.DaveG.ca] | `-- Installing glib-2.84.4,2... [pkg.DaveG.ca] | | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] | | `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] | | `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] | | `-- Installing python311-3.11.14... [pkg.DaveG.ca] | | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | | | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] | | `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] | | `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] | `-- Extracting glib-2.84.4,2: .......... done [pkg.DaveG.ca] | `-- Installing graphite2-1.3.14... [pkg.DaveG.ca] | `-- Extracting graphite2-1.3.14: .......... done [pkg.DaveG.ca] `-- Extracting harfbuzz-12.3.0: .......... done [pkg.DaveG.ca] `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] `-- Installing lcms2-2.17... [pkg.DaveG.ca] | `-- Installing tiff-4.7.1... [pkg.DaveG.ca] | | `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] | | `-- Installing lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting lcms2-2.17: .......... done [pkg.DaveG.ca] `-- Installing libXrandr-1.5.4... [pkg.DaveG.ca] `-- Extracting libXrandr-1.5.4: .......... done [pkg.DaveG.ca] `-- Installing xorg-fonts-truetype-7.7_1... [pkg.DaveG.ca] | `-- Installing encodings-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting encodings-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing font-bh-ttf-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg.DaveG.ca] | `-- Installing font-misc-ethiopic-1.0.4... [pkg.DaveG.ca] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg.DaveG.ca] | `-- Installing font-misc-meltho-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg.DaveG.ca] Extracting openjdk17-17.0.17+10.1_1: .......... 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 python311-3.11.14: -- 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 openjdk17-17.0.17+10.1_1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> cdk-chemistry-2.7.1 depends on file: /usr/local/openjdk17/bin/java - found ===> Returning to build of cdk-chemistry-2.7.1 ===> cdk-chemistry-2.7.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] 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. ===> cdk-chemistry-2.7.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of cdk-chemistry-2.7.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for cdk-chemistry-2.7.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for cdk-chemistry-2.7.1 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] cdk [pom] [INFO] cdk-base [pom] [INFO] cdk-interfaces [jar] [INFO] cdk-core [jar] [INFO] cdk-standard [jar] [INFO] cdk-atomtype [jar] [INFO] cdk-valencycheck [jar] [INFO] cdk-misc [pom] [INFO] cdk-diff [jar] [INFO] cdk-test [jar] [INFO] cdk-data [jar] [INFO] cdk-storage [pom] [INFO] cdk-ioformats [jar] [INFO] cdk-silent [jar] [INFO] cdk-isomorphism [jar] [INFO] cdk-datadebug [jar] [INFO] cdk-ctab [jar] [INFO] cdk-io [jar] [INFO] cdk-tool [pom] [INFO] cdk-formula [jar] [INFO] cdk-dict [jar] [INFO] cdk-pdb [jar] [INFO] cdk-libiocml [jar] [INFO] cdk-smiles [jar] [INFO] cdk-extra [jar] [INFO] cdk-smarts [jar] [INFO] cdk-reaction [jar] [INFO] cdk-descriptor [pom] [INFO] cdk-fingerprint [jar] [INFO] cdk-cip [jar] [INFO] cdk-signature [jar] [INFO] cdk-charges [jar] [INFO] cdk-forcefield [jar] [INFO] cdk-sdg [jar] [INFO] cdk-builder3dtools [jar] [INFO] cdk-builder3d [jar] [INFO] cdk-qsar [jar] [INFO] cdk-ionpot [jar] [INFO] cdk-qsaratomic [jar] [INFO] cdk-qsarbond [jar] [INFO] cdk-hash [jar] [INFO] cdk-fragment [jar] [INFO] cdk-model [jar] [INFO] cdk-qsarmolecular [jar] [INFO] cdk-qsarcml [jar] [INFO] cdk-qsarionpot [jar] [INFO] cdk-qsarprotein [jar] [INFO] cdk-display [pom] [INFO] cdk-render [jar] [INFO] cdk-renderbasic [jar] [INFO] cdk-renderawt [jar] [INFO] cdk-renderextra [jar] [INFO] cdk-control [jar] [INFO] cdk-qm [jar] [INFO] cdk-iordf [jar] [INFO] cdk-libiomd [jar] [INFO] cdk-pdbcml [jar] [INFO] cdk-jniinchi-support [jar] [INFO] cdk-inchi [jar] [INFO] cdk-group [jar] [INFO] cdk-pcore [jar] [INFO] cdk-structgen [jar] [INFO] cdk-tautomer [jar] [INFO] cdk-legacy [jar] [INFO] cdk-app [pom] [INFO] cdk-depict [jar] [INFO] cdk-bundle [jar] [INFO] cdk-annotation [jar] [INFO] cdk-test-atomtype [jar] [INFO] cdk-log4j [jar] [INFO] cdk-test-core [jar] [INFO] cdk-test-standard [jar] [INFO] cdk-test-valencycheck [jar] [INFO] cdk-qsarsubstance [jar] [INFO] cdk-test-extra [jar] [INFO] [INFO] ----------------------< org.openscience.cdk:cdk >----------------------- [INFO] Building cdk 2.7.1 [1/75] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk/2.7.1/cdk-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-base >-------------------- [INFO] Building cdk-base 2.7.1 [2/75] [INFO] from base/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-base --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-base/2.7.1/cdk-base-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-interfaces >----------------- [INFO] Building cdk-interfaces 2.7.1 [3/75] [INFO] from base/interfaces/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-interfaces --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/interfaces/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-interfaces --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 86 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/interfaces/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-interfaces --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-interfaces --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-interfaces --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-interfaces --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/interfaces/target/cdk-interfaces-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-interfaces --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/interfaces/target/cdk-interfaces-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-interfaces/2.7.1/cdk-interfaces-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/interfaces/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-interfaces/2.7.1/cdk-interfaces-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-core >-------------------- [INFO] Building cdk-core 2.7.1 [4/75] [INFO] from base/core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 81 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/BondRef.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/BondRef.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java uses or overrides a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java: Recompile with -Xlint:removal for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/io/setting/SettingManager.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/src/main/java/org/openscience/cdk/io/setting/SettingManager.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-core --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-core --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-core --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/target/cdk-core-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-core --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/target/cdk-core-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-core/2.7.1/cdk-core-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/core/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-core/2.7.1/cdk-core-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-standard >------------------ [INFO] Building cdk-standard 2.7.1 [5/75] [INFO] from base/standard/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-standard --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-standard --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 89 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/src/main/java/org/openscience/cdk/geometry/BondTools.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/src/main/java/org/openscience/cdk/geometry/BondTools.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-standard --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-standard --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-standard --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-standard --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/target/cdk-standard-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-standard --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/target/cdk-standard-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-standard/2.7.1/cdk-standard-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/standard/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-standard/2.7.1/cdk-standard-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-atomtype >------------------ [INFO] Building cdk-atomtype 2.7.1 [6/75] [INFO] from base/atomtype/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-atomtype --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-atomtype --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-atomtype --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-atomtype --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-atomtype --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-atomtype --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/target/cdk-atomtype-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-atomtype --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/target/cdk-atomtype-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-atomtype/2.7.1/cdk-atomtype-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/atomtype/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-atomtype/2.7.1/cdk-atomtype-2.7.1.pom [INFO] [INFO] ----------------< org.openscience.cdk:cdk-valencycheck >---------------- [INFO] Building cdk-valencycheck 2.7.1 [7/75] [INFO] from base/valencycheck/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-valencycheck --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-valencycheck --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-valencycheck --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-valencycheck --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-valencycheck --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-valencycheck --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/target/cdk-valencycheck-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-valencycheck --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/target/cdk-valencycheck-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-valencycheck/2.7.1/cdk-valencycheck-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/valencycheck/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-valencycheck/2.7.1/cdk-valencycheck-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-misc >-------------------- [INFO] Building cdk-misc 2.7.1 [8/75] [INFO] from misc/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-misc --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-misc/2.7.1/cdk-misc-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-diff >-------------------- [INFO] Building cdk-diff 2.7.1 [9/75] [INFO] from misc/diff/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-diff --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-diff --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 24 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomDiff.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomDiff.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomDiff.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-diff --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-diff --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-diff --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-diff --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/target/cdk-diff-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-diff --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/target/cdk-diff-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-diff/2.7.1/cdk-diff-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/diff/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-diff/2.7.1/cdk-diff-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-test >-------------------- [INFO] Building cdk-test 2.7.1 [10/75] [INFO] from base/test/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/src/main/java/org/openscience/cdk/test/interfaces/AbstractAtomContainerTest.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/src/main/java/org/openscience/cdk/test/interfaces/AbstractAtomContainerTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-test --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-test --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/target/cdk-test-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/target/cdk-test-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test/2.7.1/cdk-test-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test/2.7.1/cdk-test-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-data >-------------------- [INFO] Building cdk-data 2.7.1 [11/75] [INFO] from base/data/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-data --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-data --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 41 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/src/main/java/org/openscience/cdk/AtomContainer.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/src/main/java/org/openscience/cdk/AtomContainer.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/src/main/java/org/openscience/cdk/AtomContainer.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/src/main/java/org/openscience/cdk/AtomContainer.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-data --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-data --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-data --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-data --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/target/cdk-data-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-data --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/target/cdk-data-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-data/2.7.1/cdk-data-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/data/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-data/2.7.1/cdk-data-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-storage >------------------- [INFO] Building cdk-storage 2.7.1 [12/75] [INFO] from storage/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-storage --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-storage/2.7.1/cdk-storage-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-ioformats >------------------ [INFO] Building cdk-ioformats 2.7.1 [13/75] [INFO] from storage/ioformats/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-ioformats --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-ioformats --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 102 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ioformats/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-ioformats --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-ioformats --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-ioformats --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-ioformats --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ioformats/target/cdk-ioformats-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-ioformats --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ioformats/target/cdk-ioformats-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-ioformats/2.7.1/cdk-ioformats-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ioformats/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-ioformats/2.7.1/cdk-ioformats-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-silent >------------------- [INFO] Building cdk-silent 2.7.1 [14/75] [INFO] from base/silent/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-silent --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-silent --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 38 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-silent --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-silent --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-silent --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-silent --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/target/cdk-silent-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-silent --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/target/cdk-silent-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-silent/2.7.1/cdk-silent-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/silent/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-silent/2.7.1/cdk-silent-2.7.1.pom [INFO] [INFO] ----------------< org.openscience.cdk:cdk-isomorphism >----------------- [INFO] Building cdk-isomorphism 2.7.1 [15/75] [INFO] from base/isomorphism/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-isomorphism --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-isomorphism --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 31 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-isomorphism --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-isomorphism --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-isomorphism --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-isomorphism --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/target/cdk-isomorphism-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-isomorphism --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/target/cdk-isomorphism-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-isomorphism/2.7.1/cdk-isomorphism-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/isomorphism/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-isomorphism/2.7.1/cdk-isomorphism-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-datadebug >------------------ [INFO] Building cdk-datadebug 2.7.1 [16/75] [INFO] from base/datadebug/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-datadebug --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-datadebug --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 37 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugBond.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/src/main/java/org/openscience/cdk/debug/DebugBond.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-datadebug --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-datadebug --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-datadebug --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-datadebug --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/target/cdk-datadebug-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-datadebug --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/target/cdk-datadebug-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-datadebug/2.7.1/cdk-datadebug-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/datadebug/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-datadebug/2.7.1/cdk-datadebug-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-ctab >-------------------- [INFO] Building cdk-ctab 2.7.1 [17/75] [INFO] from storage/ctab/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-ctab --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-ctab --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 15 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/MDLReader.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/MDLReader.java uses or overrides a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/MDLReader.java: Recompile with -Xlint:removal for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-ctab --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-ctab --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-ctab --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-ctab --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/target/cdk-ctab-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-ctab --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/target/cdk-ctab-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-ctab/2.7.1/cdk-ctab-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/ctab/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-ctab/2.7.1/cdk-ctab-2.7.1.pom [INFO] [INFO] ---------------------< org.openscience.cdk:cdk-io >--------------------- [INFO] Building cdk-io 2.7.1 [18/75] [INFO] from storage/io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-io --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-io --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/src/main/java/org/openscience/cdk/io/CMLReader.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/src/main/java/org/openscience/cdk/io/CMLReader.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/src/main/java/org/openscience/cdk/io/program/GaussianInputWriter.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/src/main/java/org/openscience/cdk/io/program/GaussianInputWriter.java: Recompile with -Xlint:removal for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-io --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-io --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-io --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-io --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/target/cdk-io-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-io --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/target/cdk-io-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-io/2.7.1/cdk-io-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/io/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-io/2.7.1/cdk-io-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-tool >-------------------- [INFO] Building cdk-tool 2.7.1 [19/75] [INFO] from tool/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-tool --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-tool/2.7.1/cdk-tool-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-formula >------------------- [INFO] Building cdk-formula 2.7.1 [20/75] [INFO] from tool/formula/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-formula --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-formula --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 22 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/src/main/java/org/openscience/cdk/formula/IsotopeContainer.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/src/main/java/org/openscience/cdk/formula/IsotopeContainer.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/src/main/java/org/openscience/cdk/formula/rules/IsotopePatternRule.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/src/main/java/org/openscience/cdk/formula/rules/IsotopePatternRule.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/src/main/java/org/openscience/cdk/formula/rules/IsotopePatternRule.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-formula --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-formula --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-formula --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-formula --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/target/cdk-formula-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-formula --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/target/cdk-formula-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-formula/2.7.1/cdk-formula-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/formula/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-formula/2.7.1/cdk-formula-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-dict >-------------------- [INFO] Building cdk-dict 2.7.1 [21/75] [INFO] from base/dict/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-dict --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-dict --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-dict --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-dict --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-dict --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-dict --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/target/cdk-dict-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-dict --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/target/cdk-dict-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-dict/2.7.1/cdk-dict-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/dict/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-dict/2.7.1/cdk-dict-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-pdb >--------------------- [INFO] Building cdk-pdb 2.7.1 [22/75] [INFO] from storage/pdb/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-pdb --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-pdb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdb/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-pdb --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-pdb --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-pdb --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-pdb --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdb/target/cdk-pdb-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-pdb --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdb/target/cdk-pdb-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-pdb/2.7.1/cdk-pdb-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdb/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-pdb/2.7.1/cdk-pdb-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-libiocml >------------------ [INFO] Building cdk-libiocml 2.7.1 [23/75] [INFO] from storage/libiocml/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-libiocml --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-libiocml --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/src/main/java/org/openscience/cdk/libio/cml/Convertor.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/src/main/java/org/openscience/cdk/libio/cml/Convertor.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/src/main/java/org/openscience/cdk/libio/cml/Convertor.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-libiocml --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-libiocml --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-libiocml --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-libiocml --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/target/cdk-libiocml-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-libiocml --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/target/cdk-libiocml-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-libiocml/2.7.1/cdk-libiocml-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiocml/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-libiocml/2.7.1/cdk-libiocml-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-smiles >------------------- [INFO] Building cdk-smiles 2.7.1 [24/75] [INFO] from storage/smiles/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-smiles --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-smiles --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/src/main/java/org/openscience/cdk/io/MoSSOutputReader.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/src/main/java/org/openscience/cdk/io/MoSSOutputReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-smiles --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-smiles --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-smiles --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-smiles --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/target/cdk-smiles-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-smiles --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/target/cdk-smiles-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-smiles/2.7.1/cdk-smiles-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/smiles/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-smiles/2.7.1/cdk-smiles-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-extra >-------------------- [INFO] Building cdk-extra 2.7.1 [25/75] [INFO] from misc/extra/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-extra --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-extra --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 47 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeReader.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeReader.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/src/main/java/org/openscience/cdk/io/CrystClustReader.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/src/main/java/org/openscience/cdk/io/CrystClustReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-extra --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-extra --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-extra --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-extra --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/target/cdk-extra-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-extra --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/target/cdk-extra-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-extra/2.7.1/cdk-extra-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/extra/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-extra/2.7.1/cdk-extra-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-smarts >------------------- [INFO] Building cdk-smarts 2.7.1 [26/75] [INFO] from tool/smarts/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-smarts --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/smarts/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-smarts --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/smarts/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-smarts --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-smarts --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-smarts --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-smarts --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/smarts/target/cdk-smarts-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-smarts --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/smarts/target/cdk-smarts-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-smarts/2.7.1/cdk-smarts-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/smarts/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-smarts/2.7.1/cdk-smarts-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-reaction >------------------ [INFO] Building cdk-reaction 2.7.1 [27/75] [INFO] from base/reaction/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-reaction --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-reaction --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/src/main/java/org/openscience/cdk/reaction/ReactionEngine.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/src/main/java/org/openscience/cdk/reaction/ReactionEngine.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/src/main/java/org/openscience/cdk/reaction/ReactionEngine.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-reaction --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-reaction --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-reaction --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-reaction --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/target/cdk-reaction-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-reaction --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/target/cdk-reaction-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-reaction/2.7.1/cdk-reaction-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/reaction/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-reaction/2.7.1/cdk-reaction-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-descriptor >----------------- [INFO] Building cdk-descriptor 2.7.1 [28/75] [INFO] from descriptor/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-descriptor --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-descriptor/2.7.1/cdk-descriptor-2.7.1.pom [INFO] [INFO] ----------------< org.openscience.cdk:cdk-fingerprint >----------------- [INFO] Building cdk-fingerprint 2.7.1 [29/75] [INFO] from descriptor/fingerprint/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-fingerprint --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-fingerprint --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 17 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-fingerprint --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-fingerprint --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-fingerprint --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-fingerprint --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/target/cdk-fingerprint-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-fingerprint --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/target/cdk-fingerprint-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-fingerprint/2.7.1/cdk-fingerprint-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/fingerprint/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-fingerprint/2.7.1/cdk-fingerprint-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-cip >--------------------- [INFO] Building cdk-cip 2.7.1 [30/75] [INFO] from descriptor/cip/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-cip --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-cip --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-cip --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-cip --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-cip --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-cip --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/target/cdk-cip-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-cip --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/target/cdk-cip-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-cip/2.7.1/cdk-cip-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/cip/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-cip/2.7.1/cdk-cip-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-signature >------------------ [INFO] Building cdk-signature 2.7.1 [31/75] [INFO] from descriptor/signature/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-signature --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/signature/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-signature --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/signature/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-signature --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-signature --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-signature --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-signature --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/signature/target/cdk-signature-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-signature --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/signature/target/cdk-signature-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-signature/2.7.1/cdk-signature-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/signature/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-signature/2.7.1/cdk-signature-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-charges >------------------- [INFO] Building cdk-charges 2.7.1 [32/75] [INFO] from tool/charges/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-charges --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-charges --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 10 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/src/main/java/org/openscience/cdk/charges/InductivePartialCharges.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/src/main/java/org/openscience/cdk/charges/InductivePartialCharges.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-charges --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-charges --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-charges --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-charges --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/target/cdk-charges-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-charges --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/target/cdk-charges-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-charges/2.7.1/cdk-charges-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/charges/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-charges/2.7.1/cdk-charges-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-forcefield >----------------- [INFO] Building cdk-forcefield 2.7.1 [33/75] [INFO] from tool/forcefield/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-forcefield --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-forcefield --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 11 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java: Recompile with -Xlint:removal for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-forcefield --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-forcefield --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-forcefield --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-forcefield --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/target/cdk-forcefield-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-forcefield --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/target/cdk-forcefield-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-forcefield/2.7.1/cdk-forcefield-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/forcefield/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-forcefield/2.7.1/cdk-forcefield-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-sdg >--------------------- [INFO] Building cdk-sdg 2.7.1 [34/75] [INFO] from tool/sdg/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-sdg --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 9 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-sdg --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 12 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/sdg/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-sdg --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-sdg --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-sdg --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-sdg --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/sdg/target/cdk-sdg-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-sdg --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/sdg/target/cdk-sdg-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-sdg/2.7.1/cdk-sdg-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/sdg/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-sdg/2.7.1/cdk-sdg-2.7.1.pom [INFO] [INFO] ---------------< org.openscience.cdk:cdk-builder3dtools >--------------- [INFO] Building cdk-builder3dtools 2.7.1 [35/75] [INFO] from tool/builder3dtools/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-builder3dtools --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-builder3dtools --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-builder3dtools --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-builder3dtools --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-builder3dtools --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-builder3dtools --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/target/cdk-builder3dtools-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-builder3dtools --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/target/cdk-builder3dtools-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-builder3dtools/2.7.1/cdk-builder3dtools-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3dtools/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-builder3dtools/2.7.1/cdk-builder3dtools-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-builder3d >------------------ [INFO] Building cdk-builder3d 2.7.1 [36/75] [INFO] from tool/builder3d/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-builder3d --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-builder3d --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-builder3d --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-builder3d --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-builder3d --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-builder3d --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/target/cdk-builder3d-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-builder3d --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/target/cdk-builder3d-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-builder3d/2.7.1/cdk-builder3d-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/builder3d/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-builder3d/2.7.1/cdk-builder3d-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-qsar >-------------------- [INFO] Building cdk-qsar 2.7.1 [37/75] [INFO] from descriptor/qsar/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsar --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsar --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 11 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsar/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractAtomicDescriptor.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractAtomicDescriptor.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsar --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsar --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsar --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsar --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsar/target/cdk-qsar-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsar --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsar/target/cdk-qsar-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsar/2.7.1/cdk-qsar-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsar/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsar/2.7.1/cdk-qsar-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-ionpot >------------------- [INFO] Building cdk-ionpot 2.7.1 [38/75] [INFO] from descriptor/ionpot/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-ionpot --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/ionpot/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-ionpot --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-ionpot --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-ionpot --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-ionpot --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-ionpot --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/ionpot/target/cdk-ionpot-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-ionpot --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/ionpot/target/cdk-ionpot-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-ionpot/2.7.1/cdk-ionpot-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/ionpot/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-ionpot/2.7.1/cdk-ionpot-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-qsaratomic >----------------- [INFO] Building cdk-qsaratomic 2.7.1 [39/75] [INFO] from descriptor/qsaratomic/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsaratomic --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsaratomic --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 29 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsaratomic/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsaratomic --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsaratomic --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsaratomic --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsaratomic --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsaratomic/target/cdk-qsaratomic-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsaratomic --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsaratomic/target/cdk-qsaratomic-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsaratomic/2.7.1/cdk-qsaratomic-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsaratomic/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsaratomic/2.7.1/cdk-qsaratomic-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-qsarbond >------------------ [INFO] Building cdk-qsarbond 2.7.1 [40/75] [INFO] from descriptor/qsarbond/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsarbond --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsarbond --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarbond/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsarbond --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsarbond --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsarbond --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsarbond --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarbond/target/cdk-qsarbond-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsarbond --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarbond/target/cdk-qsarbond-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarbond/2.7.1/cdk-qsarbond-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarbond/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarbond/2.7.1/cdk-qsarbond-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-hash >-------------------- [INFO] Building cdk-hash 2.7.1 [41/75] [INFO] from tool/hash/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-hash --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/hash/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-hash --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 35 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/hash/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-hash --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-hash --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-hash --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-hash --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/hash/target/cdk-hash-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-hash --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/hash/target/cdk-hash-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-hash/2.7.1/cdk-hash-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/hash/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-hash/2.7.1/cdk-hash-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-fragment >------------------ [INFO] Building cdk-fragment 2.7.1 [42/75] [INFO] from tool/fragment/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-fragment --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-fragment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-fragment --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-fragment --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-fragment --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-fragment --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/target/cdk-fragment-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-fragment --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/target/cdk-fragment-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-fragment/2.7.1/cdk-fragment-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/fragment/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-fragment/2.7.1/cdk-fragment-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-model >-------------------- [INFO] Building cdk-model 2.7.1 [43/75] [INFO] from tool/model/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-model --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-model --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/src/main/java/org/openscience/cdk/fingerprint/model/Bayesian.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/src/main/java/org/openscience/cdk/fingerprint/model/Bayesian.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/src/main/java/org/openscience/cdk/fingerprint/model/Bayesian.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-model --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-model --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-model --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-model --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/target/cdk-model-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-model --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/target/cdk-model-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-model/2.7.1/cdk-model-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/model/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-model/2.7.1/cdk-model-2.7.1.pom [INFO] [INFO] ---------------< org.openscience.cdk:cdk-qsarmolecular >---------------- [INFO] Building cdk-qsarmolecular 2.7.1 [44/75] [INFO] from descriptor/qsarmolecular/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsarmolecular --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsarmolecular --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 61 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptor.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptor.java: Recompile with -Xlint:removal for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsarmolecular --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsarmolecular --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsarmolecular --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsarmolecular --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/target/cdk-qsarmolecular-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsarmolecular --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/target/cdk-qsarmolecular-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarmolecular/2.7.1/cdk-qsarmolecular-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarmolecular/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarmolecular/2.7.1/cdk-qsarmolecular-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-qsarcml >------------------- [INFO] Building cdk-qsarcml 2.7.1 [45/75] [INFO] from descriptor/qsarcml/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsarcml --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarcml/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsarcml --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarcml/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsarcml --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsarcml --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsarcml --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsarcml --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarcml/target/cdk-qsarcml-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsarcml --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarcml/target/cdk-qsarcml-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarcml/2.7.1/cdk-qsarcml-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarcml/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarcml/2.7.1/cdk-qsarcml-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-qsarionpot >----------------- [INFO] Building cdk-qsarionpot 2.7.1 [46/75] [INFO] from descriptor/qsarionpot/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsarionpot --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarionpot/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsarionpot --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsarionpot --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsarionpot --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsarionpot --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsarionpot --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarionpot/target/cdk-qsarionpot-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsarionpot --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarionpot/target/cdk-qsarionpot-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarionpot/2.7.1/cdk-qsarionpot-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarionpot/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarionpot/2.7.1/cdk-qsarionpot-2.7.1.pom [INFO] [INFO] ----------------< org.openscience.cdk:cdk-qsarprotein >----------------- [INFO] Building cdk-qsarprotein 2.7.1 [47/75] [INFO] from descriptor/qsarprotein/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsarprotein --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsarprotein --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java uses or overrides a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsarprotein --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsarprotein --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsarprotein --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsarprotein --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/target/cdk-qsarprotein-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsarprotein --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/target/cdk-qsarprotein-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarprotein/2.7.1/cdk-qsarprotein-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarprotein/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarprotein/2.7.1/cdk-qsarprotein-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-display >------------------- [INFO] Building cdk-display 2.7.1 [48/75] [INFO] from display/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-display --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-display/2.7.1/cdk-display-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-render >------------------- [INFO] Building cdk-render 2.7.1 [49/75] [INFO] from display/render/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-render --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-render --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-render --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-render --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-render --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-render --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/target/cdk-render-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-render --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/target/cdk-render-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-render/2.7.1/cdk-render-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/render/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-render/2.7.1/cdk-render-2.7.1.pom [INFO] [INFO] ----------------< org.openscience.cdk:cdk-renderbasic >----------------- [INFO] Building cdk-renderbasic 2.7.1 [50/75] [INFO] from display/renderbasic/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-renderbasic --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-renderbasic --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 45 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-renderbasic --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-renderbasic --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-renderbasic --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-renderbasic --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/target/cdk-renderbasic-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-renderbasic --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/target/cdk-renderbasic-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-renderbasic/2.7.1/cdk-renderbasic-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderbasic/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-renderbasic/2.7.1/cdk-renderbasic-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-renderawt >------------------ [INFO] Building cdk-renderawt 2.7.1 [51/75] [INFO] from display/renderawt/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-renderawt --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderawt/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-renderawt --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderawt/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-renderawt --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-renderawt --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-renderawt --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-renderawt --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderawt/target/cdk-renderawt-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-renderawt --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderawt/target/cdk-renderawt-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-renderawt/2.7.1/cdk-renderawt-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderawt/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-renderawt/2.7.1/cdk-renderawt-2.7.1.pom [INFO] [INFO] ----------------< org.openscience.cdk:cdk-renderextra >----------------- [INFO] Building cdk-renderextra 2.7.1 [52/75] [INFO] from display/renderextra/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-renderextra --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderextra/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-renderextra --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderextra/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-renderextra --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-renderextra --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-renderextra --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-renderextra --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderextra/target/cdk-renderextra-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-renderextra --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderextra/target/cdk-renderextra-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-renderextra/2.7.1/cdk-renderextra-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/display/renderextra/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-renderextra/2.7.1/cdk-renderextra-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-control >------------------- [INFO] Building cdk-control 2.7.1 [53/75] [INFO] from misc/control/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-control --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/control/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-control --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/control/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-control --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-control --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-control --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-control --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/control/target/cdk-control-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-control --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/control/target/cdk-control-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-control/2.7.1/cdk-control-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/control/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-control/2.7.1/cdk-control-2.7.1.pom [INFO] [INFO] ---------------------< org.openscience.cdk:cdk-qm >--------------------- [INFO] Building cdk-qm 2.7.1 [54/75] [INFO] from misc/qm/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qm --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/qm/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qm --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qm --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qm --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qm --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qm --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/qm/target/cdk-qm-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qm --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/qm/target/cdk-qm-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qm/2.7.1/cdk-qm-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/qm/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qm/2.7.1/cdk-qm-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-iordf >-------------------- [INFO] Building cdk-iordf 2.7.1 [55/75] [INFO] from storage/iordf/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-iordf --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-iordf --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLWriter.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLWriter.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-iordf --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-iordf --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-iordf --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-iordf --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/target/cdk-iordf-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-iordf --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/target/cdk-iordf-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-iordf/2.7.1/cdk-iordf-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/iordf/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-iordf/2.7.1/cdk-iordf-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-libiomd >------------------- [INFO] Building cdk-libiomd 2.7.1 [56/75] [INFO] from storage/libiomd/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-libiomd --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiomd/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-libiomd --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiomd/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-libiomd --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-libiomd --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-libiomd --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-libiomd --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiomd/target/cdk-libiomd-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-libiomd --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiomd/target/cdk-libiomd-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-libiomd/2.7.1/cdk-libiomd-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/libiomd/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-libiomd/2.7.1/cdk-libiomd-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-pdbcml >------------------- [INFO] Building cdk-pdbcml 2.7.1 [57/75] [INFO] from storage/pdbcml/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-pdbcml --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdbcml/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-pdbcml --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdbcml/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-pdbcml --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-pdbcml --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-pdbcml --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-pdbcml --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdbcml/target/cdk-pdbcml-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-pdbcml --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdbcml/target/cdk-pdbcml-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-pdbcml/2.7.1/cdk-pdbcml-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/pdbcml/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-pdbcml/2.7.1/cdk-pdbcml-2.7.1.pom [INFO] [INFO] --------------< org.openscience.cdk:cdk-jniinchi-support >-------------- [INFO] Building cdk-jniinchi-support 2.7.1 [58/75] [INFO] from storage/jniinchi-support/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-jniinchi-support --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/jniinchi-support/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-jniinchi-support --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/jniinchi-support/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-jniinchi-support --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-jniinchi-support --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-jniinchi-support --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-jniinchi-support --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/jniinchi-support/target/cdk-jniinchi-support-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-jniinchi-support --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/jniinchi-support/target/cdk-jniinchi-support-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-jniinchi-support/2.7.1/cdk-jniinchi-support-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/jniinchi-support/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-jniinchi-support/2.7.1/cdk-jniinchi-support-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-inchi >-------------------- [INFO] Building cdk-inchi 2.7.1 [59/75] [INFO] from storage/inchi/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-inchi --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-inchi --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-inchi --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-inchi --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-inchi --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-inchi --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/target/cdk-inchi-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-inchi --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/target/cdk-inchi-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-inchi/2.7.1/cdk-inchi-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/storage/inchi/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-inchi/2.7.1/cdk-inchi-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-group >-------------------- [INFO] Building cdk-group 2.7.1 [60/75] [INFO] from tool/group/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-group --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/group/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-group --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 17 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/group/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-group --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-group --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-group --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-group --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/group/target/cdk-group-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-group --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/group/target/cdk-group-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-group/2.7.1/cdk-group-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/group/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-group/2.7.1/cdk-group-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-pcore >-------------------- [INFO] Building cdk-pcore 2.7.1 [61/75] [INFO] from tool/pcore/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-pcore --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/pcore/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-pcore --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 9 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/pcore/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-pcore --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-pcore --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-pcore --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-pcore --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/pcore/target/cdk-pcore-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-pcore --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/pcore/target/cdk-pcore-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-pcore/2.7.1/cdk-pcore-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/pcore/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-pcore/2.7.1/cdk-pcore-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-structgen >------------------ [INFO] Building cdk-structgen 2.7.1 [62/75] [INFO] from tool/structgen/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-structgen --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-structgen --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 10 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/src/main/java/org/openscience/cdk/structgen/RandomGenerator.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/src/main/java/org/openscience/cdk/structgen/RandomGenerator.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-structgen --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-structgen --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-structgen --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-structgen --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/target/cdk-structgen-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-structgen --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/target/cdk-structgen-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-structgen/2.7.1/cdk-structgen-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/structgen/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-structgen/2.7.1/cdk-structgen-2.7.1.pom [INFO] [INFO] ------------------< org.openscience.cdk:cdk-tautomer >------------------ [INFO] Building cdk-tautomer 2.7.1 [63/75] [INFO] from tool/tautomer/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-tautomer --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-tautomer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-tautomer --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-tautomer --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-tautomer --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-tautomer --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/target/cdk-tautomer-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-tautomer --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/target/cdk-tautomer-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-tautomer/2.7.1/cdk-tautomer-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/tool/tautomer/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-tautomer/2.7.1/cdk-tautomer-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-legacy >------------------- [INFO] Building cdk-legacy 2.7.1 [64/75] [INFO] from legacy/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- javacc-maven-plugin:2.6:javacc (javacc) @ cdk-legacy --- Java Compiler Compiler Version 5.0 (Parser Generator) (type "javacc" with no arguments for help) Reading from file /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/javacc/org/openscience/cdk/iupac/parser/NomParser.jj . . . File "TokenMgrError.java" does not exist. Will create one. File "ParseException.java" does not exist. Will create one. File "Token.java" does not exist. Will create one. File "SimpleCharStream.java" does not exist. Will create one. Parser generated successfully. [INFO] Processed 1 grammar [INFO] [INFO] --- javacc-maven-plugin:2.6:jjtree-javacc (javacc) @ cdk-legacy --- Java Compiler Compiler Version 5.0 (Tree Builder) (type "jjtree" with no arguments for help) Reading from file /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/jjtree/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt . . . File "Node.java" does not exist. Will create one. File "SimpleNode.java" does not exist. Will create one. File "ASTStart.java" does not exist. Will create one. File "ASTReaction.java" does not exist. Will create one. File "ASTGroup.java" does not exist. Will create one. File "ASTSmarts.java" does not exist. Will create one. File "ASTAtom.java" does not exist. Will create one. File "ASTLowAndBond.java" does not exist. Will create one. File "ASTOrBond.java" does not exist. Will create one. File "ASTExplicitHighAndBond.java" does not exist. Will create one. File "ASTImplicitHighAndBond.java" does not exist. Will create one. File "ASTNotBond.java" does not exist. Will create one. File "ASTSimpleBond.java" does not exist. Will create one. File "ASTExplicitAtom.java" does not exist. Will create one. File "ASTLowAndExpression.java" does not exist. Will create one. File "ASTOrExpression.java" does not exist. Will create one. File "ASTExplicitHighAndExpression.java" does not exist. Will create one. File "ASTImplicitHighAndExpression.java" does not exist. Will create one. File "ASTNotExpression.java" does not exist. Will create one. File "ASTRecursiveSmartsExpression.java" does not exist. Will create one. File "ASTTotalHCount.java" does not exist. Will create one. File "ASTImplicitHCount.java" does not exist. Will create one. File "ASTExplicitConnectivity.java" does not exist. Will create one. File "ASTAtomicNumber.java" does not exist. Will create one. File "ASTHybrdizationNumber.java" does not exist. Will create one. File "ASTCharge.java" does not exist. Will create one. File "ASTRingConnectivity.java" does not exist. Will create one. File "ASTPeriodicGroupNumber.java" does not exist. Will create one. File "ASTTotalConnectivity.java" does not exist. Will create one. File "ASTValence.java" does not exist. Will create one. File "ASTRingMembership.java" does not exist. Will create one. File "ASTSmallestRingSize.java" does not exist. Will create one. File "ASTAliphatic.java" does not exist. Will create one. File "ASTNonCHHeavyAtom.java" does not exist. Will create one. File "ASTAromatic.java" does not exist. Will create one. File "ASTAnyAtom.java" does not exist. Will create one. File "ASTAtomicMass.java" does not exist. Will create one. File "ASTRingIdentifier.java" does not exist. Will create one. File "ASTChirality.java" does not exist. Will create one. File "ASTElement.java" does not exist. Will create one. File "SMARTSParserTreeConstants.java" does not exist. Will create one. File "SMARTSParserVisitor.java" does not exist. Will create one. File "JJTSMARTSParserState.java" does not exist. Will create one. Annotated grammar generated successfully in /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/target/javacc-1769263173589/node/SMARTSParser.jj Java Compiler Compiler Version 5.0 (Parser Generator) (type "javacc" with no arguments for help) Reading from file /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/target/javacc-1769263173589/node/SMARTSParser.jj . . . File "TokenMgrError.java" does not exist. Will create one. File "ParseException.java" does not exist. Will create one. File "Token.java" does not exist. Will create one. File "SimpleCharStream.java" does not exist. Will create one. Parser generated successfully. [INFO] Processed 1 grammar [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-legacy --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-legacy --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 238 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlus.java: Some input files use or override a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlus.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java: Recompile with -Xlint:removal for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/java/org/openscience/cdk/graph/BiconnectivityInspector.java: Some input files use unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/src/main/java/org/openscience/cdk/graph/BiconnectivityInspector.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-legacy --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-legacy --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-legacy --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-legacy --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/target/cdk-legacy-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-legacy --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/target/cdk-legacy-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/legacy/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.pom [INFO] [INFO] --------------------< org.openscience.cdk:cdk-app >--------------------- [INFO] Building cdk-app 2.7.1 [65/75] [INFO] from app/pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-app --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-app/2.7.1/cdk-app-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-depict >------------------- [INFO] Building cdk-depict 2.7.1 [66/75] [INFO] from app/depict/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-depict --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-depict --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/target/classes [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java uses or overrides a deprecated API. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java: Recompile with -Xlint:deprecation for details. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java uses unchecked or unsafe operations. [INFO] /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-depict --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-depict --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-depict --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-depict --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/target/cdk-depict-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-depict --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/target/cdk-depict-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-depict/2.7.1/cdk-depict-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/app/depict/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-depict/2.7.1/cdk-depict-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-bundle >------------------- [INFO] Building cdk-bundle 2.7.1 [67/75] [INFO] from bundle/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-bundle --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ cdk-bundle --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-bundle --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ cdk-bundle --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-bundle --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-bundle --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/target/cdk-bundle-2.7.1.jar [INFO] [INFO] --- maven-shade-plugin:2.2:shade (default) @ cdk-bundle --- [INFO] Including org.openscience.cdk:cdk-interfaces:jar:2.7.1 in the shaded jar. [INFO] Including javax.vecmath:vecmath:jar:1.5.2 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-core:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-standard:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-atomtype:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-valencycheck:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-diff:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-data:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-ioformats:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-silent:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-isomorphism:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-datadebug:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-io:jar:2.7.1 in the shaded jar. [INFO] Including xerces:xercesImpl:jar:2.8.0 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-formula:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-dict:jar:2.7.1 in the shaded jar. [INFO] Including xom:xom:jar:1.3.7 in the shaded jar. [INFO] Including xalan:xalan:jar:2.7.2 in the shaded jar. [INFO] Including xalan:serializer:jar:2.7.2 in the shaded jar. [INFO] Including xml-apis:xml-apis:jar:1.3.03 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-pdb:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-ctab:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-libiocml:jar:2.7.1 in the shaded jar. [INFO] Including org.blueobelisk:cmlxom:jar:4.0 in the shaded jar. [INFO] Including org.blueobelisk:euclid:jar:2.0 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.11.0 in the shaded jar. [INFO] Including org.apache.logging.log4j:log4j-1.2-api:jar:2.17.1 in the shaded jar. [INFO] Including org.apache.logging.log4j:log4j-api:jar:2.17.1 in the shaded jar. [INFO] Including org.apache.commons:commons-lang3:jar:3.0 in the shaded jar. [INFO] Including org.apache.commons:commons-math:jar:2.2 in the shaded jar. [INFO] Including joda-time:joda-time:jar:1.6.2 in the shaded jar. [INFO] Including org.ccil.cowan.tagsoup:tagsoup:jar:1.2 in the shaded jar. [INFO] Including junit:junit:jar:4.13.2 in the shaded jar. [INFO] Including org.hamcrest:hamcrest-core:jar:2.2 in the shaded jar. [INFO] Including org.hamcrest:hamcrest:jar:2.2 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-smiles:jar:2.7.1 in the shaded jar. [INFO] Including uk.ac.ebi.beam:beam-core:jar:1.3.4 in the shaded jar. [INFO] Including uk.ac.ebi.beam:beam-func:jar:1.3.4 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-extra:jar:2.7.1 in the shaded jar. [INFO] Including gov.nist.math:jama:jar:1.0.3 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-smarts:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-reaction:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-fingerprint:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-cip:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-signature:jar:2.7.1 in the shaded jar. [INFO] Including com.github.gilleain.signatures:signatures:jar:1.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-charges:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-forcefield:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-sdg:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-builder3dtools:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-builder3d:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsar:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-ionpot:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsaratomic:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsarbond:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-hash:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-fragment:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-model:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsarmolecular:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsarcml:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsarionpot:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qsarprotein:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-render:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-renderbasic:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-renderawt:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-renderextra:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-control:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-qm:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-iordf:jar:2.7.1 in the shaded jar. [INFO] Including org.apache.jena:jena-core:jar:2.7.4 in the shaded jar. [INFO] Including org.apache.jena:jena-iri:jar:0.9.4 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.6.4 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-libiomd:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-pdbcml:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-inchi:jar:2.7.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-api:jar:1.0.1 in the shaded jar. [INFO] Including net.java.dev.jna:jna:jar:5.10.0 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-core:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-darwin-aarch64:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-darwin-x86-64:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-linux-arm:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-linux-x86:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-linux-x86-64:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-win32-x86:jar:1.0.1 in the shaded jar. [INFO] Including io.github.dan2097:jna-inchi-win32-x86-64:jar:1.0.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-jniinchi-support:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-group:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-pcore:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-structgen:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-tautomer:jar:2.7.1 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-legacy:jar:2.7.1 in the shaded jar. [INFO] Including jgrapht:jgrapht:jar:0.6.0 in the shaded jar. [INFO] Including org.openscience.cdk:cdk-depict:jar:2.7.1 in the shaded jar. [INFO] Including org.freehep:freehep-graphicsio-pdf:jar:2.4 in the shaded jar. [INFO] Including org.freehep:freehep-graphics2d:jar:2.4 in the shaded jar. [INFO] Including org.freehep:freehep-graphicsio:jar:2.4 in the shaded jar. [INFO] Including org.freehep:freehep-io:jar:2.2.2 in the shaded jar. [INFO] Including org.freehep:freehep-graphicsio-tests:jar:2.4 in the shaded jar. [INFO] Including org.freehep:freehep-graphicsbase:jar:2.4 in the shaded jar. [INFO] Including org.freehep:freehep-graphicsio-ps:jar:2.4 in the shaded jar. [INFO] Replacing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/target/cdk-2.7.1.jar with /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/target/cdk-bundle-2.7.1-shaded.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-bundle --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/target/cdk-bundle-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-bundle/2.7.1/cdk-bundle-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-bundle/2.7.1/cdk-bundle-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-annotation >----------------- [INFO] Building cdk-annotation 2.7.1 [68/75] [INFO] from base/annotation/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-annotation --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/annotation/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-annotation --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-annotation --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-annotation --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-annotation --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-annotation --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/annotation/target/cdk-annotation-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-annotation --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/annotation/target/cdk-annotation-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-annotation/2.7.1/cdk-annotation-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/annotation/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-annotation/2.7.1/cdk-annotation-2.7.1.pom [INFO] [INFO] ---------------< org.openscience.cdk:cdk-test-atomtype >---------------- [INFO] Building cdk-test-atomtype 2.7.1 [69/75] [INFO] from base/test-atomtype/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test-atomtype --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-atomtype/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test-atomtype --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test-atomtype --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test-atomtype --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-test-atomtype --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-test-atomtype --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-atomtype/target/cdk-test-atomtype-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test-atomtype --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-atomtype/target/cdk-test-atomtype-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-atomtype/2.7.1/cdk-test-atomtype-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-atomtype/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-atomtype/2.7.1/cdk-test-atomtype-2.7.1.pom [INFO] [INFO] -------------------< org.openscience.cdk:cdk-log4j >-------------------- [INFO] Building cdk-log4j 2.7.1 [70/75] [INFO] from misc/log4j/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-log4j --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-log4j --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/log4j/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-log4j --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-log4j --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-log4j --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-log4j --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/log4j/target/cdk-log4j-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-log4j --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/log4j/target/cdk-log4j-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-log4j/2.7.1/cdk-log4j-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/log4j/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-log4j/2.7.1/cdk-log4j-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-test-core >------------------ [INFO] Building cdk-test-core 2.7.1 [71/75] [INFO] from base/test-core/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-core/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test-core --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test-core --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test-core --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-test-core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-test-core --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-core/target/cdk-test-core-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test-core --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-core/target/cdk-test-core-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-core/2.7.1/cdk-test-core-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-core/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-core/2.7.1/cdk-test-core-2.7.1.pom [INFO] [INFO] ---------------< org.openscience.cdk:cdk-test-standard >---------------- [INFO] Building cdk-test-standard 2.7.1 [72/75] [INFO] from base/test-standard/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test-standard --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-standard/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test-standard --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test-standard --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test-standard --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-test-standard --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-test-standard --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-standard/target/cdk-test-standard-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test-standard --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-standard/target/cdk-test-standard-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-standard/2.7.1/cdk-test-standard-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-standard/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-standard/2.7.1/cdk-test-standard-2.7.1.pom [INFO] [INFO] -------------< org.openscience.cdk:cdk-test-valencycheck >-------------- [INFO] Building cdk-test-valencycheck 2.7.1 [73/75] [INFO] from base/test-valencycheck/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test-valencycheck --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-valencycheck/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test-valencycheck --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test-valencycheck --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test-valencycheck --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-test-valencycheck --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-test-valencycheck --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-valencycheck/target/cdk-test-valencycheck-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test-valencycheck --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-valencycheck/target/cdk-test-valencycheck-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-valencycheck/2.7.1/cdk-test-valencycheck-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/base/test-valencycheck/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-valencycheck/2.7.1/cdk-test-valencycheck-2.7.1.pom [INFO] [INFO] ---------------< org.openscience.cdk:cdk-qsarsubstance >---------------- [INFO] Building cdk-qsarsubstance 2.7.1 [74/75] [INFO] from descriptor/qsarsubstance/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-qsarsubstance --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarsubstance/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-qsarsubstance --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarsubstance/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-qsarsubstance --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-qsarsubstance --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-qsarsubstance --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-qsarsubstance --- [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarsubstance/target/cdk-qsarsubstance-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-qsarsubstance --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarsubstance/target/cdk-qsarsubstance-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarsubstance/2.7.1/cdk-qsarsubstance-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/descriptor/qsarsubstance/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-qsarsubstance/2.7.1/cdk-qsarsubstance-2.7.1.pom [INFO] [INFO] -----------------< org.openscience.cdk:cdk-test-extra >----------------- [INFO] Building cdk-test-extra 2.7.1 [75/75] [INFO] from misc/test-extra/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test-extra --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/test-extra/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test-extra --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test-extra --- [INFO] Not copying test resources [INFO] [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test-extra --- [INFO] Not compiling test sources [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cdk-test-extra --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-test-extra --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/test-extra/target/cdk-test-extra-2.7.1.jar [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test-extra --- [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/test-extra/target/cdk-test-extra-2.7.1.jar to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-extra/2.7.1/cdk-test-extra-2.7.1.jar [INFO] Installing /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/misc/test-extra/pom.xml to /wrkdirs/usr/ports/science/cdk/work/.m2/repository/org/openscience/cdk/cdk-test-extra/2.7.1/cdk-test-extra-2.7.1.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for cdk 2.7.1: [INFO] [INFO] cdk ................................................ SUCCESS [ 0.340 s] [INFO] cdk-base ........................................... SUCCESS [ 0.006 s] [INFO] cdk-interfaces ..................................... SUCCESS [ 4.851 s] [INFO] cdk-core ........................................... SUCCESS [ 5.571 s] [INFO] cdk-standard ....................................... SUCCESS [ 3.870 s] [INFO] cdk-atomtype ....................................... SUCCESS [ 0.391 s] [INFO] cdk-valencycheck ................................... SUCCESS [ 0.397 s] [INFO] cdk-misc ........................................... SUCCESS [ 0.008 s] [INFO] cdk-diff ........................................... SUCCESS [ 0.518 s] [INFO] cdk-test ........................................... SUCCESS [ 0.986 s] [INFO] cdk-data ........................................... SUCCESS [ 11.302 s] [INFO] cdk-storage ........................................ SUCCESS [ 0.005 s] [INFO] cdk-ioformats ...................................... SUCCESS [ 7.093 s] [INFO] cdk-silent ......................................... SUCCESS [ 6.324 s] [INFO] cdk-isomorphism .................................... SUCCESS [ 4.415 s] [INFO] cdk-datadebug ...................................... SUCCESS [ 11.551 s] [INFO] cdk-ctab ........................................... SUCCESS [ 6.195 s] [INFO] cdk-io ............................................. SUCCESS [ 10.041 s] [INFO] cdk-tool ........................................... SUCCESS [ 0.005 s] [INFO] cdk-formula ........................................ SUCCESS [ 6.150 s] [INFO] cdk-dict ........................................... SUCCESS [ 1.577 s] [INFO] cdk-pdb ............................................ SUCCESS [ 2.559 s] [INFO] cdk-libiocml ....................................... SUCCESS [ 0.831 s] [INFO] cdk-smiles ......................................... SUCCESS [ 1.623 s] [INFO] cdk-extra .......................................... SUCCESS [ 5.861 s] [INFO] cdk-smarts ......................................... SUCCESS [ 4.122 s] [INFO] cdk-reaction ....................................... SUCCESS [ 5.088 s] [INFO] cdk-descriptor ..................................... SUCCESS [ 0.004 s] [INFO] cdk-fingerprint .................................... SUCCESS [ 4.173 s] [INFO] cdk-cip ............................................ SUCCESS [ 0.995 s] [INFO] cdk-signature ...................................... SUCCESS [ 0.609 s] [INFO] cdk-charges ........................................ SUCCESS [ 0.983 s] [INFO] cdk-forcefield ..................................... SUCCESS [ 2.406 s] [INFO] cdk-sdg ............................................ SUCCESS [ 5.648 s] [INFO] cdk-builder3dtools ................................. SUCCESS [ 1.070 s] [INFO] cdk-builder3d ...................................... SUCCESS [ 1.269 s] [INFO] cdk-qsar ........................................... SUCCESS [ 0.692 s] [INFO] cdk-ionpot ......................................... SUCCESS [ 0.031 s] [INFO] cdk-qsaratomic ..................................... SUCCESS [ 4.986 s] [INFO] cdk-qsarbond ....................................... SUCCESS [ 0.485 s] [INFO] cdk-hash ........................................... SUCCESS [ 4.611 s] [INFO] cdk-fragment ....................................... SUCCESS [ 0.769 s] [INFO] cdk-model .......................................... SUCCESS [ 0.739 s] [INFO] cdk-qsarmolecular .................................. SUCCESS [ 4.735 s] [INFO] cdk-qsarcml ........................................ SUCCESS [ 0.469 s] [INFO] cdk-qsarionpot ..................................... SUCCESS [ 0.023 s] [INFO] cdk-qsarprotein .................................... SUCCESS [ 0.893 s] [INFO] cdk-display ........................................ SUCCESS [ 0.004 s] [INFO] cdk-render ......................................... SUCCESS [ 1.593 s] [INFO] cdk-renderbasic .................................... SUCCESS [ 6.075 s] [INFO] cdk-renderawt ...................................... SUCCESS [ 1.065 s] [INFO] cdk-renderextra .................................... SUCCESS [ 0.408 s] [INFO] cdk-control ........................................ SUCCESS [ 0.149 s] [INFO] cdk-qm ............................................. SUCCESS [ 0.027 s] [INFO] cdk-iordf .......................................... SUCCESS [ 0.292 s] [INFO] cdk-libiomd ........................................ SUCCESS [ 0.219 s] [INFO] cdk-pdbcml ......................................... SUCCESS [ 0.241 s] [INFO] cdk-jniinchi-support ............................... SUCCESS [ 0.068 s] [INFO] cdk-inchi .......................................... SUCCESS [ 0.191 s] [INFO] cdk-group .......................................... SUCCESS [ 0.189 s] [INFO] cdk-pcore .......................................... SUCCESS [ 0.174 s] [INFO] cdk-structgen ...................................... SUCCESS [ 0.128 s] [INFO] cdk-tautomer ....................................... SUCCESS [ 0.092 s] [INFO] cdk-legacy ......................................... SUCCESS [ 6.837 s] [INFO] cdk-app ............................................ SUCCESS [ 0.003 s] [INFO] cdk-depict ......................................... SUCCESS [ 6.959 s] [INFO] cdk-bundle ......................................... SUCCESS [ 4.967 s] [INFO] cdk-annotation ..................................... SUCCESS [ 0.029 s] [INFO] cdk-test-atomtype .................................. SUCCESS [ 0.250 s] [INFO] cdk-log4j .......................................... SUCCESS [ 0.227 s] [INFO] cdk-test-core ...................................... SUCCESS [ 0.309 s] [INFO] cdk-test-standard .................................. SUCCESS [ 0.318 s] [INFO] cdk-test-valencycheck .............................. SUCCESS [ 0.325 s] [INFO] cdk-qsarsubstance .................................. SUCCESS [ 0.324 s] [INFO] cdk-test-extra ..................................... SUCCESS [ 0.407 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:49 min [INFO] Finished at: 2026-01-24T13:59:54Z [INFO] ------------------------------------------------------------------------ =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cdk-chemistry-2.7.1 depends on file: /usr/local/openjdk17/bin/java - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for cdk-chemistry-2.7.1 ===> Generating temporary packing list install -m 0644 /wrkdirs/usr/ports/science/cdk/work/cdk-cdk-2.7.1/bundle/target/cdk-2.7.1.jar /wrkdirs/usr/ports/science/cdk/work/stage/usr/local/share/java/classes/cdk-2.7.1.jar ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-01-24T13:56:32+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=0835676e361b' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for cdk-chemistry-2.7.1 ===> Building cdk-chemistry-2.7.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for cdk-chemistry-2.7.1 build of science/cdk | cdk-chemistry-2.7.1 ended at Sat Jan 24 09:00:37 EST 2026 build time: 00:04:06