Renjin, randomForest and Fiji


#1

Hi,

I’m currently working with Renjin. I had to replace the shipped version with the latest Renjin version. This is my jars folder:

-rw-r--r--@   1 twagner  admin    235438 May 22 10:57 JLargeArrays-1.6.jar
-rw-r--r--@   1 twagner  admin   1175798 May 22 10:56 JTransforms-3.1.jar
-rw-r--r--@   1 twagner  staff    117846 Mar 28 19:05 JWlz-1.4.0.jar
-rw-r--r--@   1 twagner  staff   1351223 Mar 28 19:05 T2-NIT-1.1.1.jar
-rw-r--r--@   1 twagner  staff      6306 Mar 28 19:05 T2-TreelineGraph-1.1.1.jar
-rw-r--r--@   1 twagner  staff    635940 Mar 28 19:05 VIB-lib-2.1.1.jar
-rw-r--r--@   1 twagner  staff     46280 Mar 28 19:05 VectorString-2.0.0.jar
-rw-r--r--@   1 twagner  staff     21967 Mar 28 19:05 ahocorasick-0.2.4.jar
-rw-r--r--@   1 twagner  staff     94264 Mar 28 19:05 ant-junit.jar
-rw-r--r--@   1 twagner  staff     11814 Mar 28 19:05 ant-launcher.jar
-rw-r--r--@   1 twagner  staff    436656 Mar 28 19:05 ant-nodeps.jar
-rw-r--r--@   1 twagner  staff   1327716 Mar 28 19:05 ant.jar
-rw-r--r--@   1 twagner  staff     74544 Mar 28 19:05 args4j-2.0.25.jar
-rw-r--r--@   1 twagner  staff     46022 Mar 28 19:05 asm-4.0.jar
-rw-r--r--@   1 twagner  staff     19614 Mar 28 19:05 asm-analysis-4.0.jar
-rw-r--r--@   1 twagner  staff     37776 Mar 28 19:05 asm-commons-4.0.jar
-rw-r--r--@   1 twagner  staff     21982 Mar 28 19:05 asm-tree-4.0.jar
-rw-r--r--@   1 twagner  staff     36995 Mar 28 19:05 asm-util-4.0.jar
-rw-r--r--@   1 twagner  staff    145982 Mar 28 19:05 autocomplete-2.5.8.jar
-rw-r--r--@   1 twagner  staff     17008 Mar 28 19:05 base64-2.3.8.jar
-rw-r--r--@   1 twagner  staff   8004326 Mar 28 19:05 batik-1.8.jar
-rw-r--r--@   1 twagner  staff    377042 Mar 28 19:05 batik-anim-1.8.jar
-rw-r--r--@   1 twagner  staff    301028 Mar 28 19:05 batik-awt-util-1.8.jar
-rw-r--r--@   1 twagner  staff    529674 Mar 28 19:05 batik-bridge-1.8.jar
-rw-r--r--@   1 twagner  staff    256539 Mar 28 19:05 batik-css-1.8.jar
-rw-r--r--@   1 twagner  staff    140057 Mar 28 19:05 batik-dom-1.8.jar
-rw-r--r--@   1 twagner  staff     10347 Mar 28 19:05 batik-ext-1.8.jar
-rw-r--r--@   1 twagner  staff    144227 Mar 28 19:05 batik-gvt-1.8.jar
-rw-r--r--@   1 twagner  staff     55269 Mar 28 19:05 batik-parser-1.8.jar
-rw-r--r--@   1 twagner  staff     17156 Mar 28 19:05 batik-script-1.8.jar
-rw-r--r--@   1 twagner  staff    217196 Mar 28 19:05 batik-svg-dom-1.8.jar
-rw-r--r--@   1 twagner  staff    177875 Mar 28 19:05 batik-svggen-1.8.jar
-rw-r--r--@   1 twagner  staff    107737 Mar 28 19:05 batik-util-1.8.jar
-rw-r--r--@   1 twagner  staff     26777 Mar 28 19:05 batik-xml-1.8.jar
-rw-r--r--@   1 twagner  staff    192035 Mar 28 19:05 bcmail-jdk14-138.jar
-rw-r--r--@   1 twagner  staff   1551468 Mar 28 19:05 bcprov-jdk14-138.jar
-rw-r--r--@   1 twagner  staff    534320 Mar 28 19:05 bigdataviewer-core-3.0.3.jar
-rw-r--r--@   1 twagner  staff     66391 Mar 28 19:05 bigdataviewer-vistools-1.0.0-beta-4.jar
drwxr-xr-x@  16 twagner  admin       544 May  8 09:33 bio-formats
-rw-r--r--@   1 twagner  staff     60250 Mar 28 19:05 blas-0.8.jar
-rw-r--r--@   1 twagner  staff    389033 Mar 28 19:05 bsh-2.0b6.jar
-rw-r--r--@   1 twagner  staff     10822 Mar 28 19:05 bytelist-1.0.11.jar
-rw-r--r--@   1 twagner  staff   3622815 Mar 28 19:05 clojure-1.8.0.jar
-rw-r--r--@   1 twagner  staff    152436 Mar 28 19:05 codemodel-2.6.jar
-rw-r--r--@   1 twagner  staff    531557 Mar 28 19:05 collections-generic-4.01.jar
-rw-r--r--@   1 twagner  staff    263865 Mar 28 19:05 commons-codec-1.8.jar
-rw-r--r--@   1 twagner  staff    241367 Mar 28 19:05 commons-compress-1.4.1.jar
-rw-r--r--@   1 twagner  staff    315805 Mar 28 19:05 commons-lang3-3.1.jar
-rw-r--r--@   1 twagner  staff     60686 Mar 28 19:05 commons-logging-1.1.1.jar
-rw-r--r--@   1 twagner  staff    988514 Mar 28 19:05 commons-math-2.2.jar
-rw-r--r--@   1 twagner  staff   2213560 Mar 28 19:05 commons-math3-3.6.1.jar
-rw-r--r--@   1 twagner  staff    415578 Mar 28 19:05 commons-vfs2-2.0.jar
-rw-r--r--@   1 twagner  staff    167028 Mar 28 19:05 datasets-0.8.1906.jar
-rw-r--r--@   1 twagner  staff    346556 Mar 28 19:05 ejml-0.24.jar
-rw-r--r--@   1 twagner  staff     82778 Mar 28 19:05 eventbus-1.4.jar
-rw-r--r--@   1 twagner  staff     69111 Mar 28 19:05 f2jutil-0.8.jar
-rw-r--r--@   1 twagner  staff     89475 Mar 28 19:05 fake-2.0.0-SNAPSHOT.jar
-rw-r--r--@   1 twagner  staff    224324 Mar 28 19:05 ffmpeg-2.6.1-0.11.jar
-rw-r--r--@   1 twagner  staff     10106 Mar 28 19:05 fiji-2.0.0-SNAPSHOT.jar
-rw-r--r--@   1 twagner  staff    117749 Mar 28 19:05 fiji-compat-2.0.2.jar
-rw-r--r--@   1 twagner  staff     89331 Mar 28 19:05 fiji-lib-2.1.1.jar
-rw-r--r--@   1 twagner  staff     32494 Mar 28 19:05 fiji-scripting-2.0.0-SNAPSHOT.jar
-rw-r--r--@   1 twagner  staff    340318 Mar 28 19:05 filters-2.0.235.jar
-rw-r--r--@   1 twagner  staff     21029 Mar 28 19:05 gcc-runtime-0.8.1906.jar
-rw-r--r--@   1 twagner  staff     16854 Mar 28 19:05 gentyref-1.1.0.jar
-rw-r--r--@   1 twagner  staff    345605 Mar 28 19:05 gluegen-rt-2.3.2.jar
-rw-r--r--@   1 twagner  staff       345 Mar 28 19:05 gluegen-rt-main-2.3.2.jar
-rw-r--r--    1 twagner  admin     33299 Apr  3 17:26 gpcj-2.2.0.jar
-rw-r--r--@   1 twagner  staff     94199 Mar 28 19:05 grDevices-0.8.1906.jar
-rw-r--r--@   1 twagner  staff    131797 Mar 28 19:05 graphics-0.8.1906.jar
-rw-r--r--@   1 twagner  staff   4468297 Mar 28 19:05 groovy-2.3.6.jar
-rw-r--r--@   1 twagner  staff    231952 Mar 28 19:05 gson-2.7.jar
-rw-r--r--@   1 twagner  staff   2308517 Mar 28 19:05 guava-19.0.jar
-rw-r--r--@   1 twagner  staff     45024 Mar 28 19:05 hamcrest-core-1.3.jar
-rw-r--r--    1 twagner  admin   2177678 May  8 09:31 ij-1.51n.jar
-rw-r--r--@   1 twagner  staff    155483 Mar 28 19:05 ij1-patcher-0.12.5.jar
-rw-r--r--    1 twagner  admin     95802 Apr  3 17:26 ij_blob-1.4.9.jar
-rw-r--r--@   1 twagner  staff     31881 Mar 28 19:05 image4j-0.7.jar
-rw-r--r--@   1 twagner  staff     10069 Mar 28 19:05 imagej-2.0.0-rc-59.jar
-rw-r--r--@   1 twagner  staff    459708 Mar 28 19:05 imagej-common-0.24.3.jar
-rw-r--r--@   1 twagner  staff    717206 Mar 28 19:05 imagej-deprecated-0.1.1.jar
-rw-r--r--@   1 twagner  staff     23302 Mar 28 19:05 imagej-launcher-4.0.5.jar
-rw-r--r--@   1 twagner  staff    304657 Mar 28 19:05 imagej-legacy-0.23.5.jar
-rw-r--r--@   1 twagner  staff     12736 Mar 28 19:05 imagej-notebook-0.2.1.jar
-rw-r--r--@   1 twagner  staff   1720138 Mar 28 19:05 imagej-ops-0.36.0.jar
-rw-r--r--@   1 twagner  staff    362073 Mar 28 19:05 imagej-plugins-commands-0.7.0.jar
-rw-r--r--@   1 twagner  staff     50870 Mar 28 19:05 imagej-plugins-tools-0.3.0.jar
-rw-r--r--@   1 twagner  staff     22403 Mar 28 19:05 imagej-plugins-uploader-ssh-0.3.1.jar
-rw-r--r--@   1 twagner  staff     17992 Mar 28 19:05 imagej-plugins-uploader-webdav-0.2.1.jar
-rw-r--r--@   1 twagner  staff     30789 Mar 28 19:05 imagej-scripting-0.5.1.jar
-rw-r--r--@   1 twagner  staff     10412 Mar 28 19:05 imagej-ui-awt-0.3.0.jar
-rw-r--r--@   1 twagner  staff    262016 Mar 28 19:05 imagej-ui-swing-0.21.1.jar
-rw-r--r--@   1 twagner  staff    244237 Mar 28 19:05 imagej-updater-0.8.2.jar
-rw-r--r--@   1 twagner  staff    604774 Mar 28 19:05 imglib2-3.2.1.jar
-rw-r--r--@   1 twagner  staff    434250 Mar 28 19:05 imglib2-algorithm-0.6.2.jar
-rw-r--r--@   1 twagner  staff     19754 Mar 28 19:05 imglib2-algorithm-fft-0.1.2.jar
-rw-r--r--@   1 twagner  staff    154999 Mar 28 19:05 imglib2-algorithm-gpl-0.1.5.jar
-rw-r--r--@   1 twagner  staff     34761 Mar 28 19:05 imglib2-ij-2.0.0-beta-35.jar
-rw-r--r--@   1 twagner  staff     78654 Mar 28 19:05 imglib2-realtransform-2.0.0-beta-34.jar
-rw-r--r--@   1 twagner  staff    141094 Mar 28 19:05 imglib2-roi-0.4.4.jar
-rw-r--r--@   1 twagner  staff     62591 Mar 28 19:05 imglib2-ui-2.0.0-beta-31.jar
-rw-r--r--@   1 twagner  staff     36450 Mar 28 19:05 invokebinder-1.2.jar
-rw-r--r--@   1 twagner  staff   1117661 Mar 28 19:05 itext-2.1.5.jar
-rw-r--r--@   1 twagner  staff   1621481 Mar 28 19:05 itextpdf-5.1.1.jar
-rw-r--r--@   1 twagner  staff   1944932 Mar 28 19:05 j3dcore-1.6.0-scijava-2.jar
-rw-r--r--@   1 twagner  staff   1047514 Mar 28 19:05 j3dutils-1.6.0-scijava-2.jar
-rw-r--r--@   1 twagner  staff    479044 Mar 28 19:05 jacl.jar
-rw-r--r--@   1 twagner  staff    258160 Mar 28 19:05 jai-codec-1.1.3.jar
-rw-r--r--@   1 twagner  staff   1900631 Mar 28 19:05 jai-core-1.1.3.jar
-rw-r--r--@   1 twagner  staff     37424 Mar 28 19:05 jama-1.0.3.jar
-rw-r--r--@   1 twagner  staff     96121 Mar 28 19:05 java-cup-0.11a.jar
-rw-r--r--@   1 twagner  staff    237500 Mar 28 19:05 javacpp-0.11.jar
-rw-r--r--@   1 twagner  staff    750581 Mar 28 19:05 javassist-3.20.0-GA.jar
-rw-r--r--@   1 twagner  staff   1291811 Mar 28 19:05 jcodings-1.0.10.jar
-rw-r--r--@   1 twagner  staff    330246 Mar 28 19:05 jcommon-1.0.23.jar
-rw-r--r--@   1 twagner  staff     33887 Mar 28 19:05 jdatepicker-1.3.2.jar
-rw-r--r--@   1 twagner  staff    304924 Mar 28 19:05 jdom2-2.0.6.jar
-rw-r--r--@   1 twagner  staff    553982 Mar 28 19:05 jep-2.4.2.jar
-rw-r--r--@   1 twagner  staff    385729 Mar 28 19:05 jffi-1.2.7-native.jar
-rw-r--r--@   1 twagner  staff    145708 Mar 28 19:05 jffi-1.2.7.jar
-rw-r--r--@   1 twagner  staff   1565065 Mar 28 19:05 jfreechart-1.0.19.jar
-rw-r--r--@   1 twagner  staff     33832 Mar 28 19:05 jgoodies-common-1.7.0.jar
-rw-r--r--@   1 twagner  staff    117714 Mar 28 19:05 jgoodies-forms-1.7.2.jar
-rw-r--r--@   1 twagner  staff    245266 Mar 28 19:05 jgrapht-0.8.3.jar
-rw-r--r--@   1 twagner  staff    809964 Mar 28 19:05 jgraphx-1.10.4.1.jar
-rw-r--r--@   1 twagner  staff   9704798 Mar 28 19:05 jhdf5-14.12.5.jar
-rw-r--r--@   1 twagner  staff   2098069 Mar 28 19:05 jhotdraw-7.6.0.jar
-rw-r--r--@   1 twagner  staff     18579 Mar 28 19:05 jitk-tps-2.1.0.jar
-rw-r--r--@   1 twagner  staff   1137286 Mar 28 19:05 jna-4.2.2.jar
-rw-r--r--@   1 twagner  staff    312931 Mar 28 19:05 jnr-constants-0.8.5.jar
-rw-r--r--@   1 twagner  staff     34939 Mar 28 19:05 jnr-enxio-0.4.jar
-rw-r--r--@   1 twagner  staff    645516 Mar 28 19:05 jnr-ffi-1.0.7.jar
-rw-r--r--@   1 twagner  staff     61632 Mar 28 19:05 jnr-netdb-1.1.2.jar
-rw-r--r--@   1 twagner  staff    156638 Mar 28 19:05 jnr-posix-3.0.1.jar
-rw-r--r--@   1 twagner  staff     21112 Mar 28 19:05 jnr-unixsocket-0.3.jar
-rw-r--r--@   1 twagner  staff    219943 Mar 28 19:05 jnr-x86asm-1.0.2.jar
-rw-r--r--@   1 twagner  staff     66496 Mar 28 19:05 joal-2.3.2.jar
-rw-r--r--@   1 twagner  staff       345 Mar 28 19:05 joal-main-2.3.2.jar
-rw-r--r--@   1 twagner  staff    219608 Mar 28 19:05 jocl-2.3.2.jar
-rw-r--r--@   1 twagner  staff       345 Mar 28 19:05 jocl-main-2.3.2.jar
-rw-r--r--@   1 twagner  staff    629506 Mar 28 19:05 joda-time-2.9.4.jar
-rw-r--r--@   1 twagner  staff   3414448 Mar 28 19:05 jogl-all-2.3.2.jar
-rw-r--r--@   1 twagner  staff       345 Mar 28 19:05 jogl-all-main-2.3.2.jar
-rw-r--r--@   1 twagner  staff    187904 Mar 28 19:05 joni-2.1.1.jar
-rw-r--r--@   1 twagner  staff   1469651 Mar 28 19:05 jpedalSTD-2.80b11.jar
-rw-r--r--@   1 twagner  staff   8264971 Mar 28 19:05 jruby-core-1.7.12.jar
-rw-r--r--@   1 twagner  staff  10757761 Mar 28 19:05 jruby-stdlib-1.7.12.jar
-rw-r--r--@   1 twagner  staff    756883 Mar 28 19:05 js.jar
-rw-r--r--@   1 twagner  staff    229086 Mar 28 19:05 jsch-0.1.49.jar
-rw-r--r--@   1 twagner  staff    293671 Mar 28 19:05 jsoup-1.7.2.jar
-rw-r--r--@   1 twagner  staff    498954 Mar 28 19:05 jtransforms-2.4.jar
-rw-r--r--@   1 twagner  staff     40973 Mar 28 19:05 jung-api-2.0.1.jar
-rw-r--r--@   1 twagner  staff     62328 Mar 28 19:05 jung-graph-impl-2.0.1.jar
-rw-r--r--@   1 twagner  staff  37423189 Mar 28 19:05 jython-shaded-2.7.0.jar
-rw-r--r--@   1 twagner  staff     71904 Mar 28 19:05 jzlib-1.1.2.jar
-rw-r--r--@   1 twagner  staff    339283 Mar 28 19:05 kryo-2.24.0.jar
-rw-r--r--@   1 twagner  staff   1102985 Mar 28 19:05 languagesupport-2.5.8.jar
-rw-r--r--@   1 twagner  staff    960384 Mar 28 19:05 lapack-0.8.jar
-rw-r--r--@   1 twagner  staff    874626 Mar 28 19:05 legacy-imglib1-1.1.6.jar
-rwxr-xr-x@   1 twagner  staff    489884 Mar 28 19:05 log4j-1.2.17.jar
-rw-r--r--@   1 twagner  staff    304075 Mar 28 19:05 logback-classic-1.1.7.jar
-rw-r--r--@   1 twagner  staff    470782 Mar 28 19:05 logback-core-1.1.7.jar
drwxr-xr-x@   7 twagner  admin       238 Mar 28 19:05 macosx
-rw-r--r--@   1 twagner  staff    413342 Mar 28 19:05 mapdb-1.0.3.jar
-rw-r--r--@   1 twagner  staff     40987 Mar 28 19:05 markdownj-0.3.0-1.0.2b4.jar
-rw-r--r--@   1 twagner  staff     94421 Mar 28 19:05 maven-scm-api-1.4.jar
-rw-r--r--@   1 twagner  staff     40066 Mar 28 19:05 maven-scm-provider-svn-commons-1.4.jar
-rw-r--r--@   1 twagner  staff     69858 Mar 28 19:05 maven-scm-provider-svnexe-1.4.jar
-rw-r--r--@   1 twagner  staff    211185 Mar 28 19:05 metadata-extractor-2.6.2.jar
-rw-r--r--@   1 twagner  staff   1338906 Mar 28 19:05 methods-0.8.1906.jar
-rw-r--r--@   1 twagner  staff     76784 Mar 28 19:05 miglayout-3.7.4-swing.jar
-rw-r--r--@   1 twagner  staff   2011420 Mar 28 19:05 mines-jtk-20151125.jar
-rw-r--r--@   1 twagner  staff     59648 Mar 28 19:05 minimaven-2.2.0.jar
-rw-r--r--@   1 twagner  staff      4965 Mar 28 19:05 minlog-1.2.jar
-rw-r--r--@   1 twagner  staff    338032 Mar 28 19:05 mpicbg-1.1.1.jar
-rw-r--r--@   1 twagner  staff     51460 Mar 28 19:05 mpicbg-trakem2-1.2.3.jar
-rw-r--r--@   1 twagner  staff    268984 Mar 28 19:05 mtj-1.0.4.jar
-rw-r--r--@   1 twagner  staff     32927 Mar 28 19:05 nailgun-server-0.9.1.jar
-rw-r--r--@   1 twagner  staff     17848 Mar 28 19:05 native-lib-loader-2.1.4.jar
-rw-r--r--@   1 twagner  staff   4590070 Mar 28 19:05 netcdf-4.3.19.jar
-rw-r--r--@   1 twagner  staff    604886 Mar 28 19:05 netlib-java-0.9.3-renjin-patched-2.jar
-rw-r--r--@   1 twagner  staff     25501 Mar 28 19:05 object-inspector-0.1.jar
-rw-r--r--@   1 twagner  staff     41755 Mar 28 19:05 objenesis-2.1.jar
-rw-r--r--@   1 twagner  staff     53325 Mar 28 19:05 op-finder-0.1.0.jar
-rw-r--r--@   1 twagner  staff     25965 Mar 28 19:05 opencsv-2.4.jar
-rw-r--r--@   1 twagner  admin     80720 May  8 13:27 opencsv-3.9(1).jar
-rw-r--r--@   1 twagner  staff     14124 Mar 28 19:05 options-1.1.jar
-rw-r--r--    1 twagner  admin      1937 May 11 09:25 original-renjin-guava-17.0b.jar
-rw-r--r--@   1 twagner  staff     41801 Mar 28 19:05 pal-optimization-2.0.0.jar
-rw-r--r--@   1 twagner  staff     43742 Mar 28 19:05 parsington-1.0.0.jar
-rw-r--r--@   1 twagner  staff     49987 Mar 28 19:05 pentaho-package-manager-1.0.8.jar
-rw-r--r--@   1 twagner  staff    110019 Mar 28 19:05 perf4j-0.9.13.jar
-rw-r--r--@   1 twagner  staff    250546 Mar 28 19:05 plexus-utils-1.5.6.jar
-rw-r--r--@   1 twagner  staff    431722 Mar 28 19:05 postgresql-8.2-507.jdbc3.jar
-rw-r--r--@   1 twagner  admin    143349 Jun  2 14:17 randomForest-4.6-12-b49.jar
-rw-r--r--@   1 twagner  staff     25429 Mar 28 19:05 regexp-1.3.jar
-rw-r--r--@   1 twagner  admin     76416 Jun  6 09:31 renjin-appl-0.8.2387.jar
-rw-r--r--@   1 twagner  admin   3299487 Jun  6 09:30 renjin-core-0.8.2387.jar
-rw-r--r--@   1 twagner  admin    101589 Jun  6 14:27 renjin-gnur-runtime-0.8.2387.jar
-rw-r--r--    1 twagner  admin   2294551 May 11 09:25 renjin-guava-17.0b.jar
-rw-r--r--@   1 twagner  admin     17796 Jun  6 09:28 renjin-script-engine-0.8.2387.jar
-rw-r--r--@   1 twagner  staff   1188593 Mar 28 19:05 rhino-1.7.6.jar
-rw-r--r--@   1 twagner  staff   1056316 Mar 28 19:05 rsyntaxtextarea-2.5.8.jar
-rw-r--r--@   1 twagner  staff   9807458 Mar 28 19:05 scala-compiler-2.12.1.jar
-rw-r--r--@   1 twagner  staff   5272325 Mar 28 19:05 scala-library-2.12.1.jar
-rw-r--r--@   1 twagner  staff    201174 Mar 28 19:05 scala-parser-combinators_2.12.0-M4-1.0.4.jar
-rw-r--r--@   1 twagner  staff   3538697 Mar 28 19:05 scala-reflect-2.12.1.jar
-rw-r--r--@   1 twagner  staff    547860 Mar 28 19:05 scala-xml_2.12-1.0.6.jar
-rw-r--r--@   1 twagner  staff    539245 Mar 28 19:05 scala-xml_2.12.0-M4-1.0.5.jar
-rw-r--r--@   1 twagner  staff   1043053 Mar 28 19:05 scifio-0.31.1.jar
-rw-r--r--@   1 twagner  staff     22079 Mar 28 19:05 scifio-bf-compat-2.0.2.jar
-rw-r--r--@   1 twagner  staff     25511 Mar 28 19:05 scifio-cli-0.3.3.jar
-rw-r--r--@   1 twagner  staff     29573 Mar 28 19:05 scifio-hdf5-0.1.1.jar
-rw-r--r--@   1 twagner  staff    991166 Mar 28 19:05 scifio-jai-imageio-1.1.0.jar
-rw-r--r--@   1 twagner  staff     17511 Mar 28 19:05 scifio-lifesci-0.7.0.jar
-rw-r--r--@   1 twagner  staff    114183 Mar 28 19:05 scifio-ome-xml-0.14.2.jar
-rw-r--r--@   1 twagner  staff     24546 Mar 28 19:05 scifio-tools-0.14.0.jar
-rw-r--r--@   1 twagner  staff    769598 Mar 28 19:05 scijava-common-2.62.1.jar
-rw-r--r--@   1 twagner  staff      7599 Mar 28 19:05 scijava-config-2.0.1.jar
-rw-r--r--@   1 twagner  staff     41988 Mar 28 19:05 scijava-expression-parser-2.1.1.jar
-rw-r--r--@   1 twagner  staff     23520 Mar 28 19:05 scijava-plugins-commands-0.2.2.jar
-rw-r--r--@   1 twagner  staff      9347 Mar 28 19:05 scijava-plugins-platforms-0.2.1.jar
-rw-r--r--@   1 twagner  staff      4399 Mar 28 19:05 scijava-plugins-text-markdown-0.1.2.jar
-rw-r--r--@   1 twagner  staff      4343 Mar 28 19:05 scijava-plugins-text-plain-0.1.2.jar
-rw-r--r--@   1 twagner  staff     48790 Mar 28 19:05 scijava-ui-awt-0.1.5.jar
-rw-r--r--@   1 twagner  staff    126798 Mar 28 19:05 scijava-ui-swing-0.9.1.jar
-rw-r--r--@   1 twagner  staff    181414 Mar 28 19:05 script-editor-0.1.2.jar
-rw-r--r--@   1 twagner  staff     12051 Mar 28 19:05 scripting-beanshell-0.3.1.jar
-rw-r--r--@   1 twagner  staff      9275 Mar 28 19:05 scripting-clojure-0.1.5.jar
-rw-r--r--@   1 twagner  staff     15708 Mar 28 19:05 scripting-groovy-0.2.5.jar
-rw-r--r--@   1 twagner  staff     18968 Mar 28 19:05 scripting-java-0.4.0.jar
-rw-r--r--@   1 twagner  staff      7817 Mar 28 19:05 scripting-javascript-0.4.3.jar
-rw-r--r--@   1 twagner  staff      8272 Mar 28 19:05 scripting-jruby-0.2.4.jar
-rw-r--r--@   1 twagner  staff     15428 Mar 28 19:05 scripting-jython-0.4.0.jar
-rw-r--r--@   1 twagner  staff      7180 Mar 28 19:05 scripting-renjin-0.2.1.jar
-rw-r--r--@   1 twagner  staff      7078 Mar 28 19:05 scripting-scala-0.2.0.jar
-rwxr-xr-x@   1 twagner  staff     41071 Mar 28 19:05 slf4j-api-1.7.21.jar
-rw-r--r--@   1 twagner  staff    273449 Mar 28 19:05 snakeyaml-1.13.jar
-rw-r--r--@   1 twagner  staff    109316 Mar 28 19:05 spim_data-2.2.0.jar
-rw-r--r--@   1 twagner  staff    759376 Mar 28 19:05 stats-0.8.1906.jar
-rw-r--r--@   1 twagner  staff      8640 Mar 28 19:05 swing-checkbox-tree-1.0.1.jar
-rw-r--r--@   1 twagner  staff     12591 Mar 28 19:05 swing-worker-1.1.jar
-rw-r--r--@   1 twagner  staff   1389926 Mar 28 19:05 swingx-1.6.1.jar
-rw-r--r--@   1 twagner  staff   2523218 Mar 28 19:05 trove4j-3.0.3.jar
-rw-r--r--@   1 twagner  staff    126892 Mar 28 19:05 udunits-4.3.18.jar
-rw-r--r--@   1 twagner  staff     49711 Mar 28 19:05 ui-behaviour-1.1.0.jar
-rw-r--r--@   1 twagner  staff    394440 Mar 28 19:05 utils-0.8.1906.jar
-rw-r--r--@   1 twagner  staff    164203 Mar 28 19:05 vecmath-1.6.0-scijava-2.jar
-rw-r--r--@   1 twagner  staff      9625 Mar 28 19:05 weave_jy2java-2.0.0-SNAPSHOT.jar
-rw-r--r--@   1 twagner  staff   8991494 Mar 28 19:05 weka-dev-3.9.0.jar
-rw-r--r--@   1 twagner  staff       935 Mar 28 19:05 xerbla-0.8.jar
-rw-r--r--@   1 twagner  staff   1212965 Mar 28 19:05 xercesImpl-2.8.1.jar
-rwxr-xr-x@   1 twagner  staff    195119 Mar 28 19:05 xml-apis-1.3.03.jar
-rw-r--r--@   1 twagner  staff     85686 Mar 28 19:05 xml-apis-ext-1.3.04.jar
-rw-r--r--@   1 twagner  staff    645023 Mar 28 19:05 xmlgraphics-commons-2.1.jar
-rw-r--r--@   1 twagner  staff    117333 Mar 28 19:05 xmpcore-5.1.2.jar
-rw-r--r--@   1 twagner  staff     94672 Mar 28 19:05 xz-1.0.jar
-rw-r--r--@   1 twagner  staff    192394 Mar 28 19:05 yecht-1.0.jar

These are my dependencies:

 	<dependencies>
		<dependency>
   	 		<groupId>net.imagej</groupId>
   	 		<artifactId>ij</artifactId>
   	 		 <version>1.51d</version>
		</dependency>
		<dependency>
   	 		<groupId>com.opencsv</groupId>
   	 		<artifactId>opencsv</artifactId>
  	 		<version>3.9</version>
		</dependency>
		<dependency>
   	 		<groupId>org.apache.commons</groupId>
   			<artifactId>commons-math3</artifactId>
    		<version>3.3</version>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
				<version>4.12</version>
		</dependency>
		<dependency>
	    	<groupId>org.renjin</groupId>
	    	<artifactId>renjin-script-engine</artifactId>
	    	<version>0.8.2387</version>
	 	</dependency>
		<dependency>
		    <groupId>org.renjin.cran</groupId>
		    <artifactId>randomForest</artifactId>
		    <version>4.6-12-b49</version>
		</dependency>
		<dependency>
		    <groupId>sc.fiji</groupId>
		    <artifactId>fiji-lib</artifactId>
		    <version>2.1.1</version>
		</dependency>
		<dependency>
		    <groupId>de.biomedical-imaging.ij</groupId>
		    <artifactId>ij_blob</artifactId>
		    <version>1.4.9</version>
		</dependency>

	</dependencies>

If I train a random forest in Fiji and compare it with original R installation using the same data I get a twice as high error rate when using Fiji. However, if I run a minimal example in eclipse I get the same error rate as in original R:

public static void main(String[] args) {
		RenjinScriptEngineFactory factory = new RenjinScriptEngineFactory();
		
		RenjinScriptEngine engine = factory.getScriptEngine();
		 try {
			 	engine.eval("v <- version");
				SEXP s = (SEXP) engine.eval("v$version.string");
				IJ.log("Verison: " + s);
				engine.eval("library(randomForest)");
				engine.eval("load(\"training_data.RData\");");
				engine.eval("usedFeatures <- c(\"HuMoment_0\",\"HuMoment_1\",\"HuMoment_2\",\"HuMoment_3\",\"HuMoment_4\",\"HuMoment_5\",\"HuMoment_6\",\"MEAN_0\",\"gSD_0\",\"gMEAN_0\");");
				engine.eval("labels <- data[,1];");
				engine.eval("model <- randomForest(as.factor(labels)~.,data=data[,usedFeatures],ntree=50,importance=TRUE,mtry=4);");
				double[] ooberror =   ((DoubleVector) engine.eval("tail(model$err.rate[,c(\"OOB\")],n=1)")).toDoubleArray();
				System.out.println("Estimated error rate: " + ooberror[0]*100 );
				
			} catch (ScriptException e) {
				e.printStackTrace();
			}

	}

Maybe @ctrueden has an idea why the results differ? Maybe I missed and component when updating to the latest Renjin?

BTW: The output of

engine.eval("v <- version");
				SEXP s = (SEXP) engine.eval("v$version.string");
				IJ.log("Verison: " + s);

is 0.8.2387 in Fiji and in eclipse (as expected).

Best
Thorsten


#2

Maybe someone can tell me if there are other jar files which influence Renjin in Fiji besides
renjin-appl-0.8.2387.jar
renjin-core-0.8.2387.jar
renjin-gnur-runtime-0.8.2387.jar
renjin-guava-17.0b.jar
renjin-script-engine-0.8.2387.ja


#3

@twagner can you also reproduce this behaviour by using Rserve or JRI?

I wonder that you use Renjin because many tests with R packages (with native components - C, Fortran)
still fail (Even if the (green) successful tests suggest otherwise):

http://packages.renjin.org/package/org.renjin.cran/randomForest

http://packages.renjin.org/package/org.renjin.cran/spatstat (if you click on deldir you see that the tests failed!)


#4

No, I didnt try Rserve or JRI. I’m using Renjin because it is easy to use, randomForests works nicely, it is easy to distribute to different users and I can stuck with java.


#5

@twagner Yes, I agree. The advantages to have a full blown R interpreter in Java which could use all native package dependencies would be terrific.

At the moment however many packages of R which rely on native c code will not work by default and the plot devices aren’t implemented, either.

However it is interresting how they want to archive this:

http://www.renjin.org/blog/2016-01-31-introducing-gcc-bridge.html


#6

@Bio7 it works pretty well!

randomForest is mostly Fortran code for example.

Often the problems with packages are the small details. For example, I just looked at spatstat.utils and see that it compiles, but the NAMESPACE file includes useDynLib("spat.utils") and so Renjin looks for a R_init_spat.utils method to call when loading the compiled native code. Apparently there is a special rule in GNU R that . are replaced with _ in dynamically-linked libraries, so Renjin should be looking instead for R_init_spat_utils. It’s getting all those little rules right that makes full compatibility time consuming (but achievable!)


#7

@akbertram Great to hear. Thanks for the clarification.

The spatstat library callable from a Java interpreter would be a dream;-)

Will there be a Renjin plot device available in the near future, too?


#8

Just for completeness:

I’ve opened an issue here:
https://github.com/bedatadriven/renjin/issues/322

I will keep the forum updated.


#9

Solved! I replaced the following files with the latest one:
datasets-0.8.1906.jar
gcc-runtimg-0.8.1906.jar
graphics-0.8.1906.jar
grDevices-0.8.1906.jar
methods-0.8.1906.jar
utils-0.8.1906.jar
stats-0.8.1906.jar

See the github issue for more information.


#10

Glad you solved it, @twagner.

Why did you have to upgrade the shipped version? Bug-fixes? New features?

It would be awesome if you could file a PR against the scijava/scripting-renjin repository which updates to the newest version. Then we can upgrade it in ImageJ2 core.


#11

@ctrueden
Yes, there were important changes which makes training and prediction of the randomForests many times faster. And as this issues shows, the older version performs (in terms of accuracy) much worse.

How can I change the ${renjin-script.version} variable in the POM.xml inside the scripting-renjin repository?

Best
Thorsten


#12

If you worry about performance, why bother with R at all vs. Java implementations of RF (Weka, H2O, KNIME, …)?


#13

To be honest: I just prototyping in Java for Fiji (I have to implement it c++ later) and already knew Renjin from other projects. That is the reason why I’m not put any effort in using other libraries. But even for prototyping performance can be critical (testing). Furthermore, there are other nice tools implemented in R (automatic variable selection) which I would like to use.