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Bugzilla – Bug 741 |
broken jython after update |
Last modified: 2014-09-25 06:51:21 CDT |
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NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug. The Fiji project now uses GitHub Issues for issue tracking. Please file all new issues there. |
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Hello Fiji team, many of the functions in jython do not seem to work after the new update (the life-line version saved me :-)). Same error on Windows and MacOSx. For instance import os print os.path.isdir('/foobar') gives Started Macro.py at Wed May 07 21:58:51 CEST 2014 Traceback (most recent call last): File "<iostream>", line 2, in <module> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", line 195, in isdir File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", line 195, in isdir java.lang.IncompatibleClassChangeError: Found class com.kenai.jffi.InvocationBuffer, but interface was expected at com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) at org.python.posix.LibC$jaffl$0.stat$raw(Unknown Source) at org.python.posix.LibC$jaffl$0.stat(Unknown Source) at org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200) at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207) at org.python.modules.posix.PosixModule$StatFunction.__call__(PosixModule.java:966) at posixpath$py.isdir$17(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py:198) at posixpath$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py) at org.python.core.PyTableCode.call(PyTableCode.java:165) at org.python.core.PyBaseCode.call(PyBaseCode.java:134) at org.python.core.PyFunction.__call__(PyFunction.java:317) at org.python.pycode._pyx1.f$0(<iostream>:2) at org.python.pycode._pyx1.call_function(<iostream>) at org.python.core.PyTableCode.call(PyTableCode.java:165) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.Py.runCode(Py.java:1261) at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235) at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:230) at Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:73) at common.RefreshScripts.runScript(RefreshScripts.java:328) at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225) at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) java.lang.IncompatibleClassChangeError: java.lang.IncompatibleClassChangeError: Found class com.kenai.jffi.InvocationBuffer, but interface was expected java.lang.NullPointerException: null at javax.swing.JComponent.scrollRectToVisible(JComponent.java:3070) at fiji.scripting.ErrorHandler.scrollToVisible(ErrorHandler.java:96) at fiji.scripting.TextEditor.markCompileEnd(TextEditor.java:2063) at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1229) at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) Information about your version of Java: os.arch => x86_64 os.name => Mac OS X os.version => 10.8.5 java.version => 1.6.0_65 java.vendor => Apple Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_65-b14-462-11M4609 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 20.65-b04-462 java.vm.vendor => Apple Inc. java.vm.info => mixed mode java.awt.graphicsenv => apple.awt.CGraphicsEnvironment java.specification.name => Java Platform API Specification java.specification.version => 1.6 sun.cpu.endian => little sun.desktop => null file.separator => / The up-to-date check says: REMIND_LATER Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: null ij.dir => /Applications/Fiji.app Information about the version of each plugin: 4ccfd999:554f1fa4:387faf3d 20131002182226 :00c8c9c 2c93d9a6:2d9d2593:be71a9c0 20130903145716 :00efaa6 9770ed7e:40cf929f:0606b3ee 20130522114921 :011890f bdf6dc82:91b262e7:09001cd1 20130627164644 :019970f 13ce586a:be23db6b:315fb93c 20131106185955 :02ea642 426d64f4:be49972e:be49972e 20131002182232 :0307564 8c8f6d33:ac4c137b:ac4c137b 20130627164708 :0326851 dc0a9d07:01345c54:3449bd49 20140109165231 :034fe21 ec8c284f:6ee6ad0c:68f9f317 20130214000150 :0433ba9 6cfb774f:b8f734bb:b8f734bb 20140109165236 :04478f7 24590873:d3ccdd03:d3ccdd03 20130214000150 :044f3fe 015d8a2e:9cbf5db5:8de91f6b 20130903145706 :04782f0 6738a701:d6932866:d6932866 20130627164702 :04a4a5c 6bd9ca65:0954132b:637e808e 20140221152117 :05b1de4 30420365:5a23ed73:5a23ed73 20130214000150 :069ebf3 84d76592:53d3f4e0:53d3f4e0 20130214000150 :06c89a7 3f876cb1:205f633a:205f633a 20130214000150 :07e9a49 08453207:08453207:08453207 20130214000150 :0845320 738cf583:36e9a80a:bca93bda 20140109165229 :087a0a0 a058419c:e976dd2f:0194333b 20140325102448 :08a4dae 3ea9130d:791596f0:791596f0 20140325102402 :096abf5 09868b51:09868b51:09868b51 20130214000150 :09868b5 0aadfa58:b3b7277b:b3b7277b 20130214000150 :09e22a2 b0e5ec4f:f9fb1b1e:7b2063a5 20130728100324 :0a2a17f fb827967:5dbb3afe:1bf26607 20140221152119 :0a5d89f 0a93f0be:0a93f0be:0a93f0be 20130214000150 :0a93f0b 1cea16c4:5674b1fc:c120c076 20140109165229 :0af0912 cd9eda33:239d2a49:f25c125a 20130430095628 :0b76869 079072d5:3f320e23:0bfab9b2 20130728100335 :0bc2f58 61ab84fd:2a4992aa:2a4992aa 20130627164710 :0bd5f17 283a7027:9263e996:9263e996 20130214000150 :0c2a5e1 72ea2fc2:73af3a23:73af3a23 20130522115000 :0d4057e 2335d2f7:425d0ca9:39c6a187 20140325102256 :0d70010 8725145c:442562b0:4c699a2e 20130728100311 :0d8d4be 6478da40:1d98f525:1d98f525 20130214000150 :0dccf16 36be42c0:7ba6da96:1d35149e 20131002182227 :0de1ed9 58e12d38:0756c7da:0756c7da 20130430095625 :0e15c07 69e33649:d2b46052:d2b46052 20130430095637 :0e17d4e 1dd37acb:dcf3e354:dcf3e354 20131106190016 :0eec001 4b7c50dc:c2bc4887:c2bc4887 20130430095636 :0f0b618 0f44924c:0f44924c:0f44924c 20130214000150 :0f44924 1a215d3d:25bd369d:e6d5fe76 20130430095619 :0fb2aba 30fe4811:431e6ee1:0117adfc 20130522114940 :0ff27f6 6e73f072:7a97d173:e43858a8 20140325102301 :10502f4 10ab7036:10ab7036:b7e560e5 20130214000150 :10ab703 c95cbe14:4cf90d1d:fc10f5f6 20140221152114 :11b4297 9c65dc22:528ce9f7:43458c1d 20130627164625 :12ab1b9 68c7e388:8140b70b:ae096325 20130903145717 :133cff4 ffa4b5e4:6d536854:6d536854 20130214000150 :1383353 1398b098:1398b098:1398b098 20130214000150 :1398b09 2bd28388:f2516a22:f2516a22 20130522114938 :139ef92 431a3747:4cead5ae:4cead5ae 20130214000150 :13d94c1 95e82eac:0f992270:c877ab64 20131002182226 :144906c 0de19f82:a4621a87:a4621a87 20130522114957 :1506fc3 a480dab5:5e63ab6d:b7e6ebe8 20130627164643 :150e165 64d30616:13d82a9a:ecc81996 20131106185933 :15260b1 e9c6b155:014024f1:2e801b15 20131106185858 :152b09a 7222de21:aaed1bde:40e5c3d0 20130214000150 :15f3494 975368e0:213d521b:213d521b 20130627164714 :16012d5 166036ab:166036ab:166036ab 20130214000150 :166036a b2275d1c:f7a5eb30:4918803a 20130214000150 :16bbe0c 6f58c779:11dc44ca:fd83b09e 20131002182227 :171c90f 68b5039b:0dc5c1a8:4a8bf900 20131106185923 :1728149 174a4b19:174a4b19:174a4b19 20130214000150 :174a4b1 97576758:7caa08fd:2f3fb8f8 20131002182222 :179685f 53b934a5:21896ddd:980cba3f 20130728100341 :17eeef0 c0edb63b:3b1f88b2:4ed7ae8c 20130617220549 :18606e8 97d046c8:9467908f:9467908f 20130627164712 :186e052 f0dde207:5b731066:5b731066 20130627164652 :1902ce8 2750162f:ee9e5ec5:ee9e5ec5 20130627164705 :19181db 95a9e32c:c395f259:925450a6 20130728100334 :1941524 08119256:c7a3730c:6bea0bb0 20130529112540 :1a10f15 1a6345a2:1a6345a2:1a6345a2 20130214000150 :1a6345a 5a40b171:9017d436:63e90571 20130214000150 :1ad3be0 25fdd56a:2545e299:5f7905f1 20140109165218 :1ad6b45 e094b1c1:44ab48c3:5633cb6f 20130214000150 :1b71cda b6014f87:f81e1832:f81e1832 20140325102359 :1b7b2d4 d0970734:b7d19372:b7d19372 20130627164708 :1bc31e9 8e9a382a:6bf46a19:e77edfe4 20140325102301 :1bef7c8 9a4bddf7:40e38844:40e38844 20140325102402 :1c18921 19335ace:fc1a3d5e:28e1ad96 20130522114949 :1c88458 1cee26bc:1cee26bc:1cee26bc 20130214000150 :1cee26b eadb2593:64b484df:281c847d 20130728100319 :1d44a0d a3420fc4:aab1f90e:0130eaa3 20140507194130 :1d7294a cd63c0bf:92f964a3:92f964a3 20130522114951 :1daf580 981f35fd:f48d5b7d:a7d5f82c 20130214000150 :1dedefe 4bf490fc:4986d4a9:4986d4a9 20140507194127 :1deeabc 61a74a7e:2c344e2f:304d96ad 20130214000150 :1dfc974 1eb5c9ef:1eb5c9ef:1eb5c9ef 20130214000150 :1eb5c9e c2f213f2:0abfb748:95082cfe 20131106185951 :1eb9422 748e0dec:fac9aaf3:52b8f2ca 20130627164644 :1ee97bd 30f498a1:3b681b12:774f56bf 20140109165218 :1f0b3f8 ee97218b:f3679f41:f3679f41 20130522115001 :1f35cae 106c63d5:97a86bf6:97a86bf6 20130430095638 :1f4f9e5 09d3a31a:34a7400a:34a7400a 20130430095635 :1f65630 202a7fb9:202a7fb9:202a7fb9 20130214000150 :202a7fb 48a4132f:ebf1fa4f:ebf1fa4f 20130617220622 :2079ca3 43405316:fb978da1:ed0e2581 20130903145717 :20bc295 20e2cec7:20e2cec7:20e2cec7 20130621073128 :20e2cec 2104ef52:2104ef52:2104ef52 20130214000150 :2104ef5 34578b7a:f19576cf:f19576cf 20130430095635 :2136ee1 4446b45a:e25b18ee:e25b18ee 20140507194122 :213e2d0 bac30d9e:3515d95e:633579fc 20130214000150 :216b590 9379a218:00ae7525:c9d69a61 20131002182226 :2197aa2 513d98b0:25b9b371:25b9b371 20140325102400 :21e64d4 a53af77b:d9198d71:ed143caa 20130430095535 :22863fd 22fd045b:22fd045b:22fd045b 20130214000150 :22fd045 232cc1e4:232cc1e4:232cc1e4 20130214000150 :232cc1e 590e0603:ae8aa869:a76de30a 20130214000150 :238f8b7 b1a5b585:1d14f6c6:3bbd89c8 20130617220607 :2398f66 23cae80c:23cae80c:23cae80c 20130214000150 :23cae80 cedb6d82:f7cc7817:2362f25c 20130214000150 :242749d 204ad6d9:7f6eef1b:7f6eef1b 20130522115000 :248a32e 357b1056:8156e009:8156e009 20130214000150 :24d47d7 c946fe7e:30421f1a:582cf7c7 20140221152112 :24e0bde d7c670b5:f555145a:f555145a 20130728100353 :253c6df 83895477:0a5b1beb:34181783 20140221152128 :259df97 726af6cb:5ad6878a:5ad6878a 20130430095636 :263158a 265850b3:265850b3:265850b3 20130214000150 :265850b def4038f:787984b3:d558718f 20130522114956 :265cb26 c1327662:79025585:50b28793 20140221152106 :2716120 bcee12e8:0be27539:0be27539 20140221152127 :279a86b 0f832edd:81589f14:1651ecce 20131106190022 :27c6f58 97baa7b5:de42e047:de42e047 20130627164653 :27de591 f5f5d72d:64b58031:48ecb5fe 20131002182219 :27f8eeb eedac93f:52476ec4:effdb45e 20130903145717 :2837db0 26250ca7:c150f381:c150f381 20131002182232 :28a6b42 eff3a295:639027a3:639027a3 20130627164712 :295ba57 3e3b75d2:c970805d:8e60f732 20130214000150 :29d38d7 c716cfad:c357e934:69c529de 20130529112547 :2a26b5e 7caabb2a:c5a9c9bf:c5a9c9bf 20130903145720 :2a72259 d9e0bf3a:1d693ab8:60903c8f 20130430095617 :2b318f7 c92bc1d4:2928de88:ba375fb6 20130522114921 :2bd4340 6cb70056:c1c6fcd4:e43dfba7 20130627164645 :2bd9a85 84c6ebeb:1dc1193a:1dc1193a 20130627164710 :2bda1f6 0e158e32:8cdb360f:8cdb360f 20131106190017 :2bde09b 5c14a520:d1d3073e:45a3b5e7 20130430095605 :2ce2c00 516ababa:a275e857:a275e857 20130627164650 :2cee6c3 d3dc14cc:bc3ea362:bc3ea362 20130214000150 :2d33401 27e145ac:05f63f9c:a1c84eee 20130214000150 :2d9491a f31b9812:ca52ad89:2f40baca 20130430095620 :2daf8bd 2dc5d027:2dc5d027:2dc5d027 20130214000150 :2dc5d02 27d2690c:8627f7ec:c5261e10 20130522114954 :2dcaf5b 55a173bf:799c302a:799c302a 20130627164658 :2dd01db 7848c98b:ddff4a15:cbb5750c 20131002182224 :2e5652c f943680c:7685f113:e18ae199 20140109165210 :2eeefe6 8c194ae9:d8fbc303:d8fbc303 20140325102453 :2ef6f1e faf3590e:b3a6dfc8:b3a6dfc8 20130627164708 :2fc7f2b 907bd39d:8f13b98c:8f13b98c 20130627164650 :30100de 28046446:9ce1257d:fdf7a057 20130214000150 :30bafe0 839b37bc:80e1da52:653d576f 20131106185955 :310cdb6 95af1ff3:dca3038a:e752ccac 20130522114941 :31333d7 2cb7f9c7:689d562e:0070496c 20131002182219 :319297f 3fbb225b:0c583e31:66b82737 20140221152118 :31d2070 4c6e9c10:b32fe26e:2d196b9f 20130627164648 :31f9aa9 6759f7b5:c8cc463f:72027754 20130522114943 :320b761 32aabe78:32aabe78:32aabe78 20130214000150 :32aabe7 32d24a27:32d24a27:32d24a27 20130214000150 :32d24a2 e229121f:77fa5f41:c87493e1 20140325102447 :332f660 5b7ea1e1:b0be5c35:4c3c0562 20130903145712 :336ead7 0b6a9aff:fd6990df:dbc12f34 20131124211403 :33b6af8 4136049b:62d5cd6d:97058b48 20140109165223 :3406abc ff79458d:984820cd:464a2e8a 20130627164631 :347fb7e ade5d7d9:e6e0879f:e6e0879f 20130214000150 :34b7341 184d9580:d91a130e:d91a130e 20130709124555 :34d0deb 34dfe8f4:34dfe8f4:34dfe8f4 20130214000150 :34dfe8f 6ce54af8:747ead7e:5f124d58 20140221152121 :351a73c c2708786:1c927295:db268567 20140221152124 :3569266 fc45d44e:027485e0:027485e0 20130903145721 :3582cd5 1910f7d0:35de4ecb:d9674003 20131106185918 :35c256a 7b7d78b4:854de8ea:391eb005 20130214000150 :363190d b6a2df10:9b100a5d:9b100a5d 20131002182231 :369b635 55f79ce5:c3ab5cd0:c3ab5cd0 20130214000150 :36b6b0d 91d6774f:81ee7dda:831d5b93 20130214000150 :36cdef5 74eb0251:4dd61c5a:008da5fc 20130728100310 :37afe6e 76812dce:45409dcf:25d93bd6 20130903145707 :37da6fe 272da056:b8955e06:fe3586fb 20140221152056 :3877215 b851408d:46e4714e:46e4714e 20131106190009 :38b2c2b d57f5101:162ac456:3c299a45 20130430095606 :397b46c d3aa0468:2dbaef27:eb94a247 20131106185925 :398ab19 39d4aaaf:39d4aaaf:39d4aaaf 20130214000150 :39d4aaa 9373a092:2bfe6962:310d12cb 20130903145711 :39eba37 64be498f:fb0a03d7:cf45b5a3 20140507194117 :3a44600 27359058:67e005e1:67e005e1 20140221152106 :3aacabe 02bc6560:8b5fc706:7a3e1a44 20140109165222 :3ae2fa1 96ab42df:8aff2407:77ccabc8 20130903145716 :3b5dda7 f5f8ecef:54105758:9b28d112 20131002182219 :3b9cd74 4b051b74:2a0a96ae:2a0a96ae 20130627164713 :3bac3fb fd9298bb:258c8496:258c8496 20131002182235 :3ca141d 4bcc3453:2c1b23d1:46d835ce 20140221152107 :3cd39ba 1d0f1a86:b9041587:b9041587 20140507194123 :3d2962d 7a2916d6:39f45f23:f23b1754 20131106185958 :3da60e9 48b257aa:d060d203:43c804dd 20140221152114 :3dad25a 032b5ee0:a7f44d64:897b14f6 20130627164641 :3e21f65 581a3b53:c57906e2:c57906e2 20130627164651 :3e4163b 3ea0d59d:3ea0d59d:3ea0d59d 20130214000150 :3ea0d59 276e8559:46172d0e:f7ccca79 20131002182222 :3ea7f59 4a859b01:d852debb:7f15de44 20130903145706 :3eaa025 4f964c3f:1f0d1725:a877c584 20130214000150 :3f54d48 1df8fa3c:ae0ec97b:e8cbfe99 20140221152116 :3fbce45 25ee5004:56c5a359:4450a30c 20131002182225 :3fc3355 d23b07fd:89eeb017:5cc73b2d 20130430095557 :3fd7941 b976cd2c:f5835d94:989747c9 20140109165230 :3fda2de 70139a6f:372f52d6:5c1c3ab5 20130728100311 :3ff339d 4cd7e966:09dd6436:283cbd26 20131002182227 :4060273 19c93860:accf2661:d258c6ee 20130627164640 :407ca02 546ef145:a5fc0c94:baf0d89e 20130430095536 :40b40cc 1c41e9ff:4199e180:4199e180 20130214000150 :4124ed0 41d82921:41d82921:41d82921 20130214000150 :41d8292 ab93324a:11097a44:06b1f91c 20130728100340 :4234b85 6ff3b71c:66eb19e0:fbcca133 20131106190006 :4250a4f 42556198:42556198:42556198 20130214000150 :4255619 6a1f8608:d62e5bb8:d62e5bb8 20140507194125 :429311f 596fa687:2e716db7:4d76a873 20140507194119 :4294cf9 aa6dcdbb:c3683c76:4787bb4e 20140221152121 :433f2bc ee5ed229:a89451d3:f8f3cddc 20140109165237 :435878b 67507798:3ced777f:262afe0f 20130723222006 :4382808 a74fe43c:342c20d9:ce6fae5c 20131009105156 :43ca129 37ed52c8:35dfa2bd:bf3f68d9 20130430095556 :43e9c64 fc615298:505a9692:70a63a6e 20130522114948 :44f1985 98a674fc:75c078e3:3e89db63 20130214000150 :45bce17 5a9c725e:20c1fca1:20c1fca1 20130627164704 :460995d 8c33e42d:d4b801ab:d81d2e53 20130903145718 :4630427 4e5f9362:27fae44c:1b412fbf 20130627164633 :465d5f7 665e87f1:70d3a12d:2e95f8bf 20130728100315 :46a37da 72879ca4:1022e9ea:79160dfc 20130430095617 :46b2ddd ed1d53ab:b9bd6f19:b9bd6f19 20131106190012 :46ea6dc eb55dffc:dd4d209c:c9d8974a 20130728100342 :472c08c 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jars/ij-updater-ssh-2.0.0-beta-7.7.jar 6f60a5ac 20140221152120 jars/ij-updater-webdav-2.0.0-beta-7.7.jar 27161205 20140221152106 jars/ij-util-awt-2.0.0-beta-7.7.jar 11b4297f 20140221152114 jars/ij-util-swing-2.0.0-beta-7.7.jar 7390168e 20140325102322 jars/ij1-patcher-0.1.1.jar be2287e8 20130214000150 jars/imagescience-2.4.1.jar 780fae40 20130214000150 jars/imageware.jar 1bef7c8a 20140325102301 jars/imglib2-2.0.0-beta-25.jar 5052ed01 20140325102257 jars/imglib2-algorithms-2.0.0-beta-25.jar e511d1cf 20140325102408 jars/imglib2-algorithms-gpl-2.0.0-beta-25.jar dac6c85a 20140325102409 jars/imglib2-algorithms-legacy-2.0.0-beta-25.jar 6d0580ab 20140325102302 jars/imglib2-ij-2.0.0-beta-25.jar a7214071 20140325102302 jars/imglib2-meta-2.0.0-beta-25.jar c9d2b877 20140325102253 jars/imglib2-ops-2.0.0-beta-25.jar f539735b 20140325102409 jars/imglib2-realtransform-2.0.0-beta-25.jar f9f1333a 20130214000150 jars/itext-2.1.5.jar c4258671 20130214000150 jars/itextpdf.jar 0dccf163 20130214000150 jars/jacl.jar 8c636e50 20130214000150 jars/jai_codec.jar 717dd8e0 20130214000150 jars/jai_core.jar e5852db5 20130728100309 jars/jai_imageio-1.0.1.jar ac77c0f5 20140221152122 jars/jama-1.0.3.jar e4ac596e 20130430095638 jars/java-cup-0.11a.jar 15f34947 20130214000150 jars/javac.jar fb25609e 20130214000150 jars/javassist-3.16.1-GA.jar ccf6c908 20130214000150 jars/jcommon-1.0.17.jar efe2e903 20131106190000 jars/jdatepicker-1.3.2.jar c295a4c5 20130430095625 jars/jdom-2.0.2.jar 64241209 20130214000150 jars/jdom-contrib.jar 166036ab 20130214000150 jars/jep.jar 55d8499c 20130214000150 jars/jfreechart-1.0.14.jar 0e15c072 20130430095625 jars/jgrapht-0.8.3.jar 0b768690 20130430095628 jars/jgraphx-1.10.4.1.jar 242749dc 20130214000150 jars/jhotdraw-7.6.0.jar 90915f54 20130214000150 jars/jna.jar 4c09d41c 20140325102411 jars/joda-time-2.2.jar 1ad3be0d 20130214000150 jars/jpedalSTD.jar 7ecaf631 20140325102357 jars/jruby-complete-1.7.11.jar 65f86378 20130214000150 jars/js.jar 2ce2c00a 20130430095605 jars/jsch-0.1.49.jar 24d47d70 20130214000150 jars/junit-4.8.1.jar 9f4f8151 20140325102322 jars/jython-2.5.2.jar 5ce5840c 20130214000150 jars/jzlib.jar d2af3ac9 20140325102302 jars/kryo-2.21-shaded.jar 5a6f6f25 20131106190031 jars/legacy-imglib1-2.0.0-SNAPSHOT.jar 35c256ae 20131106185918 jars/log4j-1.2.17.jar 7a02f3e7 20140325102413 jars/logback-classic-1.0.9.jar d9d80652 20140325102414 jars/logback-core-1.0.9.jar d1d9b590 20140109165231 jars/mapdb-0.9.7.jar 1daf5806 20130522114951 jars/markdownj-0.3.0-1.0.2b4.jar 7f0caa5d 20130214000150 jars/miglayout-3.7.3.1-swing.jar a11cfc71 20130627164648 jars/mij-1.3.6-fiji2-SNAPSHOT.jar b6bf3817 20140109165233 jars/mines-jtk-20100113.jar 5bd64fbe 20131002182230 jars/mpicbg-0.6.1-SNAPSHOT.jar 10502f4c 20140325102301 jars/native-lib-loader-2.0.0.jar a51a31db 20140325102445 jars/netcdf-4.3.19.jar f41603bf 20130214000150 jars/object-inspector-0.1.jar e0088259 20130214000150 jars/pal-optimization.jar 82577709 20130430095638 jars/pentaho-package-manager-1.0.0.jar 7af6ddeb 20140325102302 jars/perf4j-0.9.13.jar c586a356 20130214000150 jars/postgresql.jar 72184439 20130728100339 jars/rsyntaxtextarea-2.0.4.1.jar 0d70010d 20140325102256 jars/scifio-0.10.1.jar a7ba5b7d 20140325102445 jars/scifio-bf-compat-1.6.1.jar 54336bb0 20140325102445 jars/scifio-lifesci-0.4.0.jar e6f1a324 20140325102446 jars/scifio-ome-xml-0.7.0.jar 38772153 20140221152056 jars/scijava-common-2.9.0.jar eedc0cd9 20130214000150 jars/serializer-2.7.1.jar 572a727b 20131106185933 jars/slf4j-api-1.7.2.jar 9ae3dd1b 20131106185931 jars/slf4j-log4j12-1.7.2.jar 1dedefe8 20130214000150 jars/tools-1.4.2.jar 68c26a79 20131106190000 jars/udunits-4.3.18.jar 7d5ba6c5 20130214000150 jars/wavelets.jar fc6c0417 20130214000150 jars/weave_jy2java.jar 9a71e194 20130430095645 jars/weka-dev-3.7.6.jar 36cdef55 20130214000150 jars/xalan-2.7.1.jar da8b05de 20130214000150 jars/xml-apis-1.3.04.jar c432f64b 20130214000150 luts/16_colors.lut 89419f99 20130214000150 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3ee0edfa 20130214000150 plugins/Macros/batch_convert_any_to_tif.txt 55f5b6a0 20130627164704 plugins/Manual_Tracking-2.0.0-SNAPSHOT.jar 9c541ad9 20130627164700 plugins/MosaicJ_-2.0.0-SNAPSHOT.jar 04a4a5c1 20130627164702 plugins/PIV_analyser-1.1.1-SNAPSHOT.jar 219187f7 20130725160609 plugins/Personal/Close_all_forced.class e01cd8c5 20130813115544 plugins/Personal/Filter_particles.class 985fefd4 20130814152926 plugins/Personal/Message.py aeab6aa9 20130814155858 plugins/Personal/Microscope_Communicator-1.1.6.jar b726847c 20130722093324 plugins/Personal/Select_best_particle.class 039b29f5 20140507210650 plugins/Personal/automatedImgTools.py ceed8dcc 20130228143735 plugins/Personal/commons-io-2.1.jar 3e86159d 20140507210711 plugins/Personal/fileMonitoring.py c36633fb 20130904174653 plugins/Personal/maximalProjectionCommandLine.py 8f933493 20130903105859 plugins/Personal/segmentNuclei.py ded74be0 20140107191421 plugins/Personal/segment_Particles-0.2.4.jar 9a0a5e25 20130814152705 plugins/Personal/zeiss.py 19181db3 20130627164705 plugins/PointPicker_-2.0.0-SNAPSHOT.jar 964d054a 20130728100349 plugins/QuickPALM_-1.1.1-SNAPSHOT.jar 9fb03125 20130627164650 plugins/RATS_-2.0.0-SNAPSHOT.jar 5c7f3968 20130627164652 plugins/RandomJ_-1.5.1-SNAPSHOT.jar 7d1ad162 20130214000150 plugins/Reconstruct_Reader.jar 8bc6c355 20140221152128 plugins/Refresh_Javas-2.0.0-SNAPSHOT.jar 4ddf620c 20130214000150 plugins/SPIM_Opener.jar 5b5857d2 20140109165236 plugins/SPIM_Registration-2.0.0-SNAPSHOT.jar b9076c0a 20130627164652 plugins/Samples_-2.0.0-SNAPSHOT.jar 6d88799a 20140109165236 plugins/Script_Editor-2.0.0-SNAPSHOT.jar 578994ca 20130903145721 plugins/Scripts/File/Make_Screencast.bsh c70b2e6f 20130214000150 plugins/Scripts/File/Open_Samples/Adelsons_Squares.ijm 60df5674 20130522115002 plugins/Scripts/File/Open_Samples/Spirals_.ijm a3edd6db 20130214000150 plugins/Scripts/Image/Adjust/Scale_to_DPI.js 209aed52 20130214000150 plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm 1de6c712 20130709124555 plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm 459a3d09 20140411205934 plugins/Scripts/Plugins/EMBL/Automated_Fcs_Centrosomes_.py de49dfce 20140507211030 plugins/Scripts/Plugins/EMBL/Automated_Fcs_Nucleus_.py ada7d933 20140210130348 plugins/Scripts/Plugins/EMBL/concat_.py af064f17 20131002182233 plugins/Scripts/Plugins/Registration/Correct_3D_drift.py a6e496fc 20130430095637 plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh b5ee58a2 20130430095637 plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh fc46bd40 20130214000150 plugins/Scripts/Plugins/Utilities/Record_Desktop.py 9d4d012a 20130214000150 plugins/Scripts/Plugins/Utilities/Record_Window.py 8cb22fe2 20140325102447 plugins/Series_Labeler-2.0.0-SNAPSHOT.jar 7c62b5c5 20130627164714 plugins/SheppLogan_-2.0.0-SNAPSHOT.jar 332f6608 20140325102447 plugins/Sholl_Analysis-3.4.1.jar 95dc5b19 20140109165238 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar 0bd5f179 20130627164710 plugins/Siox_Segmentation-1.0.1-SNAPSHOT.jar 52fecf09 20130627164713 plugins/Skeletonize3D_-1.0.1-SNAPSHOT.jar b0820703 20130627164712 plugins/Snakuscule_-2.0.0-SNAPSHOT.jar 33b6af85 20131124211403 plugins/SplineDeformationGenerator_-2.0.0-SNAPSHOT.jar 27de591e 20130627164653 plugins/StackReg_-2.0.0-SNAPSHOT.jar 736bb192 20130627164706 plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar 64c79501 20131117123809 plugins/Stacks/Nonuniform_Background_Removal.class 59f36299 20130627164712 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar 08a4daec 20140325102448 plugins/Stitching_-2.0.0-SNAPSHOT.jar 30100de7 20130627164650 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar 685ca9dc 20130627164710 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar 2cee6c37 20130627164650 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar d822b123 20130214000150 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar 584cb5b9 20130627164714 plugins/ToAST_-25.0.1-SNAPSHOT.jar 4cf59217 20130627164712 plugins/TopoJ_-2.0.0-SNAPSHOT.jar 4de49e00 20140325102452 plugins/TrackMate_-2.2.0.jar f90d5cfd 20140507194133 plugins/Trainable_Segmentation-2.1.0-SNAPSHOT.jar 59124982 20131106190022 plugins/TrakEM2_-1.0b-SNAPSHOT.jar 8e7f3b79 20130627164651 plugins/TransformJ_-2.8.1-SNAPSHOT.jar c4e87a76 20130627164711 plugins/TurboReg_-2.0.0-SNAPSHOT.jar 9558400d 20130214000150 plugins/UnwarpJ_.jar a32dfe46 20130214000150 plugins/Utilities/Close_All_Without_Saving.txt 253c6df4 20130728100353 plugins/VIB_-2.0.0-SNAPSHOT.jar baa78901 20131002182230 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar 81279d21 20130627164659 plugins/Video_Editing-2.0.0-SNAPSHOT.jar 73396eef 20130627164709 plugins/View5D_-1.3.1-SNAPSHOT.jar 980c0ed9 20130627164715 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar 2ef6f1eb 20140325102453 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar 5f60d96e 20130724132346 plugins/Watershed_.jar 90d999fb 20140408152525 plugins/WindowsRegistry$StreamReader.class b7d30bcf 20140408152525 plugins/WindowsRegistry.class 2079ca32 20130617220622 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar 9467b1a2 20140507194131 plugins/bio-formats_plugins-5.0.1.jar 0307564a 20131002182232 plugins/blockmatching_-2.0.0-SNAPSHOT.jar 659ad6a3 20130214000150 plugins/ij-ImageIO_.jar 82f900ac 20130627164712 plugins/level_sets-1.0.1-SNAPSHOT.jar df2af815 20131002182231 plugins/mpicbg_-0.6.1-SNAPSHOT.jar 5e32d936 20130214000150 plugins/panorama_.jar 96b34801 20130214000150 plugins/readme.txt 4bd07822 20140221152129 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar 16012d5a 20130627164714 plugins/registration_3d-2.0.0-SNAPSHOT.jar d80515eb 20140408145806 plugins/testClass.class 34b7341d 20130214000150 retro/backport-util-concurrent-3.1.jar 8759ba20 20130430095631 retro/retrotranslator-runtime-1.2.9.jar a6d5a3b2 20130430095631 retro/retrotranslator-transformer-1.2.9.jar d7160d38 20130214000150 scripts/InstallJava3D.m 05a92a3c 20130214000150 scripts/IsJava3DInstalled.m ff34d026 20130214000150 scripts/Matlab3DViewerDemo_1.m 25be149f 20130214000150 scripts/Matlab3DViewerDemo_2.m cb529b6c 20130214000150 scripts/Matlab3DViewerDemo_3.m 53d2da73 20130214000150 scripts/Matlab3DViewerIntroduction.m 4bb342fa 20130214000150 scripts/Miji.m 868cd434 20130214000150 scripts/Miji_Test.m dc94c3a3 20130214000150 scripts/bfopen.m a77cab39 20130903145721 scripts/importTrackMateTracks.mI have this problem on an openSuse 13.1 64-bit system makedirs(outputPath) results in the following error: Traceback (most recent call last): File "/home/hila/Desktop/macros/DapiSegmentation_5_usingApi-a.py", line 458, in <module> outputPath = outputCreater(inputDir, inputPrefix, VERSION, ROUNDNESS_THRESHOLD, CIRC_THRESHOLD) File "/home/hila/Desktop/macros/DapiSegmentation_5_usingApi-a.py", line 175, in outputCreater makedirs(outputPath) File "/home/hila/Desktop/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py", line 149, in makedirs File "/home/hila/Desktop/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", line 171, in exists File "/home/hila/Desktop/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", line 171, in exists java.lang.IncompatibleClassChangeError: Found class com.kenai.jffi.InvocationBuffer, but interface was expected at com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) at org.python.posix.LinuxLibC$jaffl$0.__xstat64$raw(Unknown Source) and much more... removing jruby did not solve the problem. I have a different openSuse 13.1 system in which path.exists(outputPath) produces an error, iff outputPath does not exist. If outputPath exists then it works correctly.