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Re: [scipion-users] Problems with installing EM packages in Scipion from git
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From: Jose M. de la R. T. <del...@gm...> - 2016-11-14 22:18:14
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Hi Simone, The issues with the connectivity at our institute could be causing the problem as Pablo suggest. Nonetheless, I think I have seen those errors in other circumstances. First, when building Scipion from source code (from git) it build Xmipp by default and this error seems related to Java bindings, so be sure that Java jdk is properly set and everything is compiling properly without any extra EM package (just scipion install -j 5). When installing other EM packages, make sure to use the *--no-xmipp *option as stated in the How To Install wiki page. It will try to install other EM packages without building Xmipp, we are considering to change this behavior in a future and do not install Xmipp by default always. Please let us know if you manage to get Scipion properly installed with other EM packages and do not hesitate to contact us for further assistance. Bests, Jose Miguel On Mon, Nov 14, 2016 at 8:13 PM, Simone PELLEGRINO <pel...@ig...> wrote: > Hello Pablo, > > > ok that sounds like the source of the problem. We will try to keep trying > and hopefully getting some connection back soon. > > > We followed the link you sent to me, so I think we are in the right way. > > > Best > > Simone > > > > Dr. Simone Pellegrino > Integrated Structural Biology > Marat Yusupov's team > I.G.B.M.C. > 1, rue Laurent Fries > BP 10142 - 67404 Illkirch CEDEX > Tel: +33 (0)3 88 65 33 52 > > E.mail: sim...@ig... > ------------------------------ > *From:* Pablo Conesa <pc...@cn...> > *Sent:* 14 November 2016 18:47 > *To:* Simone PELLEGRINO; sci...@li... > *Subject:* Re: [scipion-users] Problems with installing EM packages in > Scipion from git > > > Dear Simone! > > > Today we've been going through a major network upgrade in our institute. > And will last for s few days. > > > This means that we will experience short disconnection periods. This will > explain those error you where getting, assuming you were trying today. > > > If so, keep trying, now for example we have connectivity, hence this email. > > One question, Have you gone through the "Github" installation > instructions? See this > <https://github.com/I2PC/scipion/wiki/How-to-Install> > > Let us know how it goes, > > > All the best, Pablo. > > > > On 14/11/16 16:05, Simone PELLEGRINO wrote: > > Dear all, > > > we are experiencing problems in installing the single EM packages from the > version of Scipion obtained from the git. The errors are the following: > > > ctffind4: > g++ -o software/em/xmipp/lib/libXmippJNI.so -shared > software/em/xmipp/libraries/bindings/java/xmipp_Pic > kingClassifier.os software/em/xmipp/libraries/bindings/java/xmipp_ProgTomographAlignment.os > software/em > /xmipp/libraries/bindings/java/xmipp_Program.os > software/em/xmipp/libraries/bindings/java/xmipp_CTFDesc > ription.os software/em/xmipp/libraries/bindings/java/xmipp_MDRow.os > software/em/xmipp/libraries/binding > s/java/xmipp_Filename.os software/em/xmipp/libraries/bindings/java/xmipp_ImageGeneric.os > software/em/xm > ipp/libraries/bindings/java/xmipp_ExceptionsHandler.os > software/em/xmipp/libraries/bindings/java/xmipp_ > Aux.os software/em/xmipp/libraries/bindings/java/xmipp_MetaData.os > software/em/xmipp/libraries/bindings > /java/xmipp_Projection.os software/em/xmipp/libraries/bindings/java/xmipp_TiltPairAligner.os > -Lsoftware > /em/xmipp/lib -Lsoftware/lib -lpthread -lXmippData -lXmippRecons > -lXmippClassif -lXmippBilib > Install file: "software/em/xmipp/lib/libXmippJNI.so" as > "software/lib/libXmippJNI.so" > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > frealign: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > motioncorr: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > resmap: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > spider: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > unblur: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > eman2.12: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > > > Does anyone know why please? With the version obtained from the webpage it > does install everything without any problem. > > Thank you very much for helping > > > Best > > Simone > > > Dr. Simone Pellegrino > Integrated Structural Biology > Marat Yusupov's team > I.G.B.M.C. > 1, rue Laurent Fries > BP 10142 - 67404 Illkirch CEDEX > Tel: +33 (0)3 88 65 33 52 > > E.mail: sim...@ig... > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
