Re: [scipion-users] Problems with installing EM packages in Scipion from git

[Pablo C. <pc...@cn...>]

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...
>
>
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