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

[Simone P. <pel...@ig...>]

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...