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

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

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...<mailto:sim...@ig...>



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