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IDProjectCategoryView StatusDate SubmittedLast Update
0003218Slicer4Core: Extensionspublic2013-07-10 10:432017-06-07 23:27
Reporterlassoan Assigned Tojcfr  
PrioritylowSeveritymajorReproducibilitysometimes
Status closedResolutionfixed 
Product Version 
Target VersionFixed in VersionSlicer 4.5.0-1 
Summary0003218: Loadable module loading from extension fails on linux
Description

Loading of loadable modules from extensions fail on certain linux computers. CLI modules work fine. See details below.

From: slicer-devel-bounces@bwh.harvard.edu [mailto:slicer-devel-bounces@bwh.harvard.edu] On Behalf Of Andras Lasso
Sent: Wednesday, July 10, 2013 12:52 PM
To: slicer-devel@bwh.harvard.edu
Subject: Re: [slicer-devel] new UKF error

I also have this error, it is reproducible with the LoadableExtensionTemplate extension (and MatlabBridge and probably with all other loadable modules distributed in an extension). After installing the LoadableExtensionTemplate extension and restarting Slicer this error is logged: “Error(s): Cannot load library /data/image/home/usr/staff/lasso/.config/NA-MIC/Extensions-22162/LoadableExtensionTemplate/lib/Slicer-4.2/qt-loadable-modules/libqSlicerLoadableModuleTemplateModule.so: (libvtkSlicerLoadableModuleTemplateModuleLogic.so: cannot open shared object file: No such file or directory)”, and the module is not loaded.

This may be related to the OS version, permissions, or other configuration settings, as I can reproduce the error on a server running Ubuntu 10.04.4 LTS, but not on a virtual machine with running Ubuntu 12.04 LTS.

Andras

From: slicer-devel-bounces@bwh.harvard.edu [mailto:slicer-devel-bounces@bwh.harvard.edu] On Behalf Of Ryan Eckbo
Sent: Wednesday, July 10, 2013 12:13 PM
To: slicer-devel@bwh.harvard.edu
Subject: [slicer-devel] new UKF error

Yesterday I had the UKF module working on Mac and Linux as a slicer build and extension build. Now this morning on Linux the extension gives
this error (after updating and building slicer):
Error(s):
CLI executable: /home/reckbo/.config/NA-MIC/Extensions-22162/UKFTractography/lib/Slicer-4.2/cli-modules/UKFTractography
/home/reckbo/.config/NA-MIC/Extensions-22162/UKFTractography/lib/Slicer-4.2/cli-modules/UKFTractography: error while loading shared libraries: libITKDeprecated-4.4.so.1: cannot open shared object file: No such file or directory
CLI executable: /home/reckbo/.config/NA-MIC/Extensions-22162/UKFTractography/lib/Slicer-4.2/cli-modules/UKFTractography
Failed to retrieve Xml Description
Fail to instantiate module "UKFTractography"

any ideas?

Also there was no mac build last night.

TagsNo tags attached.

Relationships

related to 0003730 closedjcfr Additional launcher setting are not added to the environment 
related to 0003771 closedjcfr After installing an extension, Slicer fails to load slicer/vtk/.. python module 

Activities

lassoan

lassoan

2013-07-10 10:52

developer   ~0008991

The problem is the same with the stable (Slicer 4.2.2-1) release.
lassoan

lassoan

2013-07-10 11:09

developer   ~0008992

If I manually add the /data/image/home/usr/staff/lasso/.config/NA-MIC/Extensions-22162/LoadableExtensionTemplate/lib/Slicer-4.2/qt-loadable-modules directory to the LD_LIBRARY_PATH path before starting Slicer then everything works.
jcfr

jcfr

2013-07-12 08:48

administrator   ~0009025

Fixed in r22170
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22170
lassoan

lassoan

2013-10-23 21:29

developer   ~0010214

Unfortunately, this issue is still present in Slicer-4.3.1. It fails exactly the same way on my linux computer and also reported by a user (http://na-mic.org/Mantis/view.php?id=3456).

If I add the following lines to the SlicerLauncherSettings.ini file's [LibraryPaths] section then everything works well:

15\path=/data/image/home/usr/staff/lasso/.config/NA-MIC/Extensions-22599/MatlabBridge/lib/Slicer-4.3/qt-loadable-modules
16\path=/data/image/home/usr/staff/lasso/.config/NA-MIC/Extensions-22599/MatlabBridge/lib/Slicer-4.3/cli-modules

This may be related to the OS version, permissions, or other configuration settings, as I can reproduce the error on a server running Ubuntu 10.04.4 LTS, but not on a virtual machine with running Ubuntu 12.04 LTS.
lassoan

lassoan

2014-04-24 18:48

developer   ~0011667

Extension install fails for one more linux user:
http://slicer-devel.65872.n3.nabble.com/Saving-the-scene-tt4031452.html

It might not be the highest priority but probably should not be set to low priority.
lassoan

lassoan

2014-05-12 07:04

developer   ~0011719

Reports keep coming...

From: slicer-users-bounces@bwh.harvard.edu [mailto:slicer-users-bounces@bwh.harvard.edu] On Behalf Of Csaba Pinter
Sent: May 8, 2014 1:20 PM
To: Csaba Pinter; Strugari, Matthew SCA
Cc: slicer-users@bwh.harvard.edu
Subject: Re: [slicer-users] SlicerRT

Hi Matthew,

I have the same problem, see
https://dl.dropboxusercontent.com/u/3143581/screenshots/20140507_LinuxSlicerRTModules.png

Please try to apply the workaround as explained here:
http://www.na-mic.org/Bug/view.php?id=3218 (comment on 2013-10-24)

Let me know how it goes!

Cheers,
csaba

From: slicer-users-bounces@bwh.harvard.edu [mailto:slicer-users-bounces@bwh.harvard.edu] On Behalf Of Csaba Pinter
Sent: May 6, 2014 18:00
To: Strugari, Matthew SCA
Cc: slicer-users@bwh.harvard.edu
Subject: Re: [slicer-users] SlicerRT

Re-including the Slicer users mailing list...

SlicerRT have worked on Ubuntu 12.04 and we didn’t release a new version since then, so I don’t have an obvious answer. I’ll check tomorrow on my Linux computer in the lab.

Cheers,
csaba

From: Strugari, Matthew SCA [mailto:Matthew.Strugari@saskcancer.ca]
Sent: Tuesday, May 06, 2014 17:46
To: Csaba Pinter
Subject: RE: SlicerRT

Hi Csaba,

The Radiotherapy category does not show up and none of the of modules are present within the entire loaded module list.

Matthew

-----Original Message-----
From: Csaba Pinter [mailto:csaba.pinter@queensu.ca]
Sent: Tue 5/6/2014 15:42
To: Strugari, Matthew SCA
Cc: slicer-users@bwh.harvard.edu
Subject: RE: SlicerRT

Re-including the Slicer users mailing list...

The SlicerRT extension does not show up as an individual module, but as several modules in the Radiotherapy category. See module descriptions here:
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
Can you find these?

csaba

From: Strugari, Matthew SCA [mailto:Matthew.Strugari@saskcancer.ca]
Sent: Tuesday, May 06, 2014 17:07
To: Csaba Pinter
Subject: RE: SlicerRT

I am using the Linux platform. Specifically Ubuntu 12.04.

I have not been able to use SlicerRT since the March 14th nightly build. The module is displayed as installed and enabled but it does not show up anywhere within Slicer.

Matthew

-----Original Message-----
From: Csaba Pinter [mailto:csaba.pinter@queensu.ca]
Sent: Tue 5/6/2014 14:34
To: Strugari, Matthew SCA
Subject: RE: SlicerRT

Which platform are you on?

In the last several days the nightly builds got unstable due to migration from VTK version 5 to 6, so in any case I suggest using the nightly for April 24 (when the last successful Windows build happened).

csaba

From: slicer-users-bounces@bwh.harvard.edu<mailto:slicer-users-bounces@bwh.harvard.edu> [mailto:slicer-users-bounces@bwh.harvard.edu] On Behalf Of Strugari, Matthew SCA
Sent: May 6, 2014 11:19
To: slicer-users@bwh.harvard.edu<mailto:slicer-users@bwh.harvard.edu>
Subject: [slicer-users] SlicerRT

How can I get the SlicerRT module to load in the Slicer nightly builds? I have installed it through the Extensions Manager but I have not been able to load and use it on the last few nightly builds.

Thanks.

Matthew
lassoan

lassoan

2014-05-12 07:08

developer   ~0011720

Another probable occurrence:

On Mon, May 12, 2014 at 5:43 AM, elena bresciani wrote:
Dear all,
I'm using 3D slicer 4.3.1 on linux-64, I downloaded successfully the Vmtk extension from the extension manager but I can't find it between modules. I restarted the application and checked that the module is enabled but I still can't find it.
Any suggestion?
Thank you very much
Best regards
Elena
pinter

pinter

2014-07-18 09:41

developer   ~0012194

Another occurrence:
http://slicer-devel.65872.n3.nabble.com/Install-extension-from-file-on-linux-td4032106.html
lassoan

lassoan

2014-07-18 11:05

developer   ~0012196

Apparently, many users have this issue (the above cases are just those that we hear about). It might not be the highest priority issue right now, but probably this issue should not stay at low priority.
jcfr

jcfr

2017-06-07 23:27

administrator   ~0014638

Fix committed to 2145-support-for-installing-extension-from-file branch.

Related Changesets

Slicer: 2145-support-for-installing-extension-from-file a12652fe

2013-07-12 12:47:38

jcfr

Details Diff 		BUG: Fix launcher settings to allow loading of extension in unix build tree

This commit restores the correct loading of extension installed in a Slicer
build tree. It contains a fix related to ITKv4 transition and fix related
to transition from DCMTK static libraries to shared libraries (r21914)

Following the transition to ITKv4, the libraries (*.so) were built in the
lib directory [1] whereas in ITKv3, the libraries were built in the bin
directory [2].

[1] https://github.com/Kitware/ITK/blob/1839b74bacfd455dd917b086466c882ed29606ba/CMakeLists.txt#L164-174
[2] https://github.com/Kitware/ITK/blob/v3.20.1/CMakeLists.txt#L93-99

Following the transition to using DCMTK shared libraries (r21914 [3]), a
follow-up commit (r21942 [4]) has been pushed to ensure Slicer could be
started from a build tree on windows.

[3] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21914
[4] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21942

In both case (ITKv4 and DCMTK), Slicer could be started successfully from
a build tree on Windows (thanks to the launcher settings), and started
successfully on Unix system (thanks to rpath). On the other hand, since
the launcher settings were incorrect on unix system, the loading of
installed extensions (having rpath stripped) in a unix build tree was
failing.

Fixes 0003218

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22170 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockCTKAppLauncherSettings.cmake Diff File

Issue History

Date Modified Username Field Change
2013-07-10 10:43 lassoan New Issue
2013-07-10 10:43 lassoan Status new => assigned
2013-07-10 10:43 lassoan Assigned To => jcfr
2013-07-10 10:52 lassoan Note Added: 0008991
2013-07-10 11:09 lassoan Note Added: 0008992
2013-07-10 11:12 jcfr Priority normal => high
2013-07-10 11:12 jcfr Target Version => Slicer 4.3.0
2013-07-12 08:48 jcfr Note Added: 0009025
2013-07-12 08:48 jcfr Status assigned => resolved
2013-07-12 08:48 jcfr Fixed in Version => Slicer 4.3.0
2013-07-12 08:48 jcfr Resolution open => fixed
2013-10-23 21:29 lassoan Note Added: 0010214
2013-10-23 21:30 lassoan Status resolved => assigned
2014-03-07 09:48 jcfr Priority high => low
2014-03-07 09:48 jcfr Status assigned => acknowledged
2014-03-07 09:48 jcfr Fixed in Version Slicer 4.3.0 =>
2014-03-07 09:48 jcfr Target Version Slicer 4.3.0 =>
2014-04-24 18:48 lassoan Note Added: 0011667
2014-05-12 07:04 lassoan Note Added: 0011719
2014-05-12 07:08 lassoan Note Added: 0011720
2014-07-18 09:41 pinter Note Added: 0012194
2014-07-18 11:05 lassoan Note Added: 0012196
2014-07-22 11:06 jcfr Relationship added related to 0003730
2014-07-22 13:50 jcfr Relationship added related to 0003771
2017-03-30 15:06 inorton Status acknowledged => closed
2017-03-30 15:06 inorton Fixed in Version => Slicer 4.5.0-1
2017-06-07 23:27 jcfr Changeset attached => Slicer 2145-support-for-installing-extension-from-file a12652fe
2017-06-07 23:27 jcfr Note Added: 0014638