0004041: packaging issues on MacOS version (at least on r24523) - MantisBT

ID	Project	Category	View Status	Date Submitted	Last Update

0004041	Slicer4	Core: Base Code	public	2015-09-09 07:15	2018-03-02 11:07

Reporter	fbudin	Assigned To	jcfr
Priority	normal	Severity	major	Reproducibility	always
Status	closed	Resolution	fixed
Product Version
Target Version		Fixed in Version	Slicer 4.6.0

Summary	0004041: packaging issues on MacOS version (at least on r24523)
Description	When Slicer starts, I get the following error messages in the log: Message 1: Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSDemonWarpLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSDemonWarpLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSDemonWarpLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSDWICleanupLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSDWICleanupLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKCommon-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSDWICleanupLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSFitLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSFitLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKCommon-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSFitLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSLabelStatsLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSLabelStatsLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSLabelStatsLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSResampleLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSResampleLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSResampleLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSResizeLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSResizeLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSResizeLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSROIAutoLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSROIAutoLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSROIAutoLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSStripRotationLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSStripRotationLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSStripRotationLib.dylib Reason: image not found) Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSTransformConvertLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSTransformConvertLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libBRAINSTransformConvertLib.dylib Reason: image not found) Message 2: Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libPerformMetricTestLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libPerformMetricTestLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKCommon-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libPerformMetricTestLib.dylib Reason: image not found) Message 3: Error(s): Cannot load library /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libVBRAINSDemonWarpLib.dylib: (dlopen(/Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libVBRAINSDemonWarpLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib Referenced from: /Users/fbudin/Desktop/Slicer.app/Contents/lib/Slicer-4.4/cli-modules/libVBRAINSDemonWarpLib.dylib Reason: image not found) This concerns mostly the BRAINSTool libraries. To fix it, I had to manually fix the rpath in the libraries using the following script: #!/bin/tcsh set searchFor="Dashboards" foreach myfile ($*) echo "File: $myfile" set myline=`otool -l $myfile \|grep $searchFor` foreach line ($myline) if(`echo $line \|grep -c $searchFor` > 0 ) then set libname=$line:t install_name_tool -change "$line" "@rpath/lib/Slicer-4.4/$libname" $myfile endif end end
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fbudin 2015-10-06 07:30 developer ~0013339	I just realized that the libraries from BRAINS are packaged twice in Slicer for the MacOS package: once in ./Contents/lib/Slicer-4.4/cli-modules, and once in ./Contents/lib/Slicer-4.4. I am not sure why this is the case, but the ones that are in ./Contents/lib/Slicer-4.4 are correctly patched to point to the libraries packaged in Slicer (eg: @rpath/lib/Slicer-4.4/libITKIOBMP-4.8.1.dylib), when the ones in ./Contents/lib/Slicer-4.4/cli-modules are not (eg: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib)

jcfr 2016-07-19 18:33 administrator ~0014044	Fixed in r25241 See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=25241

Import 2017-06-07 23:51:09: master 3fb107bc 2016-07-19 18:27:10 jcfr Details Diff	COMP: BRAINSTools: Address MacOSX packaging issue. Fix 0004041 $ git shortlog 7859819..47dc8e6 --no-merges Isaiah Norton (1): COMP: Address MacOSX packaging issue. The BRAINS CMAKE_OSX_RPATH default no longer matched the Slicer default [1]. Due to this setting, the RPATH for BRAINS libraries was not being detected and replaced correctly by the Slicer fixup_bundle procedure. Specifically, as far as I can tell, having a pre-set `@rpath` in the installed libraries caused the fixup_bundle procedure to copy the (fixed) libraries into the `Slicer-4.5` base directory, rather than fixing in-place the libraries in `Slicer-4.5/cli-modules`. This caused two copies of the libraries to be included in the distribution bundle [2], one of which was un-patched. This un-patched version is referred to by all other libraries, causing dlopen failures. The end result is that BRAINS could not be used in shared-library mode on Mac [3]. See: [1] https://github.com/Slicer/ITK/commit/8ac0d6013b76238f9d84de906c14b493addf8ac8 [2] http://www.na-mic.org/Bug/view.php?id=4041 [3] http://massmail.spl.harvard.edu/public-archives/slicer-users/2016/010782.html From: Isaiah Norton <isaiah.norton@gmail.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@25241 3bd1e089-480b-0410-8dfb-8563597acbee
	mod - SuperBuild.cmake		Diff File

Date Modified	Username	Field	Change
2015-09-09 07:15	fbudin	New Issue
2015-09-09 07:15	fbudin	Status	new => assigned
2015-09-09 07:15	fbudin	Assigned To	=> jcfr
2015-10-06 07:30	fbudin	Note Added: 0013339
2016-07-19 18:33	jcfr	Note Added: 0014044
2016-07-19 18:33	jcfr	Status	assigned => resolved
2016-07-19 18:33	jcfr	Fixed in Version	=> Slicer 4.6.0
2016-07-19 18:33	jcfr	Resolution	open => fixed
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master 3fb107bc
2018-03-02 11:07	jcfr	Status	resolved => closed