[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=721112

Susi Lehtola  changed:

   What|Removed |Added

 Blocks|505154 (FE-SCITECH) |





Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=505154
[Bug 505154] Tracker: Review Requests for Science and Technology related
packages
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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=721112

Ankur Sinha (FranciscoD)  changed:

   What|Removed |Added

 Status|ASSIGNED|CLOSED
 Resolution|--- |WONTFIX
Last Closed||2018-01-07 16:46:08



--- Comment #20 from Ankur Sinha (FranciscoD)  ---
I'm going to close this as WONTFIX. I'm not working on medical applications
anymore so I'm not the best person to maintain this package now.

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=721112

Richard Shaw hobbes1...@gmail.com changed:

   What|Removed |Added

 CC|hobbes1...@gmail.com|
   Assignee|hobbes1...@gmail.com|nob...@fedoraproject.org



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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=721112
Bug 721112 depends on bug 483663, which changed state.

Bug 483663 Summary: Review Request: tetgen - A tetrahedral mesh generator
https://bugzilla.redhat.com/show_bug.cgi?id=483663

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=721112

Dominik 'Rathann' Mierzejewski domi...@greysector.net changed:

   What|Removed |Added

   See Also|https://bugzilla.redhat.com |
   |/show_bug.cgi?id=483663 |
 Depends On||483663



--- Comment #19 from Dominik 'Rathann' Mierzejewski domi...@greysector.net ---
tetgen is free software now and I've just approved Sandro's package, so it can
be unbundled from vmtk.


Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=483663
[Bug 483663] Review Request: tetgen - A tetrahedral mesh generator
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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=721112

Dominik 'Rathann' Mierzejewski domi...@greysector.net changed:

   What|Removed |Added

 Blocks||505154 (FE-SCITECH)




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=505154
[Bug 505154] Tracker: Review Requests for Science and Technology related
packages
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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=721112

Bug 721112 depends on bug 539387, which changed state.

Bug 539387 Summary: Review Request: InsightToolkit - Medical imaging processing 
library
https://bugzilla.redhat.com/show_bug.cgi?id=539387

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #18 from Mario Ceresa mrcer...@gmail.com ---
Thanks Ankur for your efforts in packaging vmtk. You might be able to use vmtk
with netgen, which is free:
http://www.vmtk.org/Tutorials/NetgenWay/

We hope to finish ITK anytime soon -if more bundled software doesn't show up,
of course ;)

Best,
Mario

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=721112

Ankur Sinha (FranciscoD) sanjay.an...@gmail.com changed:

   What|Removed |Added

   See Also||https://bugzilla.redhat.com
   ||/show_bug.cgi?id=483663

--- Comment #17 from Ankur Sinha (FranciscoD) sanjay.an...@gmail.com ---
Hrm, cannot still build it. Depends on ITK. Also found more bundled software
*sigh* in the 1.0.1 release:

Doxygen  OpenNL  Stellar_1.0  tetgen1.4.3. I also see that tetgen is NOT free
software, as noted in the review ticket:

https://bugzilla.redhat.com/show_bug.cgi?id=483663

I'm afraid this might mean we need to drop this package altogether. I'll see if
I can speak to upstream about this.

I'll at least package stellar in the mean time:
http://www.cs.berkeley.edu/~jrs/stellar/

Thanks,
Warm regards,
Ankur

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=721112

Miroslav Suchý msu...@redhat.com changed:

   What|Removed |Added

 CC||msu...@redhat.com
  Flags||needinfo?(sanjay.ankur@gmai
   ||l.com)

--- Comment #15 from Miroslav Suchý msu...@redhat.com ---
Ping? Any progress here? Or we can close this review?

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=721112

Ankur Sinha (FranciscoD) sanjay.an...@gmail.com changed:

   What|Removed |Added

  Flags|needinfo?(sanjay.ankur@gmai |
   |l.com)  |

--- Comment #16 from Ankur Sinha (FranciscoD) sanjay.an...@gmail.com ---
Hi,

VXL has *just* been included in the repositories. I'm away and will not be able
to work on this review for another month. Please feel free to start a new
review if you need to.

Thanks,
Warm regards,
Ankur

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=721112

Bug 721112 depends on bug 567086, which changed state.

Bug 567086 Summary: Review Request: VXL - C++ Libraries for Computer Vision 
Research and Implementation
https://bugzilla.redhat.com/show_bug.cgi?id=567086

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |CURRENTRELEASE

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.


https://bugzilla.redhat.com/show_bug.cgi?id=721112

Bug 721112 depends on bug 720998, which changed state.

Bug 720998 Summary: Review Request: OpenNL - A library for solving sparse 
linear systems
https://bugzilla.redhat.com/show_bug.cgi?id=720998

   What|Old Value   |New Value

 Resolution||ERRATA
 Status|ON_QA   |CLOSED

--- Comment #14 from Ankur Sinha sanjay.an...@gmail.com 2011-08-13 03:30:55 
EDT ---
hi Richard, 

I'm waiting on vxl to be packaged. Mario's working on it. I can't get vmtk to
build in mock at the moment. Some issue with the vxl package. 

Thanks,
Ankur

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #13 from Richard Shaw hobbes1...@gmail.com 2011-07-26 14:27:21 
EDT ---
Ankur,

I found out that I was wrong about the whole python_sitelib/sitearch thing. If
there are ANY C python modules in the package then everything, including the
pure python modules go in sitearch.

Richard

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

Richard Shaw hobbes1...@gmail.com changed:

   What|Removed |Added

 Depends on||705885

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #7 from Richard Shaw hobbes1...@gmail.com 2011-07-21 10:51:19 EDT 
---
Ok, after installing the other BuildRequires I got my cmake patch working!

Next issue: 
Are you on a 32bit or 64bit system? I noticed that make install doesn't put
the libraries in /usr/lib64 on x86_64 systems. I added a %ifarch conditional to
move /usr/lib to /usr/lib64 on x86_64 and ppc64 systems.

Second issue:
I noticed it put all the python files in /usr/lib/vmtk/vmtk. I think all of
these should go into %{python_sitelib}/vmtk, right?

Richard

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #8 from Richard Shaw hobbes1...@gmail.com 2011-07-21 12:11:02 EDT 
---
Update:

I need your help to figure out what exactly is supposed to go into the -devel
package. 

I saw you had the python scripts going in there. Are they the source files
for the python libraries or are they separate from them?

I find the whole /usr/lib/vmtk/vmtk structure that make install produces
confusing...

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

Please do not reply directly to this email. All additional
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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #9 from Ankur Sinha sanjay.an...@gmail.com 2011-07-21 14:11:47 
EDT ---
 
 Well, I was trying for a few reasons. One, I'm trying to improve my cmake-fu 
 :)
 Also, hacking the link.txt is not ideal. If I can come up with a good cmake
 patch then maybe upstream will accept it (which is the best case). 
 
 Also, in retrospect, I'm wondering if we should have renamed the header file
 for OpenNL to be consistent with the library name, i.e.: nl.h - opennl.h
 
 What do you think?
 

Hrm, we certainly could do that. Although, we'd have to first look at it's
effects. I'll look into it.

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #10 from Ankur Sinha sanjay.an...@gmail.com 2011-07-21 14:19:33 
EDT ---
(In reply to comment #7)
 Ok, after installing the other BuildRequires I got my cmake patch working!
 
 Next issue: 
 Are you on a 32bit or 64bit system? I noticed that make install doesn't put
 the libraries in /usr/lib64 on x86_64 systems. I added a %ifarch conditional 
 to
 move /usr/lib to /usr/lib64 on x86_64 and ppc64 systems.

I run mock builds for a 32 bit system. I haven't tried on an x86_64 yet. 

I just looked at CMakeLists.txt. I think setting VMTK_MODULE_INSTALL_LIB_DIR
would fix this.
-DVMTK_MODULE_INSTALL_LIB_DIR:STRING=$RPM_BUILD_ROOT/%{_libdir}/ or something
on these lines. Again, I'll try it out and confirm.

 
 Second issue:
 I noticed it put all the python files in /usr/lib/vmtk/vmtk. I think all of
 these should go into %{python_sitelib}/vmtk, right?

Yes. Should. Again, setting VMTK_MODULE_INSTALL_LIB_DIR just might do the
trick.

I'll try all of this out and post :)

Thanks,
Ankur

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #11 from Ankur Sinha sanjay.an...@gmail.com 2011-07-21 14:21:05 
EDT ---
(In reply to comment #8)
 Update:
 
 I need your help to figure out what exactly is supposed to go into the -devel
 package. 
 
 I saw you had the python scripts going in there. Are they the source files
 for the python libraries or are they separate from them?
 
 I find the whole /usr/lib/vmtk/vmtk structure that make install produces
 confusing...

I'll try getting in touch with upstream for suggestions.

I'm going to be unavailable until Monday. I'll only respond after that. I
regret the inconvenience this will cause :/

Thanks,
Ankur

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #12 from Richard Shaw hobbes1...@gmail.com 2011-07-21 15:43:16 
EDT ---
(In reply to comment #10)
 (In reply to comment #7)
  Ok, after installing the other BuildRequires I got my cmake patch working!
  
  Next issue: 
  Are you on a 32bit or 64bit system? I noticed that make install doesn't 
  put
  the libraries in /usr/lib64 on x86_64 systems. I added a %ifarch 
  conditional to
  move /usr/lib to /usr/lib64 on x86_64 and ppc64 systems.
 
 I run mock builds for a 32 bit system. I haven't tried on an x86_64 yet. 

Ok, my updated spec/SRPM file[1] fixes that.


 I just looked at CMakeLists.txt. I think setting VMTK_MODULE_INSTALL_LIB_DIR
 would fix this.
 -DVMTK_MODULE_INSTALL_LIB_DIR:STRING=$RPM_BUILD_ROOT/%{_libdir}/ or something
 on these lines. Again, I'll try it out and confirm.

Didn't work for me. It appears to just control the /usr or /usr/local part of
the path, I set it to /lib64 (since it adds /usr seperately) and it ended up
putting the files in /usr/lib64/lib/vmtk/vmtk... 



  Second issue:
  I noticed it put all the python files in /usr/lib/vmtk/vmtk. I think all of
  these should go into %{python_sitelib}/vmtk, right?
 
 Yes. Should. Again, setting VMTK_MODULE_INSTALL_LIB_DIR just might do the
 trick.

Probably will not work but worth a try... The problem is all the .py files need
to go in %{python_sitelib} which is /usr/lib/pythonX.X/site-packages/ while the
.so python libraries need to go in %{python_sitearch} which can be the same as
%{python_sitelib} for 32bit systems but is /usr/lib64... for 64 bit systems.
This is easier just to manage manually.

The only side effect I've found so far is that one (and only one) of the python
.so libraries actually has a SONAME and the .so symlink is getting pulled into
the regular package instead of the -devel package. Should be easy to fix
though, there are other bigger problems...

One of the big problems is actually with vtk, not vmtk. It provides a
necessary library, libVPIC.so, but only in the -devel package, not in the main
package. Because of that I had to add a Requires for vtk-devel which pulls in a
bunch of dependencies we don't need just to get the one file we do need. I
added a BZ reference in the comment so we can watch to see when it get's fixed.

The other problem seems to be that some of the libraries from vmtk can't find
other libraries it provides. In other words, it's finding libraries in
/usr/lib{,64} but not the ones in /usr/lib{,64}/vmtk... Not sure why that is
happening.

That's enough for now I think!

[1] http://hobbes1069.fedorapeople.org/vmtk/vmtk-0.9.0-2.fc14.src.rpm

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

[bugzilla]

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #5 from Ankur Sinha sanjay.an...@gmail.com 2011-07-20 10:43:12 
EDT ---
Hi Richard,

(In reply to comment #4)
 I've made some progress trying to get it to build against the OpenNL package
 but I can't really test it because of:
 
 rpmbuild -bc rpmbuild/vmtk/SPECS/vmtk.spec
 error: Failed build dependencies:
 InsightToolkit-devel is needed by vmtk-0.9.0-2.fc14.x86_64
 vxl-devel is needed by vmtk-0.9.0-2.fc14.x86_64
 
 Because of that I've added the review request of vxl and InsightToolkit as a
 blocker for this Review Request.

I'm sorry, I forgot to mention that you need to build ITK and vxl for your
fedora system before you can test it. I for example, have a local mock repo
with these packages. 

[root@ankur ~]# ls /tmp/mock-repo/InsightToolkit-* /tmp/mock-repo/vxl-*
/tmp/mock-repo/InsightToolkit-3.20.0-5.fc16.i686.rpm   
/tmp/mock-repo/vxl-1.14.0-1.fc16.i686.rpm
/tmp/mock-repo/InsightToolkit-3.20.0-5.fc16.src.rpm
/tmp/mock-repo/vxl-1.14.0-1.fc16.src.rpm
/tmp/mock-repo/InsightToolkit-debuginfo-3.20.0-5.fc16.i686.rpm 
/tmp/mock-repo/vxl-debuginfo-1.14.0-1.fc16.i686.rpm
/tmp/mock-repo/InsightToolkit-devel-3.20.0-5.fc16.i686.rpm 
/tmp/mock-repo/vxl-devel-1.14.0-1.fc16.i686.rpm
/tmp/mock-repo/InsightToolkit-doc-3.20.0-5.fc16.i686.rpm   
/tmp/mock-repo/vxl-doc-1.14.0-1.fc16.i686.rpm
/tmp/mock-repo/InsightToolkit-examples-3.20.0-5.fc16.i686.rpm



 
 Back to this review :)
 
 The only part of the project that appears to use OpenNL is the
 DifferentialGeometry sub-project. 
 
 I've added a cmake option, USE_EXTERN_OPENNL to the main CMakeLists.txt and 
 I'm
 working on getting the headers and linking working in the CMakeLists.txt for
 DifferentialGeometry.


The package works with the fedora OpenNL which I packaged recently. You don't
need to make any tweaks. The changes I've made in the prep and build sections
are enough. 

At the moment, gdcm is broken in rawhide,(after the latest libpoppler soname
bump) so I can't build it as well :/

Thanks,
Ankur

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

--- Comment #6 from Richard Shaw hobbes1...@gmail.com 2011-07-20 11:43:55 EDT 
---
(In reply to comment #5)
 (In reply to comment #4)
  I've made some progress trying to get it to build against the OpenNL package
  but I can't really test it because of:
  
  rpmbuild -bc rpmbuild/vmtk/SPECS/vmtk.spec
  error: Failed build dependencies:
  InsightToolkit-devel is needed by vmtk-0.9.0-2.fc14.x86_64
  vxl-devel is needed by vmtk-0.9.0-2.fc14.x86_64
  
  Because of that I've added the review request of vxl and InsightToolkit as a
  blocker for this Review Request.
 
 I'm sorry, I forgot to mention that you need to build ITK and vxl for your
 fedora system before you can test it. I for example, have a local mock repo
 with these packages. 

Yup, I run a local repo as well. I'll try that.


  The only part of the project that appears to use OpenNL is the
  DifferentialGeometry sub-project. 
  
  I've added a cmake option, USE_EXTERN_OPENNL to the main CMakeLists.txt and 
  I'm
  working on getting the headers and linking working in the CMakeLists.txt for
  DifferentialGeometry.
 
 
 The package works with the fedora OpenNL which I packaged recently. You don't
 need to make any tweaks. The changes I've made in the prep and build sections
 are enough. 

Well, I was trying for a few reasons. One, I'm trying to improve my cmake-fu :)
Also, hacking the link.txt is not ideal. If I can come up with a good cmake
patch then maybe upstream will accept it (which is the best case). 

Also, in retrospect, I'm wondering if we should have renamed the header file
for OpenNL to be consistent with the library name, i.e.: nl.h - opennl.h

What do you think?

Richard

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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Richard Shaw hobbes1...@gmail.com changed:

   What|Removed |Added

 AssignedTo|nob...@fedoraproject.org|hobbes1...@gmail.com
   Flag||fedora-review?

--- Comment #2 from Richard Shaw hobbes1...@gmail.com 2011-07-19 12:01:54 EDT 
---
I'll take this one for you.

Some quick observations.

1. The %description is WAY TO LONG. 

2. I think the -devel package requires should include %{?_isa} since this isn't
a noarch pacakge:

Requires:  %{name}%{?_isa} = %{version}-%{release}

3. Could use more comments especially in %prep. I assume you're mainly removing
bundled libraries there.

Don't worry about posting a new release just yet until I can do a more in-depth
spec review.

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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Ankur Sinha sanjay.an...@gmail.com changed:

   What|Removed |Added

 Status|NEW |ASSIGNED

--- Comment #3 from Ankur Sinha sanjay.an...@gmail.com 2011-07-19 13:39:58 
EDT ---
Thank you Richard! :)

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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https://bugzilla.redhat.com/show_bug.cgi?id=721112

Richard Shaw hobbes1...@gmail.com changed:

   What|Removed |Added

 Depends on||567086(vxl),
   ||539387(InsightToolkit)

--- Comment #4 from Richard Shaw hobbes1...@gmail.com 2011-07-19 14:53:04 EDT 
---
I've made some progress trying to get it to build against the OpenNL package
but I can't really test it because of:

rpmbuild -bc rpmbuild/vmtk/SPECS/vmtk.spec
error: Failed build dependencies:
InsightToolkit-devel is needed by vmtk-0.9.0-2.fc14.x86_64
vxl-devel is needed by vmtk-0.9.0-2.fc14.x86_64

Because of that I've added the review request of vxl and InsightToolkit as a
blocker for this Review Request.

Back to this review :)

The only part of the project that appears to use OpenNL is the
DifferentialGeometry sub-project. 

I've added a cmake option, USE_EXTERN_OPENNL to the main CMakeLists.txt and I'm
working on getting the headers and linking working in the CMakeLists.txt for
DifferentialGeometry.

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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--- Comment #1 from Ankur Sinha sanjay.an...@gmail.com 2011-07-14 12:50:21 
EDT ---
Cleaned up rpmlint errors. Now there are only warnings

http://ankursinha.fedorapeople.org/vmtk/vmtk-0.9.0-2.fc15.src.rpm

http://ankursinha.fedorapeople.org/vmtk/vmtk.spec

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[Bug 721112] Review Request: vmtk - The Vascular Modeling Toolkit

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Ankur Sinha sanjay.an...@gmail.com changed:

   What|Removed |Added

 Blocks||673841(fedora-medical)
 Depends on||720998(OpenNL)
  Alias||vmtk

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