[Insight-users] trouble with InsightApplications-4.1.1

Wed May 30 11:22:31 EDT 2012

I see no such issues on my builds.

Let's start over.

1) What operating system are you running?

On Tue, May 29, 2012 at 2:25 PM, Luke Hetrick <lhetrick at nnu.edu> wrote:
> I reran the previous commands to see if that made a difference, it did not.
> I was given the same error report as before. Here is the commands I ran in
> my terminal:
>
> mkdir ITK-Build
> cd ITK-Build
> ccmake ../Superbuild .
> make
>
> then the errors begin. Thank you for your time and help on this issue.
>
>
> On Tue, May 29, 2012 at 11:34 AM, Luke Hetrick <lhetrick at nnu.edu> wrote:
>>
>> I am using the superbuild directory as my source directory for the ccmake
>> command. To clarify, after I have untarred the tar ball, I am doing the
>> following on the newly extracted InsightApplications-4.1.1 directory:
>>
>> mkdir ITK-Build
>> cd ITK-Build
>> ccmake ../Superbuild
>>
>> At that point, I get the typical cmake dialog where I configure once to
>> get some options, configure twice, then I generate the makefiles. Then I use
>> the following commands in the terminal:
>>
>> make
>>
>> Those are the exact command I have used and the exact errors I have been
>> given. I just realized that I might have messed up on the ccamke command. I
>> forgot to make it ccmake ../Superbuild . so I am trying that at the moment.
>>
>>
>>
>>
>> On Tue, May 29, 2012 at 11:22 AM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>>>
>>> Just to be clear, you are running make your superbuild directory?
>>>
>>> On Tue, May 29, 2012 at 12:45 PM, Luke Hetrick <lhetrick at nnu.edu> wrote:
>>> > Bill,
>>> >
>>> >    Well the good news is that it broke in the same spot it did last
>>> > time so
>>> > at least the error is repeatable. About 2 hrs after I ran the make
>>> > command
>>> > after I generated the makefiles, my terminal gives me this:
>>> >
>>> > Linking CXX executable imageRegTool
>>> > ../../FLTK-install/lib/libfltk.a(flstring.c.o): IN function
>>> > 'fl_strlcat':
>>> > flstring.c:(.text+0x0): multiple defination of 'fl_strlcat'
>>> >
>>> > ../VolviewPlugIns/bin/libITKFlFileWriter.a(flstring.c.o):flstring.c:(.text+0x0):
>>> > first defined here
>>> > ../../FLTK-install/lib/libfltk.a(flstring.c.o): In function
>>> > 'flstrlcpy':
>>> > flstring.c:(.text+0xd1): multiple defination of 'fl_strlcpy'
>>> >
>>> > ../VolviewPlugIns/bin/libITKFlFileWriter.a(flstring.c.o):flstring.c:(.text+0xd1):
>>> > first defined here
>>> > collect2: ld returned 1 exit status
>>> > make[5]: ***
>>> > [LandmarkInitializedMutualInformationRegistration/imageRegTool]
>>> > Error 1
>>> > make[4]: ***
>>> >
>>> > [LandmarkInitializedMutualInformationRegistration/CMakeFIles/imageRegTool.dir/all]
>>> > Error 2
>>> > make[3]: *** [all] Error 2
>>> > make[2]: *** [ITKApps-prefix/src/ITKApps-stamp/ITKApps-build] Error 2
>>> > make[1]: *** [CMakeFiles/ITKApps.dir/all] Error 2
>>> > make: *** [all] Error 2
>>> >
>>> > It successfully copies VTK and ITK from the website and can build those
>>> > directories correctly but it keeps failing about 43% in the ITKApps
>>> > section
>>> > after I run the 'make' command in the terminal. Thanks again for your
>>> > help,
>>> > at this point I know I am in a bit over my head.
>>> >
>>> > Luke H
>>> >
>>> >
>>> > On Mon, May 28, 2012 at 10:50 AM, Bill Lorensen
>>> > <bill.lorensen at gmail.com>
>>> > wrote:
>>> >>
>>> >> Output from the compilation is what I want.
>>> >>
>>> >> I do not set any cmake options for the superbuild.
>>> >>
>>> >> On Mon, May 28, 2012 at 12:30 PM, Luke Hetrick <lhetrick at nnu.edu>
>>> >> wrote:
>>> >> > Is an error log the error that the compiler throws when it runs into
>>> >> > something that causes it to fail? If so, I can run the superbuild
>>> >> > tomorrow
>>> >> > when I get to work and get error to you about noon tomorrow. What
>>> >> > options in
>>> >> > the configuration stage of the ccmake are you running when using the
>>> >> > superbuild as the source file?
>>> >> >
>>> >> >
>>> >> > On Sun, May 27, 2012 at 11:03 AM, Bill Lorensen
>>> >> > <bill.lorensen at gmail.com>
>>> >> > wrote:
>>> >> >>
>>> >> >> The superbuild should work. Can you send the error log?
>>> >> >>
>>> >> >> Bill
>>> >> >>
>>> >> >> On Thu, May 24, 2012 at 5:57 PM, Luke Hetrick <lhetrick at nnu.edu>
>>> >> >> wrote:
>>> >> >> > Bill,
>>> >> >> >
>>> >> >> >     I guess I was a bit ambitious because I ran into another
>>> >> >> > error
>>> >> >> > after
>>> >> >> > it
>>> >> >> > ran for about 4 hrs or so. It went to linking the CXX executable
>>> >> >> > imageRegTool and throws a few more errors. This time is my
>>> >> >> > ../VolviewPlugIns/bin/libFlFileWriter.a(flstring.c: is where it
>>> >> >> > breaks.
>>> >> >> > You
>>> >> >> > were not kidding when you said this was tricky to compile? I
>>> >> >> > found
>>> >> >> > some
>>> >> >> > the
>>> >> >> > software for VolView online, is this also needed for
>>> >> >> > InsightApplications?
>>> >> >> >
>>> >> >> > Luke
>>> >> >> >
>>> >> >> > On Thu, May 24, 2012 at 2:47 PM, Bill Lorensen
>>> >> >> > <bill.lorensen at gmail.com>
>>> >> >> > wrote:
>>> >> >> >>
>>> >> >> >> Luke,
>>> >> >> >>
>>> >> >> >> Yes, I have been meaning to document the ITKApp's superbuild
>>> >> >> >> more
>>> >> >> >> completely
>>> >> >> >>
>>> >> >> >> Bill
>>> >> >> >>
>>> >> >> >> On Thu, May 24, 2012 at 4:11 PM, Luke Hetrick <lhetrick at nnu.edu>
>>> >> >> >> wrote:
>>> >> >> >> > Bill,
>>> >> >> >> >
>>> >> >> >> >     I hope I am not counting my chicks before they hatch but
>>> >> >> >> > looks
>>> >> >> >> > like
>>> >> >> >> > your
>>> >> >> >> > superbuild trick is working like a champ. I removed my
>>> >> >> >> > previous
>>> >> >> >> > InsightApplications-xxxxx and just used tar -zxvf again on the
>>> >> >> >> > source
>>> >> >> >> > then
>>> >> >> >> > after creating a bin directory instead of using ccmake ..
>>> >> >> >> > inside
>>> >> >> >> > my
>>> >> >> >> > bin
>>> >> >> >> > to
>>> >> >> >> > generate the make file, I tried ccmake ../SuperBuild and it is
>>> >> >> >> > just
>>> >> >> >> > building
>>> >> >> >> > away. Thank you for the help. If it is in your power, I would
>>> >> >> >> > try
>>> >> >> >> > to
>>> >> >> >> > mention
>>> >> >> >> > the superbuild technique on the wiki or on the README file.
>>> >> >> >> > But
>>> >> >> >> > thanks
>>> >> >> >> > again.
>>> >> >> >> >
>>> >> >> >> > Luke H
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > On Thu, May 24, 2012 at 11:19 AM, Bill Lorensen
>>> >> >> >> > <bill.lorensen at gmail.com>
>>> >> >> >> > wrote:
>>> >> >> >> >>
>>> >> >> >> >> Building the ITKApps is tricky. I suggest, as a staring point
>>> >> >> >> >> you
>>> >> >> >> >> use
>>> >> >> >> >> the ITKApp superbuild:
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> On Thu, May 24, 2012 at 12:00 PM, Luke Hetrick
>>> >> >> >> >> <lhetrick at nnu.edu>
>>> >> >> >> >> wrote:
>>> >> >> >> >> > Hello,
>>> >> >> >> >> >
>>> >> >> >> >> >     I am working on a project that requires ITK software so
>>> >> >> >> >> > I
>>> >> >> >> >> > have
>>> >> >> >> >> > begun
>>> >> >> >> >> > to
>>> >> >> >> >> > install all the bit and pieces to get it up and running. I
>>> >> >> >> >> > have
>>> >> >> >> >> > CMake-2.8.7
>>> >> >> >> >> > and have already successfully installed dcmtk and FLTK to
>>> >> >> >> >> > my
>>> >> >> >> >> > knowledge.
>>> >> >> >> >> > I
>>> >> >> >> >> > have also installed VTK and the InsightToolkit from the
>>> >> >> >> >> > kitware
>>> >> >> >> >> > website
>>> >> >> >> >> > always making sure to grab the latest versions. Now I am
>>> >> >> >> >> > trying
>>> >> >> >> >> > to
>>> >> >> >> >> > build
>>> >> >> >> >> > this last InsightApplications and I am getting errors in
>>> >> >> >> >> > the
>>> >> >> >> >> > "make"
>>> >> >> >> >> > process.
>>> >> >> >> >> > After running tar -zxvf on the tared/zipped tarball, I have
>>> >> >> >> >> > ran
>>> >> >> >> >> > the
>>> >> >> >> >> > following commands:
>>> >> >> >> >> >
>>> >> >> >> >> > mkdir Bin
>>> >> >> >> >> > cd Bin
>>> >> >> >> >> > ccmake .. (at this step I instructed it where my Python.h
>>> >> >> >> >> > file
>>> >> >> >> >> > is
>>> >> >> >> >> > and
>>> >> >> >> >> > where
>>> >> >> >> >> > various dcmtk include files were located)
>>> >> >> >> >> > make
>>> >> >> >> >> >
>>> >> >> >> >> > at the final step there, I am getting to about 70% then I
>>> >> >> >> >> > throw
>>> >> >> >> >> > this
>>> >> >> >> >> > error.
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > InsightApplications-4.1.1/Bin/DigitalArchive/FlDicomQueryChooser/flqcPreferencesGUI.cxx:3:0:
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > ~/Project/InsightApplications-4.1.1/Bin/DigitalArchive/FlDicomQueryChooser/fldqcPreferecnesGUI.h:8:32:
>>> >> >> >> >> > fatal error: FL/fl_file_chooser.H: No such file or
>>> >> >> >> >> > directory
>>> >> >> >> >> > compilation terminated.
>>> >> >> >> >> >
>>> >> >> >> >> > Does anyone have any idea why it is throwing this error? I
>>> >> >> >> >> > have
>>> >> >> >> >> > tried
>>> >> >> >> >> > to
>>> >> >> >> >> > follow the documentation pages for each of the other
>>> >> >> >> >> > software
>>> >> >> >> >> > needed
>>> >> >> >> >> > to
>>> >> >> >> >> > compile this as well but I am running out of ideas to try.
>>> >> >> >> >> >
>>> >> >> >> >> > Luke H
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > _____________________________________
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>>> >> >> >> >> >
>>> >> >> >> >> > Visit other Kitware open-source projects at
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>>> >> >> >> >> >
>>> >> >> >> >> > Kitware offers ITK Training Courses, for more information
>>> >> >> >> >> > visit:
>>> >> >> >> >> > http://www.kitware.com/products/protraining.php
>>> >> >> >> >> >
>>> >> >> >> >> > Please keep messages on-topic and check the ITK FAQ at:
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>>> >> >> >> >> >
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>>> >> >> >> >> >
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
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>>
>

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