cmpiling ITK on CentOs - pcre/swig error

Beginner Questions
1

Hello,

I am trying to compile ITK on a CentOs 7 cluster. During the compilation, I get the error -
[ 56%] Completed ‘PCRE’
[ 56%] Built target PCRE
…
[ 56%] No update step for ‘swig’
[ 56%] No patch step for ‘swig’
[ 56%] Performing configure step for ‘swig’
– Swig configure successfully completed.
[ 56%] Performing build step for ‘swig’
Swig/misc.o: In function Swig_string_regex': misc.c:(.text+0x2223): undefined reference to pcre_free’
misc.c:(.text+0x22b7): undefined reference to pcre_compile' misc.c:(.text+0x22f6): undefined reference to pcre_exec’
misc.c:(.text+0x2334): undefined reference to pcre_free' Swig/misc.o: In function Swig_pcre_version’:
misc.c:(.text+0x2405): undefined reference to pcre_version' Swig/naming.o: In function name_regexmatch_value’:
naming.c:(.text+0x32): undefined reference to pcre_compile' naming.c:(.text+0x77): undefined reference to pcre_exec’
naming.c:(.text+0x83): undefined reference to `pcre_free’
collect2: error: ld returned 1 exit status
make[5]: *** [eswig] Error 1
make[4]: *** [all] Error 2
make[3]: *** [source] Error 2
make[2]: *** [Wrapping/Generators/SwigInterface/swig-prefix/src/swig-stamp/swig-build] Error 2
make[1]: *** [Wrapping/Generators/SwigInterface/CMakeFiles/swig.dir/all] Error 2
make: *** [all] Error 2

Is the swig needed? Can I skip it by choosing some option in the configure step? how do I get over the problem that it does not recognize pcre even after it was compiled during the build process?

Best,
Yaron

2

Which version of ITK are you trying to compile? pcre_free problem sounds familiar.

3

InsightToolkit-5.1.1

Yes, I read that people had it on MacOs, and there was a solution, but I am building on Linux CentOs 7.

Yaron

4

Welcome to the ITK community @Yaron! :sunny:

There should not be any issues with the CentOS 7 build – I built it yesterday :-).

Are any SWIG-related CMake options changed from their default? What are the CMake configuration options changed from the defaults?

5

Dear Matt,

Thanks for your answer.
I think I found the error. Yesterday, I built InsightToolkit-5.1.2 with the default configuration and it worked.

However, if I tried to activate the building of examples (BUILD_EXAMPLES), the python wrapper (ITK_WRAP_PYTHON), and the Module_SimpleITKFilters it fails with the same error about swig and PCRE.

The reason is that I try to install InsightToolkit on a CentOs Cluster. I do not have an administer privileges so I install it in an alternative path (to be used later on using the module package of clusters computational gridI).

After configuration, I use the command: make DESTDIR=PATH_TO_INSTALL install

As a result, make creates the following folders:

A. PATH_TO_INSTALL/usr

B. PATH_TO_INSTALL/ORIGINAL_PATH_OF_BINARIES_BUILD/Wrapping/Generators/SwigInterface/PCRE/

In the first, it places all the ITK compiles files, and in the second the PCRE.

So, when one of BUILD_EXAMPLES, ITK_WRAP_PYTHON, or module_SimpleITKFilters needs swig (I do not know which one), it does not find it due to the additional ORIGINAL_PATH_OF_BINARIES_BUILD created by cmake.

In conclusion, there is an error in the cmake file regarding the way that it install PCRE in an alternative path.

Yaron

6

Dear Yaron,

Thanks for the update.

Could you please try disabling Module_SimpleITKFilters then, installing to an alternative path.

If the behavior is the same, please try disabling ITK_WRAP_PYTHON, then installing to an alternative path.

Either of those may be building SWIG / PCRE, but SWIG / PCRE should not be installed into the install tree.

Thanks,
Matt