[Pairoscope-help] pairoscope build on RHEL 5.5

[Powers, D. <Po...@do...>]

Hi -

I wanted to share that I have built pairoscope on a RHEL 5.5 environment.  I'm not sure if others have done this or not.  Since I did not find any obvious installs on this platform through Google searching, I thought I would share how I did it, in case it might help others down the road.

( A ) Environment specifics

OS: Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Kernel: Linux  2.6.18-194.el5 #1 SMP Tue Mar 16 21:52:39 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
gcc: 4.6.1

( B ) Steps to build pairoscope:

( 1 ) build pixman 0.10.0 library from source
( 2 ) build cairo 1.6.0 from source
( 3 ) build samtools 0.1.18 from source
( 4 ) build cmake 2.8.8 from source
( 5 ) build pairoscope 0.2 from source

( C) Pairoscope specific changes

After going through ccmake and configuring the environment and building the Makefile, you can execute "make" on the command line.

I found that when I executed the "make" command, there were a lot of "error: 'function' was not declared in this scope as shown below...

[foo@bar]% make
Scanning dependencies of target pairoscope
[ 12%] Building CXX object CMakeFiles/pairoscope.dir/src/pairoscope.cpp.o
[ 25%] Building CXX object CMakeFiles/pairoscope.dir/src/YAlignmentFetcher.cpp.o
[ 37%] Building CXX object CMakeFiles/pairoscope.dir/src/YGeneView.cpp.o
In file included from /share/apps/pairoscope/src/YGeneView.h:16:0,
                 from /share/apps/pairoscope/src/YGeneView.cpp:8:
/share/apps/pairoscope/src/YTranscript.h: In constructor 'YTranscript::YTranscript()':
/share/apps/pairoscope/src/YTranscript.h:32:30: error: 'NULL' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp: In constructor 'YGeneView::YGeneView(cairo_t*, YRect, const char*, unsigned int, unsigned int, std::vector<YTranscript*>*, bool, double)':
/share/apps/pairoscope/src/YGeneView.cpp:13:32: error: 'strlen' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:15:34: error: 'strcpy' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp: In member function 'virtual void YGeneView::draw()':
/share/apps/pairoscope/src/YGeneView.cpp:44:13: error: 'stderr' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:44:53: error: 'fprintf' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:117:100: error: 'snprintf' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp: In member function 'int YGeneView::transcriptStatusPriority(char*)':
/share/apps/pairoscope/src/YGeneView.cpp:208:31: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:211:32: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:214:34: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:217:32: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:220:28: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:223:31: error: 'strcmp' was not declared in this scope
make[2]: *** [CMakeFiles/pairoscope.dir/src/YGeneView.cpp.o] Error 1
make[1]: *** [CMakeFiles/pairoscope.dir/all] Error 2
make: *** [all] Error 2

When I fixed these first errors, there were more that followed from various files.  Here is the list of five ".h" and ".cpp" files and simple changes that I made to the files to get them to compile successfully:

( 1 ) ../pairoscope/src/YTranscript.h
      add the following:
      #include <cstddef>

  ( 2 ) ../pairoscope/src/YGeneView.h
      add the following:
      #include <cstring>
      #include <stdio.h>

  ( 3 ) ../pairoscope/src/YPairView.h
      add the following:
      #include <cstdlib>

  ( 4 ) ../pairoscope/src/YDepthView.h
      add the following:
      #include <stdio.h>
      #include <cstring>

  ( 5 ) ../pairoscope/src/YPairView.cpp
      add the following:
      #include <cstring>

After I made these changes, I was able to successfully compile pairoscope as shown below:

[foo@bar]% make
[ 12%] Building CXX object CMakeFiles/pairoscope.dir/src/pairoscope.cpp.o
[ 25%] Building CXX object CMakeFiles/pairoscope.dir/src/YAlignmentFetcher.cpp.o
[ 37%] Building CXX object CMakeFiles/pairoscope.dir/src/YGeneView.cpp.o
[ 50%] Building CXX object CMakeFiles/pairoscope.dir/src/YPairView.cpp.o
[ 62%] Building CXX object CMakeFiles/pairoscope.dir/src/YView.cpp.o
[ 75%] Building CXX object CMakeFiles/pairoscope.dir/src/YDepthView.cpp.o
[ 87%] Building CXX object CMakeFiles/pairoscope.dir/src/YGenomeView.cpp.o
[100%] Building CXX object CMakeFiles/pairoscope.dir/src/YTranscriptFetcher.cpp.o
Linking CXX executable pairoscope
[100%] Built target pairoscope
[foo@bar]%

I hope this helps someone else!

Dave