Compilation error about isaac_aligner

[come-raczy]

Check if sys/stat.h exists (probably in /usr/include/sys/stat.h). If it doesn't, install the appropriate development package for your distribution.
If this doesn't help, could you please provide the following information:

• the output of 'gcc --version'
• the output of 'uname -a'
• the top 50 lines of the output of the configure script

Thanks,
Come

[choishingwan]

I have been able to solve the problem by explicitly setting all the:
export LIBRARY_PATH=$LIBRARY_PATH:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=$C_INCLUDE_PATH:$LD_LIBRARY_PATH
export CPATH=$C_PATH:$LD_LIBRARY_PATH
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$LD_LIBRARY_PATH
set to my LD_LIBRARY_PATH

However, I now got the following error while make:
[ 38%] Building CXX object c++/lib/options/CMakeFiles/isaac_options.dir/AlignOptions.cpp.o
In file included from /home/sam/programmes/sequencing_general/isaac_aligner_src/src/c++/include/workflow/alignWorkflow/BclBgzfDataSource.hh:35:0,
from /home/sam/programmes/sequencing_general/isaac_aligner_src/src/c++/include/workflow/alignWorkflow/SelectMatchesTransition.hh:54,
from /home/sam/programmes/sequencing_general/isaac_aligner_src/src/c++/include/workflow/AlignWorkflow.hh:55,
from /home/sam/programmes/sequencing_general/isaac_aligner_src/src/c++/lib/workflow/AlignWorkflow.cpp:34:
/home/sam/programmes/sequencing_general/isaac_aligner_src/src/c++/include/rta/BclBgzfTileReader.hh: In member function ‘unsigned int isaac::rta::BclBgzfTileReader::loadCompressedBcl(std::istream&, const boost::filesystem::path&, const isaac::rta::CycleBciMapper::VirtualOffset&, char_, std::size_t)’:
/home/sam/programmes/sequencing_general/isaac_aligner_src/src/c++/include/rta/BclBgzfTileReader.hh:146:17: error: cannot bind bitfield ‘tileOffset.isaac::rta::CycleBciMapper::VirtualOffset::compressedOffset’ to ‘long unsigned int&’
make[3]: *_* [c++/lib/workflow/CMakeFiles/isaac_workflow.dir/AlignWorkflow.cpp.o] Error 1
make[2]: *** [c++/lib/workflow/CMakeFiles/isaac_workflow.dir/all] Error 2
make[1]: *** [c++/bin/CMakeFiles/isaac-align.dir/rule] Error 2
make: *** [isaac-align] Error 2

Our gcc version is:

gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

and the uname -a is
Linux statgenpro.psychiatry.hku.hk 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

I suspect there is something to do with the gcc version?

Thank you for your help

[come-raczy]

Setting the include paths to the library paths seems strange.
It might be good to try from fresh with a clean environment (with none of these variables set). Or are any of these needed (e.g. to support some ubuntuesque feature like multiarch or something like that)?
Do you have another version of boost installed on your system? Or are you using the version of boost packaged with iSAAC?
Can you also provide:
echo $LIBRARY
echo $LD_LIBRARY_PATH
echo $LIBRARY_PATH
echo $C_INCLUDE_PATH
echo $C_PATH
echo $CPLUS_INCLUDE_PATH
env | grep -i boost

[choishingwan]

I have the same problem even if I have deactivated the boost library (mine was 1.55.0) and used the one provided by ISSAC, I have clean up my environment a bit and the output of the commands are:

sam@statgenpro:~$ echo $LD_LIBRARY_PATH
/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-linu x-gnu:

sam@statgenpro:~$ echo $LIBRARY_PATH
:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-lin ux-gnu:

sam@statgenpro:~$ echo $C_INCLUDE_PATH
:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-lin ux-gnu:

sam@statgenpro:~$ echo $C_PATH

sam@statgenpro:~$ echo $CPLUS_INCLUDE_PATH
:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-lin ux-gnu:

sam@statgenpro:~$ env | grep -i boost
CPLUS_INCLUDE_PATH=:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-linux-gnu:
LIBRARY_PATH=:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-linux-gnu:
LD_LIBRARY_PATH=/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-linux-gnu:
CPATH=:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-linux-gnu:
C_INCLUDE_PATH=:/home/sam/programmes/sequencing_general/bamtools/lib/:/home/sam/programmes/lib/boost_lib/lib:/usr/include/x86_64-linux-gnu:

(My sys/stat.h was located at /usr/include/x86_64-linux-gnu instead of /usr/include)

Also, I cannot arrive the part of the error using the boost library provided. I need to use my personal boost library in order to get to the error part. Else, I will get stuck at:

-- Doxygen: DOXYGEN_EXECUTABLE-NOTFOUND. Dot: /usr/bin/dot.
-- Could NOT find Markdown (missing: MARKDOWN_EXECUTABLE)
-- Markdown: MARKDOWN_EXECUTABLE-NOTFOUND.
-- Configuring incomplete, errors occurred!
Couldn't configure the project:

[come-raczy]

Looks like Roman has already fixed and pushed the issue. Can you please pull the new version and try again?
Thanks

[choishingwan]

Thank you, the new version has solved all the problems.