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XCMS / Re: XCMS mzML support
thanks, I got it to work.
The parser works fine but it takes a very long time (more than 10 min) to read in a simple 20 MB mzML file. Is there any particular reason for that?
Regards,
Stephan
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thanks, I got it to work.
The parser works fine but it takes a very long time (more than 10 min) to read in a simple 20 MB mzML file. Is there any particular reason for that?
Regards,
Stephan
2
XCMS / Re: XCMS mzML support
I'm on a LinuxMint 11 system (64 bit), which probably leaves space for a lot of things that could potentially be wrong.
BiocLite's version of XCMS works fine and so does your patched version.
Problems only start to occur when I try to get mzML support to work by out-commenting the corresponding entries in 'Makevars'.
"unable to load shared object '/home/beisken/R/x86_64-pc-linux-gnu-library/2.12/xcms/libs/xcms.so':
/home/beisken/R/x86_64-pc-linux-gnu-library/2.12/xcms/libs/xcms.so: undefined symbol: _ZNK4pwiz6msdata11RAMPAdapter9scanCountEv"
I'll look into the problem.
Regards,
Stephan
3
XCMS / Re: XCMS mzML support
many thanks for your reply.
I have successfully installed mzR and its dependency Rcpp. I had to re-archive mzR though.
For the patched XCMS version I outcommented XMLWriter.o in 'Makevars' because my compiler didn't like its library calls, i.e., it couldn't find the 'endian.hpp'.
It compiles fine but terminates while trying to test-load the program complaining about an undefined symbol in xcms.so. Guess there are some version incompatibilities?!
Have you come across that yet?
Best,
Stephan
4
XCMS / XCMS mzML support
following the instructions on the wiki page (http://http://metlinwiki.scripps.edu/mediawiki/index.php/EnableMzMLSupport), I tried to enable mzML support in XCMS.
However, if I run 'R CMD INSTALL' on the xcms_1.26.1.tar.gz (contains pulled in and modified files), the compilation fails because it cannot find 'boost/integer/endian.hpp'.
Apparently R uses the external C++ libraries rather than the ones in the archive.
Does anyone happen to know how I can use the pulled in libraries?
Regards,
Stephan