XCMS mzML support

Topic: XCMS mzML support (Read 8492 times) previous topic - next topic

XCMS mzML support

July 04, 2011, 05:06:46 AM

Hi,

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

Re: XCMS mzML support

Reply #1 – July 04, 2011, 06:27:33 AM

Hi Stephan,

mzML is a hot topic, and some changes are ahead.
There is a preliminary package mzR which you can
find at https://github.com/sneumann/mzR

This package grew out of the mzML code in XCMS,
and (c|sh)ould become the affyIO for MS in Bioconductor.

Before mzR is accepted into BioC, you will have to use
the patched XCMS version at https://github.com/sneumann/xcms
(which is highly experimental !!!!)

Please do report all your findings, we already have
a collection of files where e.g. MS2 data information
is absent, but depending on your use case it might be sufficient.

Yours,
Steffen

Re: XCMS mzML support

Reply #2 – July 05, 2011, 07:45:23 AM

Hi Steffen,

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

Re: XCMS mzML support

Reply #3 – July 05, 2011, 12:07:01 PM

Hi,

the packages were less than 24h online when I posted,

Which OS and versions do you use ?
I just verified that mzR does not yet build on Windows,
we're working on that.

Yours,
Steffen

Re: XCMS mzML support

Reply #4 – July 06, 2011, 02:53:39 AM

Hi,

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

Re: XCMS mzML support

Reply #5 – July 07, 2011, 02:09:37 AM

Hi,

Quote from: "Stephan"

Problems only start to occur when I try to get mzML support to work by out-commenting the corresponding entries in 'Makevars'.

Ah sorry, you don't do that! mzR is shipping all that pwiz stuff,
and my patched xcms is calling the IO directly from mzR.
Just install my mzR and XCMS as is, and you should be fine.

I'll try to figure how to add the packages as downloads from github,
once the packages are halfway stable. I am currently working on the windows builds.

Yours,
Steffen

Re: XCMS mzML support

Reply #6 – July 08, 2011, 05:58:20 AM

Hi,

Quote from: "sneumann"

I'll try to figure how to add the packages as downloads from github,
once the packages are halfway stable. I am currently working on the windows builds.

It seems it is working on windows, so here are some preliminary downloads:

https://github.com/sneumann/mzR/zipball/0.5.4 (source package)
https://github.com/downloads/sneumann/mzR/mzR_0.5.4.zip (Win binary)

Again, you'd need my custom XCMS from github to use these.

Yours,
Steffen

Re: XCMS mzML support

Reply #7 – July 11, 2011, 04:47:27 AM

Hi Steffen,

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

Re: XCMS mzML support

Reply #8 – July 19, 2011, 02:54:29 AM

Hi Stephan,

Quote from: "Stephan"

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?

I can reproduce that with your file, even just

Code: [Select]

mz <- openMSfile("20101004.mzML")

takes ages. So that's a problem with either pwiz or the RAMPadapter in there,
and it needs to be fixed before XCMS could possibly adopt mzR I/O.

Thanks for your report,
yours,
Steffen