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Question: R crashes when computing score on data from mzIdentML file
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gravatar for Diego Diez
2.9 years ago by
Diego Diez730
Japan
Diego Diez730 wrote:

I am testing the mzR package with some mzIdentML data following the instructions in section 3.2 of the vignette. When trying to extract the scores of each psm R crashes (see the relevant code below). When using the sample data used in the vignette (Tandem.mzid.gz in the msdata package) everything works as expected. My mzIdentML data was exported using Scaffold 4.4.5 (linux version).

> library(mzR)
Loading required package: Rcpp
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mzR_2.2.1   Rcpp_0.11.6

loaded via a namespace (and not attached):
[1] ProtGenerics_1.0.0  parallel_3.2.1      Biobase_2.28.0     
[4] codetools_0.2-11    BiocGenerics_0.14.0

> x <- openIDfile("150602Nakai_mus.mzid.gz")
> x
Identification file handle.
Filename:  foo.mzid.gz 
Number of psms:  1150 

> scr <- score(x)

 *** caught segfault ***
address 0xf1000013, cause 'memory not mapped'

Traceback:
 1: .External(list(name = "CppMethod__invoke_notvoid", address = ,     dll = list(name = "Rcpp", path = "/Library/Frameworks/R.framework/Versions/3.2_R/Resources/library/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = ,         info = ), numParameters = -1L),     , , .pointer)
 2: x@backend$getScore()
 3: .local(x, ...)
 4: score(x)
 5: score(x)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

mzr
ADD COMMENTlink modified 2.9 years ago by Laurent Gatto980 • written 2.9 years ago by Diego Diez730
1
gravatar for Laurent Gatto
2.9 years ago by
Laurent Gatto980
United Kingdom
Laurent Gatto980 wrote:

Dear Diego,

Thank you very much for the report. I have never tested any mzid files exported from Scaffold. Do you have this with every Scaffold file, of just that one? Could you check the mzIdentML version, although I don't think that should really matter. You could send the offending file for me to have a look, if you wish.

Could you also try to open the file with mzID package. It will be slower than mzR, but that would only be an issue if you have to process hundreds of files.

Hope this helps.

Laurent

 

ADD COMMENTlink written 2.9 years ago by Laurent Gatto980

Dear Laurent,

Thank you for your quick reply. I only have that single Scaffold file and no prospect of getting more soon. I checked the mzIdentML version looking at the header of the file and it seems to be 1.1.0. Also tried yesterday with the mzID package and it loaded fine, but I cannot run the score method on the obtained object (not that I really need to). Just to clarify, the file loaded fine with mzR, and could apply all the methods described in the vignette (section 3.2) up to score, which was the one causing the segfault. Unfortunately I am not sure if I can share the file with you at this moment. At any rate, I was just testing the packages with the data I had. I will most likely ask for the raw data to the core facility, and hopefully things will work better.

ADD REPLYlink written 2.9 years ago by Diego Diez730
Just to clear out, you have access to exactly the same information using mzID as mzR, so if it is critical for you you can still use mzID though the method to get scores will be different... Best Thomas > Den 16/07/2015 kl. 09.45 skrev Diego Diez [bioc] <noreply@bioconductor.org>: > > Activity on a post you are following on support.bioconductor.org > User Diego Diez wrote Comment: R crashes when computing score on data from mzIdentML file: > > Dear Laurent, > > Thank you for your quick reply. I only have that single Scaffold file and no prospect of getting more soon. I checked the mzIdentML version looking at the header of the file and it seems to be 1.1.0. Also tried yesterday with the mzID package and it loaded fine, but I cannot run the score method on the obtained object (not that I really need to). Just to clarify, the file loaded fine with mzR, and could apply all the methods described in the vignette (section 3.2) up to score, which was the one causing the segfault. Unfortunately I am not sure if I can share the file with you at this moment. At any rate, I was just testing the packages with the data I had. I will most likely ask for the raw data to the core facility, and hopefully things will work better. > > Post tags: mzr > > You may reply via email or visit C: R crashes when computing score on data from mzIdentML file
ADD REPLYlink written 2.9 years ago by Thomas Lin Pedersen70

Hi Thomas. That sounds great. I did not see in the vignette or can figure out from the methods listed in the mzID package which command should be used to obtain the scores. It is not critical but if I knew then I could test whether it also crashes R or not. Do you know how to obtain the scores with mzID?

ADD REPLYlink written 2.9 years ago by Diego Diez730

OK, one guess for the scores is to run flatten() on the mzID object and then access the "mascot:score" column in the resulting data.frame. If that is the proper way then it works just fine. Thank you.

ADD REPLYlink written 2.9 years ago by Diego Diez730

I think that's the right way.

ADD REPLYlink written 2.9 years ago by Laurent Gatto980

> Thank you for your quick reply. I only have that single Scaffold file and no prospect
> of getting more soon.I checked the mzIdentML version looking at the header of the
> file and it seems to be 1.1.0.

That's the correct version (although I think 1.0 should be supported too).

> Also tried yesterday with the mzID package and it loaded fine, but I cannot run the score
> method on the obtained object (not that I really need to).

Unfortunately, mzID and mzR do not have a consistent interface. I suppose the main reason is that they are very different under the hood, but it would be great to try to harmonise them, somehow.

> Just to clarify, the file loaded fine with mzR, and could apply all the methods described in the
> vignette (section 3.2) up to score, which was the one causing the segfault.

That could indicate that something is a bit fishy in the way Scaffold exports to mzid scores, some subtle difference in the syntax that make it incompatible with the underlying proteowizard C++ code from mzR.

> Unfortunately I am not sure if I can share the file with you at this moment. At any rate, I
> was just testing the packages with the data I had. I will most likely ask for the raw data to
> the core facility, and hopefully things will work better.

Don't hesitate to get back if you have any other questions.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Laurent Gatto980
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