mzR failed to open '.raw' file
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b.nota ▴ 340
@bnota-7379
Last seen 12 months ago
Netherlands

Hello,

I am trying to load proteomics '.raw' files into R with the mzR package, but I got an error message that it fails. I think it has something to do with the Rcpp version, because when I load the library I get a comment about the Rcpp version. I don't know how to fix it, any advice? Thanks in advance!

Ben

Here the code:

> library(mzR)
Loading required package: Rcpp
Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
>
> Ctrl9 <- openMSfile("Ctrl9.raw")
Failed to open file.
 Error in openMSfile("Ctrl9.raw") : Unable to create valid cRamp object.
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] mzR_2.6.3            Rcpp_0.12.7          BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] ProtGenerics_1.4.0  parallel_3.3.1      tools_3.3.1        
[4] Biobase_2.32.0      codetools_0.2-15    BiocGenerics_0.18.0

 

mzR .raw files • 1.1k views
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@laurent-gatto-5645
Last seen 2 days ago
Belgium

Indeed, mzR doesn't support vendor binary files. It supports all major open formats such as mzML, mzXML, ... You can convert your raw file into any of these using the msconvert software from proteowizard [1].

Best wishes,

Laurent

[1] http://proteowizard.sourceforge.net/

 

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Thank you for your quick reply, Laurent.

Do I understand correct that it is not possible to do the whole analysis in R then?

Kind regards,

Ben

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>Thank you for your quick reply, Laurent. Do I understand correct that >it is not possible to do the whole analysis in R then? Not sure what your whole analysis is, but once you have converted your files, there's a lot you can do in R. But possibly not everything. Have a look at the RforProteomics package vignettes for an overview. Best wishes, Laurent
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Entering edit mode
>Thank you for your quick reply, Laurent. Do I understand correct that >it is not possible to do the whole analysis in R then? Not sure what your whole analysis is, but once you have converted your files, there's a lot you can do in R. But possibly not everything. Have a look at the RforProteomics package vignettes for an overview. Best wishes, Laurent
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