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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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Error with openMSfile in RStudio #6

Closed thomasp85 closed 10 years ago

thomasp85 commented 10 years ago

The following error occurs when trying to load files using RStudio. The same files work fine with the regular R gui:

> ms <- openMSfile('/Users/Thomas/Desktop/004-CM_005.mzML')
Error in rampModule$open(filename, declaredOnly = TRUE) : 
  [MSDataFile::readFile()] Unsupported file format.

The problem has been observed with a range of files and on a range of systems (both mac and win). The problem is not constant (sometimes a file works in RStudio), but has only been observed using RStudio.

sneumann commented 10 years ago

I can confirm this, I had similar problems earlier on Linux. Can we have your sessionInfo() ? If you don't already, could you check the mzR devel version, which has an updated pwiz library for mzML parsing ? Thanks, Steffen

thomasp85 commented 10 years ago 
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

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

other attached packages:
[1] mzR_1.10.0  Rcpp_0.11.1 Rtsne_0.8  

loaded via a namespace (and not attached):
[1] Biobase_2.24.0      BiocGenerics_0.10.0 codetools_0.2-8     parallel_3.1.0      tools_3.1.0

I'll test out the devel version when I return from BioC2014

lgatto commented 10 years ago

@sneumann

I can confirm this, I had similar problems earlier on Linux.

Was this using RStudio or other interface?

sneumann commented 10 years ago

I have no issues with 

library(xcms)
xr <- xcmsRaw(system.file("microtofq/MM14.mzML", package="msdata"))
sessionInfo()

on rstudio Version 0.98.507

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
...
other attached packages:
[1] xcms_1.41.0        Biobase_2.22.0     BiocGenerics_0.8.0 mzR_1.11.9         Rcpp_0.11.1

@thomasp85, can you confirm that I can close the issue ?

thomasp85 commented 10 years ago

I no longer get the error with the system up to date. The problem has been though, that the error appeared in a random way (not linked to file), so I cannot say that it has disappeared with 100% certainty. But do close the issue and if it reappears we will open it again…

best

Thomas

On 02 Sep 2014, at 16:02, sneumann notifications@github.com wrote:

I have no issues with

library(xcms) xr <- xcmsRaw(system.file("microtofq/MM14.mzML", package="msdata")) sessionInfo() on rstudio Version 0.98.507

R version 3.1.1 (2014-07-10) Platform: x86_64-pc-linux-gnu (64-bit) ... other attached packages: [1] xcms_1.41.0 Biobase_2.22.0 BiocGenerics_0.8.0 mzR_1.11.9 Rcpp_0.11.1
@thomasp85, can you confirm that I can close the issue ?

— Reply to this email directly or view it on GitHub.

lgatto commented 10 years ago

Closing, as the random error seems to have disappeared. Feel free to re-open if shows up again.

axelmuller commented 8 years ago

Hi, I have a similar mzR & Rstudio problem. My problem appears to be constant and non-random though. Every time I run openMSfile() a fatal error occurs and the R session gets aborted. However, when running R from the terminal mzR works fine.

thanks for your help, Axel

the output for sessionInfo() is:

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

library(mzR) Loading required package: Rcpp sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora 23 (Workstation Edition)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] mzR_2.5.3 Rcpp_0.12.3

loaded via a namespace (and not attached): [1] ProtGenerics_1.2.1 parallel_3.2.3 tools_3.2.3 Biobase_2.30.0 codetools_0.2-14 BiocGenerics_0.16.1