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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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Invalid cvParam error on openMSfile, potentially needs updated cv terms #229

Closed jwinget closed 3 years ago

jwinget commented 3 years ago

Using mzR 2.23.0, When trying to read a file using openMSfile I get an error that ends with: Error in pwizModule$open(filename): Invalid cvParam accession "1003112".

This appears to be related to previous issues #170 and #215 which were addressed in #210 . I checked the list of cv IDs here and 1003112 is in the list, so I am curious if this list has simply not been merged into the current version of mzR.

lgatto commented 3 years ago

This is the same type of issue, but despite #210 having apparently been merged, I don't see that CV parameter in the mzR code. It might still be missing from mzR or upstream (pwiz, which we rely on).

@sneumann - do you know of this one?

sneumann commented 3 years ago

To get 1003112 in, we'd need a new pull request analogous to #210 which copies the same files over from their upstream https://github.com/ProteoWizard/pwiz/tree/master/pwiz/data/common Yours, Steffen

sneumann commented 3 years ago

Hi @jwinget , can you confirm that the github master branch solves your issue ? Yours, Steffen

jwinget commented 3 years ago

I'm having trouble installing from github:

> remotes::install_github("sneumann/mzR")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo sneumann/mzR@HEAD
Skipping 5 packages ahead of CRAN: BiocGenerics, Rhdf5lib, zlibbioc, ProtGenerics, Biobase
√  checking for file 'C:\Users\winget.jm\AppData\Local\Temp\RtmpiY8ypE\remotes1f80413da5d12\sneumann-mzR-809f9f5/DESCRIPTION' (1.2s)
-  preparing 'mzR': (48.3s)
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts (737ms)
-  checking for empty or unneeded directories (58.2s)
-  building 'mzR_2.21.2.tar.gz' (464ms)
   Warning: file 'mzR/cleanup' did not have execute permissions: corrected
   Warning: file 'mzR/configure' did not have execute permissions: corrected

* installing *source* package 'mzR' ...
** using staged installation
** libs
Error: (converted from warning) this package has a non-empty 'configure.win' file,
so building only the main architecture
* removing 'C:/Users/winget.jm/OneDrive/OneDrive - Procter and Gamble/R/R-4.0.1/library/mzR'
Error: Failed to install 'mzR' from GitHub:
  (converted from warning) installation of package ‘C:/Users/winget.jm/AppData/Local/Temp/RtmpiY8ypE/file1f80420433974/mzR_2.21.2.tar.gz’ had non-zero exit status

I was able to install 2.23.0 from BioConductor devel:

BiocManager::install(version='devel')

BiocManager::install("mzR")

This installation succeeded but I got the same cvParam error when I tried to open a file.

I also tried downloading a zip file from github and installing that but it also doesn't seem to succeed - I just get "no package" errors when I try to load it.

sneumann commented 3 years ago

Ah, building on windows tends to be a bit tricky. 1) We can push to BioC and then you can try 2.23.1. OR 2) You send me an example file to test here. It can be a blank, a QC or any non-secret mzML file. Yours, Steffen

sneumann commented 3 years ago

Hi, I can confirm that 2.23.0 couldn't read the blank.mzML I received, and that the current version (i.e. 2.23.1) can happily do echo 'library(mzR) ; ms <- openMSfile("blank.mzML") ; h <- header(ms)' | R --vanilla, error message gone. I did not check any specific content, though. Yours, Steffen