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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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Update PSI-MS.obo derived cv.cpp and cv.hpp #210

Closed sneumann closed 4 years ago

lgatto commented 4 years ago

Thanks, Steffen. Are you waiting for somebody to merge? Or just go ahead.

jorainer commented 4 years ago

There are still some failing tests that have to be fixed.

lgatto commented 4 years ago

Weird!?! Travis isn't complaining. Are there tests that are run only locally?

sneumann commented 4 years ago

Before merging I'd like someone to confirm that this fixes https://github.com/sneumann/mzR/issues/170 Or even better, we get a unit test checking for #170 . I have no idea here how to (easily) reproduce. Yours, Steffen

shubham1637 commented 4 years ago

I tried to install this update, but couldn't install the package. install_github("sneumann/mzR", ref = "feature/updateCV20191015")

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'ProtGenerics' 1.14.0 is being loaded, but >= 1.17.3 is required
ERROR: lazy loading failed for package 'mzR'
* removing 'C:/Users/shubh/Documents/R/win-library/3.5/mzR'
In R CMD INSTALL
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/shubh/AppData/Local/Temp/RtmpQ1WXbh/file19687571659f/mzR_2.19.8.tar.gz’ had non-zero exit status

I have R version 3.5.1

lgatto commented 4 years ago

@shubham1637 - you will need a more recent version of R to get the latest Bioconductor packages (for instance ProtGenerics).

shubham1637 commented 4 years ago

I tried again on R version 3.6.1. Same error

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace ‘ProtGenerics’ 1.16.0 is being loaded, but >= 1.17.3 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘mzR’
* removing ‘/home/shubham/R/x86_64-pc-linux-gnu-library/3.6/mzR’
Error: Failed to install 'mzR' from GitHub:
  (converted from warning) installation of package ‘/tmp/Rtmpi4EULF/fileeac696ba4e8/mzR_2.19.8.tar.gz’ had non-zero exit status
lgatto commented 4 years ago

You will also need the development version of Bioc (which is only available with the very latest version of R). I'm testing it at the moment.

lgatto commented 4 years ago 
BiocManager::install("sneumann/mzR", ref = "feature/updateCV20191015")

builds fine on:

> sessionInfo()
R version 3.6.1 Patched (2019-09-14 r77192)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.8.0
LAPACK: /usr/lib/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] 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     

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1
sneumann commented 4 years ago

Maybe this also fixes #215