checks are failing due to mzData

rietho / IPO

A Tool for automated Optimization of XCMS Parameters

http://bioconductor.org/packages/IPO/

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checks are failing due to mzData #71

Closed rietho closed 1 year ago

rietho commented 2 years ago

In #69 @sneumann helped to move examples from mzData to mzML after xcms dropped mzData support. However, checks in Bioconductor are still failing with:

  1 Test Suite : 
  IPO RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_ipo: Error in xcmsSet(mtbls2files[1:2], method = "centWave", peakwidth = c(12,  : 
    Chromatographic peak detection failed for all files! The first error was: Error in .mzRBackendFromContent(x): Could not determine file type for /home/biocbuild/bbs-3.15-bioc/R/library/mtbls2/mzData/MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818.mzData

Something is still going wrong in the fixed test cases.

rietho commented 2 years ago

I am not sure what causes this issue. I tested locally and the tests were running fine.

It appears that some how in https://github.com/rietho/IPO/blob/master/inst/unitTests/test_optimizeXcmsSet.R#L50 the following lines do still read in .mzData files when running on Bioconductor:

  mtbls2files <- list.files(paste(find.package("mtbls2"), "/mzML", sep=""), 
                            full.names=TRUE)

sneumann commented 2 years ago

Bioconductor is not building packages from this github repo. The Build report mentions: git_last_commit_date: 2022-04-26 11:34:28 -0400 (Tue, 26 Apr 2022) which is still without our fix.

Instead there is a BioC git at git@git.bioconductor.org:packages/IPO , see https://contributions.bioconductor.org/git-version-control.html and especially the FAQ section.

Yours, Steffen

rietho commented 1 year ago

IPO is now building without error in the devel version of Bioconductor: http://bioconductor.org/checkResults/devel/bioc-LATEST/IPO/ (the one warning is the deprecation warning)

The next steps are (per comment here)

~~Push the fix to the RELEASE_3_15 branch~~ to get to builds without error.
~~Update the maintainer email address to my gmail address (so that emails are not going to my old deactivated JR email address)~~
Email bioc-devel@r-project.org cc: lori.shepherd@roswellpark.org to un-deprecate.

rietho commented 1 year ago

Builds are now running fine. I emailed to ask for un-deprecation.

rietho commented 1 year ago

IPO is now undeprecated. So this issue is good to close.