Conflicting feature variable names when using combineFeatures twice with CV

[lgatto]

See this question for details:

1. calling combineFeatures (with CV = TRUE) to combine spectra to peptides generates fvarLabels CV.TMT6.126 ...
2. calling combineFeatures (with CV = TRUE) to combine peptides to proteins tries to generate fvarLabels CV.TMT6.126 ... and fails with error

Error in value[[3L]](cond) : duplicate 'row.names' are not allowed
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?
In addition: Warning message:
non-unique values when setting 'row.names': ‘CV.TMT6.126’, ‘CV.TMT6.127’, ‘CV.TMT6.128’, ‘CV.TMT6.129’, ‘CV.TMT6.130’, ‘CV.TMT6.131’

TODO

1. better error message
2. if CV fvarLabels are already present, add a suffix.

[PDiracDelta]

For me, putting CV = FALSE does not resolve the issue. However, solution 2 mentioned in your answer to the mentioned question does work.

[lgatto]

As noted on the support site, it should be cv in lower case:

> 
> library("MSnbase")
> library("rpx")
> px1 <- PXDataset("PXD000001")
> mztab <- pxget(px1, "PXD000001_mztab.txt")
Downloading 1 file
/home/lg390/tmp/PXD000001_mztab.txt already present.
> spec <- readMzTabData(mztab, what = "PEP", version = "0.9")
Warning message:
Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details. 
> pep <- combineFeatures(spec, groupBy = fData(spec)$sequence, fun = sum)
> ## expecting error
> prot <- combineFeatures(pep, groupBy = fData(pep)$accession, fun = sum)
Error in value[[3L]](cond) : duplicate 'row.names' are not allowed
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?
In addition: Warning message:
non-unique values when setting 'row.names': ‘CV.sub[1]’, ‘CV.sub[2]’, ‘CV.sub[3]’, ‘CV.sub[4]’, ‘CV.sub[5]’, ‘CV.sub[6]’ 
> ## now works
> prot <- combineFeatures(pep, groupBy = fData(pep)$accession, fun = sum, cv = FALSE)

I'll still see to make some changes in the package to avoid this, or at least make it explicit why the error happens.

[lgatto]

This is now properly addressed. If there is already a set of CV feature variables, the new set will be suffixed with a .1 (or .2, ... if the previous index already exists).