Running RnBeads (v1.2, BioC 3.2) fails at multiple steps
with this error message:

Error in DataFrame(..., check.names = FALSE) :
  formal argument "check.names" matched by multiple actual arguments

This can be traced to

11: DataFrame(..., check.names = FALSE)
10: is(mcols, "DataFrame")
9: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand,
       mcols = DataFrame(..., check.names = FALSE), seqlengths = seqlengths,
       seqinfo = seqinfo)
8: (function (seqnames = Rle(), ranges = NULL, strand = NULL, ...,
       seqlengths = NULL, seqinfo = NULL)
   {
       newGRanges("GRanges", seqnames = seqnames, ranges = ranges,
           strand = strand, mcols = DataFrame(..., check.names = FALSE),
           seqlengths = seqlengths, seqinfo = seqinfo)
   })(seqnames = c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1",
 ...

7: do.call(GRanges, param.list)
6: data.frame2GRanges(annot.s, chrom.column = "Chromosome", start.column = "Start",
       end.column = "End", strand.column = "Strand", assembly = assembly(rnb.set),
       sort.result = FALSE)
5: rnb.find.relative.site.coord(rnb.set, region.type, extend.by = extend.by)
4: rnb.plot.region.site.density(rnb.set, reg)
3: rnb.section.region.description(report, rnb.set, r.types)
2: rnb.run.exploratory(rnb.set, dir.reports)
1: rnb.run.analysis(dir.reports = report.dir, sample.sheet = sample.annotation,
       data.dir = idat.dir, data.type = "infinium.idat.dir")

The reason seems to be a recent change in GRanges (I'm using v 1.22.0) that does no longer require/accept check.names=F for maintaining column names:

p  = list()
p[["seqnames"]]=c("2","3","4")
p[["ranges"]]=IRanges(start=c(1,2,3), end=c(2,3,4), names=c("A","B","C"))
p[["strand"]]=c("+","+","-")
p[["var1"]]=c(7,8,9)
p[["Variable 2"]] = c(100,101,102)
do.call(GRanges, p)

GRanges object with 3 ranges and 2 metadata columns:
    seqnames    ranges strand |      var1 Variable 2
       <Rle> <IRanges>  <Rle> | <numeric>  <numeric>
  A        2    [1, 2]      + |         7        100
  B        3    [2, 3]      + |         8        101
  C        4    [3, 4]      - |         9        102
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

p[["check.names"]]=FALSE
do.call(GRanges, p)

Error in DataFrame(..., check.names = FALSE) :
  formal argument "check.names" matched by multiple actual arguments

Removing the "check.names" parameter in function data.frame2GRanges should make the pipeline work again.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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

other attached packages:
 [1] RnBeads_1.2.0                          
 [2] plyr_1.8.3                             
 [3] methylumi_2.16.0                       
 [4] minfi_1.16.0                           
 [5] bumphunter_1.10.0                      
 [6] locfit_1.5-9.1                         
 [7] iterators_1.0.8                        
 [8] foreach_1.4.3                          
 [9] Biostrings_2.38.0                      
[10] XVector_0.10.0                         
[11] SummarizedExperiment_1.0.0             
[12] lattice_0.20-33                        
[13] FDb.InfiniumMethylation.hg19_2.2.0     
[14] org.Hs.eg.db_3.2.3                     
[15] RSQLite_1.0.0                          
[16] DBI_0.3.1                              
[17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[18] GenomicFeatures_1.22.0                 
[19] AnnotationDbi_1.32.0                   
[20] reshape2_1.4.1                         
[21] scales_0.3.0                           
[22] Biobase_2.30.0                         
[23] illuminaio_0.12.0                      
[24] matrixStats_0.15.0                     
[25] limma_3.26.0                           
[26] gridExtra_2.0.0                        
[27] gplots_2.17.0                          
[28] ggplot2_1.0.1                          
[29] fields_8.3-5                           
[30] maps_3.0.0-2                           
[31] spam_1.2-1                             
[32] ff_2.2-13                              
[33] bit_1.1-12                             
[34] cluster_2.0.3                          
[35] RColorBrewer_1.1-2                     
[36] MASS_7.3-44                            
[37] GenomicRanges_1.22.0                   
[38] GenomeInfoDb_1.6.0                     
[39] IRanges_2.4.1                          
[40] S4Vectors_0.8.0                        
[41] BiocGenerics_0.16.0                    

Possibly this error is related to the version hiccup in BioC reported by Dan Tenenbaum earlier today in this list, since I installed all packages in the time interval in question. In this case it would predict that RnBead will break once the devel packages  of GRanges will be passed to production.

Hi,

You're using the current release version of GenomicRanges (1.22.0) so it doesn't look like this has anything to do with the hiccup in BioC reported by Dan earlier today (which was about devel packages making their way thru the release channel).

AFAICT what happens is the following: starting with BioC 3.2 (the current release) the GRanges() constructor was changed to always behave like if check.names=FALSE had been passed to it. As a result of this change, passing the check.names argument to it now causes an error. The entry describing that change in the NEWS file of the GenomicRanges package is:

    o GRanges() constructor no more mangles the names of the supplied metadata
       columns (e.g. if the column is "_tx_id").

There is no doubt that it could have been more explicit about passing the check.names argument now being an error.

Anyway, that change was made in devel before the BioC 3.2 release, and it seems that it broke RnBeads::data.frame2GRanges(). Unfortunately our build system didn't catch the problem because the RnBeads package contains almost no code that gets evaluated during R CMD check. And that is the real problem here IMO. More precisely: 106/120 code chunks in the vignette don't get evaluated (eval=FALSE); most man pages (including the man page for data.frame2GRanges()) either don't have examples or have them in \donttest{} directives; the package contains some unit tests but they seem very limited. This is not conform to our guidelines.

Fixing data.frame2GRanges() is easy, I'll leave it to the maintainers. Alternatively they could use makeGRangesFromDataFrame() from the GenomicRanges package and get rid of data.frame2GRanges(). BUT MOST IMPORTANTLY, I would urge them to consider (a) having running examples in all their man pages (ideally every exported function should be called at least once), and (b) put evaluated code chunks in their vignette (using eval=FALSE should be the exception, not the rule). Improving the test coverage (only 9% right now) wouldn't hurt either.

I guess chances are good that while they do this they'll find out that some of the code that is currently not evaluated is not working properly and needs to be fixed. Which is exactly what the whole exercise is about.

Sorry for the grumbling...

H.

Yes, the function in RnBeads to convert an annotation table to a data.frame was using the check.names parameter explicitly. We fixed this in RnBeads 1.3.

Hervé Pagès is right that almost all code snippets in the documentation (help pages and vignettes) are not executed. The reason is that there is a time limit on testing Bioconductor packages: R CMD check must complete within 5 minutes. Executing each example includes loading RnBeads, and thus enabling all these small chunks of test code extends the package building process to a few hours.

We created the function rnb.run.example as a solution, which not only presents the functionality of the package but also essentially tests most of its functions. We run these examples (they take more than 96 hours) before releasing new major versions. No measure is perfect, of course; you see that we sometimes overlook incompatibility issues arising when other packages are updated.

Yassen