[Debian-med-packaging] Failed test in GenomicFeatures

[Andreas Tille]

Hi,

as I previously wrote I'm working on BioConductor packages of verison
3.0.  When running the test suite of GenomicFeatures 1.18.0 I got one
error:

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
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> require("GenomicFeatures")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:GenomeInfoDb':

    species

> GenomicFeatures:::.test()
Download and preprocess the 'transcripts' data frame ... Timing stopped at: 0.212 0.008 270.411 
Error in .makeBiomartTranscripts(filters, values, mart, transcript_ids,  : 
  invalid transcript ids: ENST00000341724, ENST00000400839
Deducing exon rank from relative coordinates provided
Estimating transcript ranges.
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Prepare the 'metadata' data frame ... metadata: OK
extracting transcript information
Extracting gene IDs
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Deducing exon rank from relative coordinates provided
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .deduceExonRankings(exs, format = "gff") :
  Infering Exon Rankings.  If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName
2: In if (is.na(chrominfo)) { :
  the condition has length > 1 and only the first element will be used


RUNIT TEST PROTOCOL -- Wed Oct 22 09:23:56 2014 
*********************************************** 
Number of test functions: 29 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 29 test functions, 1 error, 0 failures
ERROR in test_makeTranscriptDbFromBiomart: Error in .makeBiomartTranscripts(filters, values, mart, transcript_ids,  : 
  invalid transcript ids: ENST00000341724, ENST00000400839

Test files with failing tests

   test_makeTranscriptDbFromBiomart.R 
     test_makeTranscriptDbFromBiomart 


Error in BiocGenerics:::testPackage("GenomicFeatures") : 
  unit tests failed for package GenomicFeatures
Calls: <Anonymous> -> <Anonymous>
Execution halted


Please let me know if you need any further information to reproduce the
problem.


Kind regards

      Andreas.

-- 
http://fam-tille.de