[Debian-med-packaging] [devteam-bioc] Failed test in GenomicFeatures

Thu Oct 23 06:46:41 UTC 2014

Hi Marc,

thanks for the quick response.  I'll add this information to the package
metadata and upload the upgraded version.

Kind regards

        Andreas.

On Wed, Oct 22, 2014 at 10:41:45AM -0700, Marc Carlson wrote:
> Hi Andreas,
> 
> This is something that can happen whenever data sources at ensembl
> are updated causing our test of the real ensembl data to become
> temporarily invalid.  We have already updated out packages to
> reflect the new data coming from ensembl.  You can see the build
> report here:
> 
> http://www.bioconductor.org/checkResults/3.0/bioc-LATEST/
> 
> And the latest released version of this software is also described
> (and available) here:
> 
> http://www.bioconductor.org/packages/3.0/bioc/html/GenomicFeatures.html
> 
> 
> Thanks!
> 
> 
>  Marc
> 
> 
> 
> On 10/22/2014 12:30 AM, Maintainer wrote:
> >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"
> >Copyright (C) 2014 The R Foundation for Statistical Computing
> >Platform: x86_64-pc-linux-gnu (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >>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.
> >
> 
> 

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