[Debian-med-packaging] Problems with test suite of new verison of Rsamtools

[Andreas Tille]

Hi,

I try to upgrade Debian packages to BioConductor 3.2.  When doing so I
stumbled upon a problem of the testsuite of Rsamtools:

> BiocGenerics:::testPackage('Rsamtools')

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 objects are masked from 'package:stats':

    IQR, mad, 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, grep, grepl, intersect, is.unsorted, lapply,
    lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

[bam_index_load] fail to load BAM index.
[fai_load] build FASTA index.
[fai_build_core] no entries in file
[fai_load] fail to open FASTA index.
[fai_load] build FASTA index.
[samopen] SAM header is present: 2 sequences.
[bam_index_load] fail to load BAM index.
[fai_load] build FASTA index.
[fai_load] build FASTA index.
[fai_load] build FASTA index.
[bam_index_core] the alignment is not sorted (EAS218_4:1:9:206:901): 2-th chr > 1-th chr
[bam_index_build2] fail to index the BAM file.
Timing stopped at: 0 0 0.001 
Error in checkTrue(warn) : Test not TRUE



RUNIT TEST PROTOCOL -- Sat Oct 31 08:43:38 2015 
*********************************************** 
Number of test functions: 180 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
Rsamtools RUnit Tests - 180 test functions, 0 errors, 1 failure
FAILURE in test_catch_samtools: Error in checkTrue(warn) : Test not TRUE


Test files with failing tests

   test_utilities.R 
     test_catch_samtools 


Error in BiocGenerics:::testPackage("Rsamtools") : 
  unit tests failed for package Rsamtools


>  sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
[1] C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] RUnit_0.4.30         Rsamtools_1.22.0     Biostrings_2.38.0   
[4] XVector_0.10.0       GenomicRanges_1.22.0 GenomeInfoDb_1.6.0  
[7] IRanges_2.4.1        S4Vectors_0.8.0      BiocGenerics_0.16.0 

loaded via a namespace (and not attached):
[1] futile.logger_1.4.1  lambda.r_1.1.7       futile.options_1.0.0
[4] BiocParallel_1.4.0   bitops_1.0-6        


Any idea what might went wrong here?

Kind regards

       Andreas.


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