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

[Morgan, Martin]

This is strange. When the Rsamtools package is installed then the following should be true
 
> fl <- system.file("unitTests", "cases", "ex1_unsort.bam", package="Rsamtools")
> file.exists(fl)
[1] TRUE

the test tries to index the bam file, and should generate an error and warnings

> Rsamtools::indexBam(fl)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/Rsamtools/unitTests/cases/ex1_unsort.bam
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  [bam_index_core] the alignment is not sorted (EAS218_4:1:9:206:901): 2-th chr > 1-th chr
2: In FUN(X[[i]], ...) : [bam_index_build2] fail to index the BAM file.

From your output below it seems like that actually occurs. The warnings should be caught by

> warn <- FALSE
> tryCatch(Rsamtools::indexBam(fl), warning=function(msg) warn <<- TRUE)
> warn
[1] TRUE

Is this what you see? Have you set some R option related to warning and error handlers?

Martin

________________________________________
From: devteam-bioc-bounces at lists.fhcrc.org [devteam-bioc-bounces at lists.fhcrc.org] on behalf of Maintainer [maintainer at bioconductor.org]
Sent: Saturday, October 31, 2015 3:52 AM
To: Bioconductor Package Maintainer
Cc: Debian Med Packaging Team
Subject: [devteam-bioc] Problems with test suite of new verison of Rsamtools

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.


--
http://fam-tille.de

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