[BioC] error in report(qa) from pkg ShortRead

[Timothée Flutre]

Hello,

I have a fastq file compressed with gzip in a directory named test/.
I would like to assess its quality. Here is what I do:

$ R
> library(ShortRead)
> qa <- qa("~/test", "fastq.gz")
> report(qa, dest="~/test")

And I get the following error message:
Error in as.data.frame(lapply(df, sprintf, fmt = fmt)) :
error in evaluating the argument 'x' in selecting a method for
function 'as.data.frame': Error in FUN(X[[1L]], ...) :
invalid format '%.3g'; use format %s for character objects

Here are more details:
> traceback()
7: as.data.frame(lapply(df, sprintf, fmt = fmt))
6: .df2a(qa[["adapterContamination"]])
5: hwrite(.df2a(qa[["adapterContamination"]]), border = 0)
4: func(x, dest, type, ...)
3: func(x, dest, type, ...)
2: report(qa, dest = "~/test")
1: report(qa, dest = "~/test")

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] ShortRead_1.22.0        GenomicAlignments_1.0.2 BSgenome_1.32.0
[4] Rsamtools_1.16.1        GenomicRanges_1.16.3    GenomeInfoDb_1.0.2
[7] Biostrings_2.32.1       XVector_0.4.0           IRanges_1.22.9
[10] BiocParallel_0.6.1      BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] BatchJobs_1.3       BBmisc_1.7          Biobase_2.24.0 [4]
bitops_1.0-6        brew_1.0-6          checkmate_1.1 [7]
codetools_0.2-8     compiler_3.1.0      DBI_0.2-7 [10] digest_0.6.4
     fail_1.2            foreach_1.4.2 [13] grid_3.1.0
hwriter_1.3.1       iterators_1.0.7 [16] lattice_0.20-29
latticeExtra_0.6-26 RColorBrewer_1.0-5 [19] RSQLite_0.11.4
sendmailR_1.1-2     stats4_3.1.0 [22] stringr_0.6.2       tools_3.1.0
        zlibbioc_1.10.0

Timothée Flutre
Chargé de Recherche / Research Scientist
INRA - Centre de Montpellier
  http://umr-agap.cirad.fr/en
  http://openwetware.org/wiki/User:Timothee_Flutre