On 30 Mar 2015, at 19:29, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 03/27/2015 11:12 AM, Nicolas Delhomme wrote:
Easy enough :-)
I'm running the RnaSeqTutorial package vignette and the chunks 6, 7 and 8 fail with that forceAndCall error.
My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11).
Nico
---------------------------------------------------------------
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Ume? Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? S-901 87 Sweden
---------------------------------------------------------------
On 27 Mar 2015, at 19:09, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
I think we'd need to see your files in order to try to reproduce this.
Dan
----- Original Message -----
From: "Nicolas Delhomme" <nicolas.delhomme at umu.se>
To: "bioC-devel" <bioc-devel at stat.math.ethz.ch>
Sent: Friday, March 27, 2015 11:04:17 AM
Subject: [Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when using ShortRead readAligned function
Hej Bioc!
I've got the following error and can't really track its origin.
Cheers,
Nico
aln2 <- readAligned(getwd(),pattern="subset.bam$",type="BAM")
Error: Input/Output
'readAligned' failed to parse files
readAligned should not be sued to read BAM files, only 'legacy' formats (old
Bowtie, MAQ, Solexa export, ...). Use GenomicAlignments::readGAlignment*
instead, everyone will be much happier. Martin
dirPath: '/Users/delhomme/Documents/Git/RnaSeqTutorial'
pattern: 'subset.bam$'
type: 'BAM'
error: "forceAndCall" is not a SPECIAL function
R Under development (unstable) (2015-02-11 r67792)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
datasets methods base
other attached packages:
[1] ShortRead_1.25.9 GenomicAlignments_1.3.32
Rsamtools_1.19.49 GenomicRanges_1.19.48
[5] GenomeInfoDb_1.3.16 Biostrings_2.35.12 XVector_0.7.4
IRanges_2.1.43
[9] S4Vectors_0.5.22 BiocParallel_1.1.21
BiocGenerics_0.13.10 RnaSeqTutorial_0.3.2
[13] easyRNASeq_2.3.4 locfit_1.5-9.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 futile.logger_1.4 bitops_1.0-6
futile.options_1.0.0 tools_3.2.0
[6] zlibbioc_1.13.3 biomaRt_2.23.5 annotate_1.45.4
RSQLite_1.0.0 lattice_0.20-30
[11] DBI_0.3.1 DESeq_1.19.0 genefilter_1.49.2
hwriter_1.3.2 grid_3.2.0
[16] LSD_3.0 Biobase_2.27.3
AnnotationDbi_1.29.20 XML_3.98-1.1
survival_2.38-1
[21] limma_3.23.11 latticeExtra_0.6-26 geneplotter_1.45.0
lambda.r_1.1.7 edgeR_3.9.14
[26] intervals_0.15.0 genomeIntervals_1.23.2 splines_3.2.0
xtable_1.7-4 RCurl_1.95-4.5
---------------------------------------------------------------
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Ume? Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? S-901 87 Sweden
---------------------------------------------------------------