[Bioc-devel] TabixFileList() constructor broken in devel
Thank you for bringing this to our attention. There were some updates made a few weeks ago to the behavior and input of 'TabixFileList()' . Its current implementation will work with a character vector as input. I will investigate further into why this change was made and if it needs to be addressed. In the meantime: TabixFileList(tbx) will throw an ERROR, but you can still use the same file that was used to create the TabixFile tbx <- open(TabixFile(fl, yieldSize=100)) TabixFileList(fl) Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Robert Castelo <robert.castelo at upf.edu>
Sent: Wednesday, December 28, 2016 11:50:58 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] TabixFileList() constructor broken in devel
Sent: Wednesday, December 28, 2016 11:50:58 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] TabixFileList() constructor broken in devel
hi,
the 'TabixFileList()' constructor in Rsamtools seems to be broken in devel:
library(Rsamtools)
example(TabixFileList) ## which actually does not construct any
'TabixFileList'
TabixFileList(tbx)
Error in as.vector(x, "character") :
cannot coerce type 'environment' to vector of type 'character'
while in release this works fine:
library(Rsamtools)
example(TabixFileList) ## which actually does not construct any
'TabixFileList'
TabixFileList(tbx)
TabixFileList of length 1
names(1): example.gtf.gz
the man page has not changed between devel and release and the current
description of the argument 'file' supports the use of a 'TabixFile'
instance as input:
file: For TabixFile(), A character(1) vector to the tabix file
path; can be remote (http://, ftp://). For ?countTabix?, a
character(1) or ?TabixFile? instance. For others, a
?TabixFile? instance.
please find below my session information for the devel run.
thanks!
robert.
sessionInfo()
R Under development (unstable) (2016-11-17 r71661)
Platform: x86_64-apple-darwin16.1.0 (64-bit)
Running under: macOS Sierra 10.12.2
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
[8] methods base
other attached packages:
[1] Rsamtools_1.27.9 Biostrings_2.43.1 XVector_0.15.0
[4] GenomicRanges_1.27.17 GenomeInfoDb_1.11.6 IRanges_2.9.14
[7] S4Vectors_0.13.5 BiocGenerics_0.21.1 setwidth_1.0-4
[10] colorout_1.1-0
loaded via a namespace (and not attached):
[1] zlibbioc_1.21.0 compiler_3.4.0 tools_3.4.0 BiocParallel_1.9.3
[5] bitops_1.0-6
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