[Bioc-devel] TabixFileList() constructor broken in devel

Shepherd, Lori Lori.Shepherd at roswellpark.org
Wed Dec 28 19:44:19 CET 2016

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:

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))

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


the 'TabixFileList()' constructor in Rsamtools seems to be broken in devel:

example(TabixFileList) ## which actually does not construct any
Error in as.vector(x, "character") :
   cannot coerce type 'environment' to vector of type 'character'

while in release this works fine:

example(TabixFileList) ## which actually does not construct any
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.



R Under development (unstable) (2016-11-17 r71661)
Platform: x86_64-apple-darwin16.1.0 (64-bit)
Running under: macOS Sierra 10.12.2

[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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