Raw Message

Message-ID: <5f0ca8b2-d7e4-4fa9-00d7-b6462f223176@upf.edu>
Date: 2016-12-28T16:50:58Z
From: Robert Castelo
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