[Bioc-devel] TabixFileList() constructor broken in devel
Martin Morgan
martin.morgan at roswellpark.org
Thu Jan 5 01:37:26 CET 2017
On 12/29/2016 12:25 PM, Vincent Carey wrote:
> A while ago Martin and I discussed the possibility of idempotence for
> TabixFile ... this seemed
> to make sense and so
>
>> TabixFile
>
> function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize =
> NA_integer_)
>
> {
>
> if (is(file, "TabixFile"))
>
> return(file)
>
> tryCatch({
>
> .io_check_exists(c(file, index))
>
> }, error = function(err) {
>
> stop(sprintf("TabixFile: %s", conditionMessage(err)),
>
> call. = FALSE)
>
> })
>
> .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize,
>
> ...)
>
> }
>
> <environment: namespace:Rsamtools>
>
>
> TabixFileList could behave similarly, working either from character paths,
> or from
>
> a list of TabixFile instances, or from a TabixFileList ... might be a
> design practice to
>
> promote for S4 programming
>
>
>> TabixFileList
>
> function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize =
> NA_integer_)
>
> {
>
> index <- as.character(index)
>
> .RsamtoolsFileList(file, index, ..., yieldSize = yieldSize,
>
> class = "TabixFile")
>
> }
>
> <environment: namespace:Rsamtools>
>
> On Thu, Dec 29, 2016 at 11:55 AM, Robert Castelo <robert.castelo at upf.edu>
> wrote:
>
>> hi Lori,
>>
>> thanks for the clarification. if this is an intended change then i'd say
>> the documentation needs to be updated since, as i showed in my email
>> below, it currently says that for functions such as 'TabixFileList()'
>> the input 'file' argument should be a 'TabixFile' instance and not a
>> character vector.
>>
>> this change also means the input is switching from a 'TabixFile'
>> instance to a 'character' vector, so pipelines or packages doing calls
>> to 'TabixFileList()' that have been passing 'TabixFile' instances as
>> arguments will have to update those calls to pass a character vector.
>>
>> i'd suggest that if there's no good reason to switch, it would be
>> safer to add the character vector as an additional possibility in the
>> input argument 'file', just as with 'countTabix()', and minimize
>> possible breaks of pipelines/packages using 'TabixFileList()'. i've
>> encountered this problem because my own package VariantFiltering calls
>> 'TabixFileList()' although is not a big deal to fix it.
>>
>> cheers,
>>
>> robert.
>>
>> On 28/12/2016 19:44, Shepherd, Lori wrote:
>>>
>>> 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)
The original behavior has been restored; both TabixFile() and
TabixFileList() are idempotent. Sorry for introducing the bug.
Martin
>>>
>>>
>>>
>>> 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
>>> 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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