[Bioc-devel] TabixFileList() constructor broken in devel
Robert Castelo
robert.castelo at upf.edu
Thu Jan 5 12:13:33 CET 2017
On 05/01/2017 01:37, Martin Morgan wrote:
> 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
>
great! thanks Martin!!
robert.
>>>>
>>>>
>>>>
>>>> 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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