[Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

[Obenchain, Valerie]

Hi,

Just wanted to let you know I saw this and will get to it as soon as
possible.

Valerie

On 10/01/2015 05:47 AM, Robert Castelo wrote:
> hi Valerie,
>
> regarding the bug you fixed about a month ago and described below, 
> there's something still not entirely correct that i did not notice then, 
> or maybe something has broken since then. Let me run the example again 
> to explain it:
>
> library(Biostrings)
> library(BiocParallel)
>
> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character, 
> BPPARAM=bpparam("SerialParam"))
> [1] "AC" "GT"
>
> ## this looks fine so far but notice the result when i call
> ## now the function 'class()' instead of 'as.character()'
>
> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=class, 
> BPPARAM=bpparam("SerialParam"))
> [1] "DNAString" "DNAString"
>
> somehow bpvec() is chopping the input into objects of a class different 
> to the original input class. this does not happen with the multicore 
> backend:
>
> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=class, 
> BPPARAM=bpparam("MulticoreParam"))
> [1] "DNAStringSet" "DNAStringSet"
>
>
> so, i guess there's still something wrong with the SerialParam backend.
>
>
> thanks!!
>
> robert.
>
>
> On 09/05/2015 12:10 AM, Obenchain, Valerie wrote:
>> Hi Robert,
>>
>> Thanks for reporting the bug. The problem was with how 'X' was split
>> before dispatching to bplapply() and affected both SerialParam and
>> SnowParam. Now fixed in release (1.2.21) and devel (1.3.52).
>>
>> Valerie
>>
>>
>>> ----- Forwarded Message -----
>>> From: "Robert Castelo"<robert.castelo at upf.edu>
>>> To: bioc-devel at r-project.org
>>> Sent: Wednesday, September 2, 2015 8:12:33 AM
>>> Subject: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem
>>>
>>> hi,
>>>
>>> I have encountered a problem when using the bpvec() function from the
>>> BiocParallel package with DNAStringSet objects and the "SerialParam"
>>> backend:
>>>
>>> library(Biostrings)
>>> library(BiocParallel)
>>>
>>>
>>> ## all correct when using the multicore backend
>>>
>>> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character, BPPARAM=bpparam())
>>> [1] "AC" "GT"
>>>
>>> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character,
>>> BPPARAM=MulticoreParam())
>>> [1] "AC" "GT"
>>>
>>>
>>> ## problem when using the SerialParam backend
>>>
>>> bpvec(X=DNAStringSet(c("AC", "GT")), FUN=as.character,
>>> BPPARAM=bpparam("SerialParam"))
>>> [1] "1" "2"
>>>
>>>
>>> the problem is that elements of the DNAStringSet object get somehow
>>> coerced to integers when using the "SerialParam" backend.
>>>
>>>
>>> this occurs in both current release and devel, please find the
>>> corresponding sessionInfo()'s below.
>>>
>>>
>>> thanks!
>>>
>>> robert.
>>>
>>> ## release
>>> sessionInfo()
>>> R version 3.2.0 (2015-04-16)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>> Running under: Fedora release 12 (Constantine)
>>>
>>> locale:
>>>    [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
>>>    [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
>>>    [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
>>>    [7] LC_PAPER=en_US.UTF8       LC_NAME=C
>>>    [9] LC_ADDRESS=C              LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>>> [8] methods   base
>>>
>>> other attached packages:
>>> [1] BiocParallel_1.2.20 Biostrings_2.36.4   XVector_0.8.0
>>> [4] IRanges_2.2.7       S4Vectors_0.6.5     BiocGenerics_0.14.0
>>> [7] vimcom_1.2-3        setwidth_1.0-4      colorout_1.1-0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] zlibbioc_1.14.0      futile.logger_1.4.1  tools_3.2.0
>>> [4] lambda.r_1.1.7       futile.options_1.0.0
>>>
>>> ## devel
>>> sessionInfo()
>>> R Under development (unstable) (2015-04-28 r68268)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>> Running under: Fedora release 12 (Constantine)
>>>
>>> locale:
>>>    [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
>>> LC_TIME=en_US.UTF8
>>>    [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8
>>> LC_MESSAGES=en_US.UTF8
>>>    [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C
>>>
>>> [10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8
>>> LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>>>    methods   base
>>>
>>> other attached packages:
>>> [1] BiocParallel_1.3.51 Biostrings_2.37.8   XVector_0.9.3
>>> IRanges_2.3.18
>>> [5] S4Vectors_0.7.14    BiocGenerics_0.15.6 vimcom_1.0-0
>>> setwidth_1.0-4
>>> [9] colorout_1.0-3
>>>
>>> loaded via a namespace (and not attached):
>>> [1] zlibbioc_1.15.0      futile.logger_1.4.1  tools_3.3.0
>>> lambda.r_1.1.7
>>> [5] futile.options_1.0.0
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
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