[BioC] multicore and DEXSeq

[Alejandro Reyes]

Dear Lynn Amon, Dear Dan,

Thanks for noticing the mistake in the vignette I will update it.

Lynn, do you have the same error when you run it using just one core?
If so, could you send me that error message?

Alejandro


> Actually, I'm still running into problems with the parallel package.  Here is my error with estimateDispersions:
>
>> glueExons <- estimateDispersions(glueExons,nCores=4)
> Estimating Cox-Reid exon dispersion estimates using 4 cores. (Progress report: one dot per 100 genes)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "fData", for signature "character"
> In addition: Warning message:
> In parallel::mclapply(allecs, FUN = funtoapply, mc.cores = mc.cores) :
>    all scheduled cores encountered errors in user code
>
>
> ________________________________________
> From: Dan Tenenbaum [dtenenba at fhcrc.org]
> Sent: Monday, July 30, 2012 1:02 PM
> To: Lynn Amon
> Cc: Lynn Amon [guest]; bioconductor at r-project.org; DEXSeq Maintainer
> Subject: Re: [BioC] multicore and DEXSeq
>
> On Mon, Jul 30, 2012 at 12:59 PM, Lynn Amon <lynn.amon at seattlebiomed.org> wrote:
>> Dan,
>> Thanks for the reply.  library(parallel) does work.  I used multicore
>> because that what vignette for DEXSeq uses.
>
> Thanks for the clarification. The DEXSeq vignette should be
> updated...Alejandro, would you mind doing that?
>
> Thanksc,
> Dan
>
>
>> Lynn
>>
>> On 7/30/12 12:55 PM, "Dan Tenenbaum" <dtenenba at fhcrc.org> wrote:
>>
>>> Hi Lynn,
>>>
>>> On Mon, Jul 30, 2012 at 12:51 PM, Lynn Amon [guest]
>>> <guest at bioconductor.org> wrote:
>>>>
>>>> Hi,
>>>> I am having trouble getting fitDespersions to recognize that I have
>>>> multicore installed. I get an error from divideWork telling me to load
>>>> parallel package but I have multicore and it detects 8 cores.  Here is
>>>> some of my script to make an exonCountSet object and then estimate
>>>> dispersions using four cores.
>>>> Thanks,
>>>> Lynn
>>>>
>>>>> glueExons <-
>>>>> read.HTSeqCounts(countfiles=file.path(bamPath,paste(rownames(samples),"/
>>>>> htseq_exons.txt",sep="")),design=samples,flattenedfile=annotationFile)
>>>>>
>>>>> sampleNames(glueExons) <- rownames(samples)
>>>>>
>>>>> expdata <- new("MIAME",name="GlueGenomics")
>>>>> experimentData(glueExons) <- expdata
>>>>>
>>>>> library(DESeq)
>>>>> genetable <- geneCountTable(glueExons)
>>>>> glue_genes <- newCountDataSet(genetable,conditions=samples)
>>>>> experimentData(glue_genes) <- expdata
>>>>>
>>>>> glueExons <- estimateSizeFactors(glueExons)
>>>>> sizeFactors(glueExons)
>>>>      WT_RY_0_12A    WT_RY_P3_12A   WT_RY_PIC_12A    WT_RY_PP_12A
>>>> IL10_RZ_0_12A
>>>>        1.0143924       0.8163463       1.2448730       0.4565408
>>>> 2.7520441
>>>>   IL10_RY_P3_12A IL10_RY_PIC_12A  IL10_RY_PP_12A
>>>>        1.1597040       0.8003611       0.9501160
>>>>>
>>>>> library(multicore)
>>>>> multicore:::detectCores()
>>>> [1] 8
>>>>> glueExons <- estimateDispersions(glueExons,nCores=4)
>>>> Estimating Cox-Reid exon dispersion estimates using 4 cores. (Progress
>>>> report: one dot per 100 genes)
>>>> Error in divideWork(cds, funtoapply = toapply, fattr =
>>>> "dispBeforeSharing",  :
>>>>    Please load first parallel package or set parameter nCores to 1...
>>>>
>>>>
>>>
>>> Load the "parallel" package, not the "multicore" package.
>>> Dan
>>>
>>>
>>>
>>>>
>>>>   -- output of sessionInfo():
>>>>
>>>> R version 2.15.0 (2012-03-30)
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>>   [7] LC_PAPER=C                 LC_NAME=C
>>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] DESeq_1.9.10       lattice_0.20-6     locfit_1.5-8
>>>> DEXSeq_1.3.14
>>>> [5] Biobase_2.17.6     BiocGenerics_0.3.0 multicore_0.1-7
>>>>
>>>> loaded via a namespace (and not attached):
>>>>   [1] annotate_1.35.3       AnnotationDbi_1.19.28 biomaRt_2.13.2
>>>>   [4] DBI_0.2-5             genefilter_1.39.0     geneplotter_1.35.0
>>>>   [7] grid_2.15.0           hwriter_1.3           IRanges_1.15.24
>>>> [10] plyr_1.7.1            RColorBrewer_1.0-5    RCurl_1.91-1
>>>> [13] RSQLite_0.11.1        splines_2.15.0        statmod_1.4.14
>>>> [16] stats4_2.15.0         stringr_0.6.1         survival_2.36-14
>>>> [19] XML_3.9-4             xtable_1.7-0
>>>>
>>>>
>>>> --
>>>> Sent via the guest posting facility at bioconductor.org.
>>>>
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>>