[BioC] multicore and DEXSeq
Alejandro Reyes
alejandro.reyes at embl.de
Wed Aug 1 14:45:24 CEST 2012
Dear Lynn,
I could not reproduce your error with my datasets. Could you send me
your ExonCountSet object, to have a closer look? With the code that you
used and the sessionInfo() output?
Alejandro
> Alejandro,
> No, I do not get the error using just one core. When I run the same exact
> script, changing nCores=4 to nCores=1, there is no error message. Thanks
> for looking into this.
> Lynn
>
>
> On 7/31/12 10:09 AM, "Alejandro Reyes" <alejandro.reyes at embl.de> wrote:
>
>> 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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>>>>
>>
>>
>
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