[BioC] multicore and DEXSeq

[Lynn Amon]

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.
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>
>