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. >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >> >> >

It looks like I can't reproduce it either. I just tried again with a clean session and it seems to go through. Thanks for your help! Lynn On 8/1/12 5:45 AM, "Alejandro Reyes" <alejandro.reyes at="" embl.de=""> wrote: >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(s ample >>>>>>>>s) >>>>>>>> ,"/ >>>>>>>> >>>>>>>> >>>>>>>>htseq_exons.txt",sep="")),design=samples,flattenedfile=annotat ionFi >>>>>>>>le >>>>>>>> ) >>>>>>>> >>>>>>>> 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 >>>>> >>> >>> >> > >