multicore and DEXSeq
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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(row names(samples),"/htseq_exons.txt",sep="")),design=samples,flattenedfil e=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... -- 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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Lynn Amon ▴ 50
@lynn-amon-5429
Last seen 9.6 years ago
I just tried library(parallel) and now it does estimateDispersions does recognize my cores. Lynn On 7/30/12 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 ),"/h >>tseq_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... > > > > -- 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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Dan Tenenbaum ★ 8.2k
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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(ro wnames(samples),"/htseq_exons.txt",sep="")),design=samples,flattenedfi le=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
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Dan, Thanks for the reply. library(parallel) does work. I used multicore because that what vignette for DEXSeq uses. 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(sample s),"/ >>>htseq_exons.txt",sep="")),design=samples,flattenedfile=annotationFi 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
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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? Thanks, 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(sampl es),"/ >>>>htseq_exons.txt",sep="")),design=samples,flattenedfile=annotationF ile) >>>> >>>> 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 >
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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@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? Thanks, 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(sampl es),"/ >>>>htseq_exons.txt",sep="")),design=samples,flattenedfile=annotationF ile) >>>> >>>> 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 >
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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(sam ples),"/ >>>>> 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 >>
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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(sam ples) >>>>>>,"/ >>>>>> >>>>>>htseq_exons.txt",sep="")),design=samples,flattenedfile=annotatio nFile >>>>>>) >>>>>> >>>>>> 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 >>> > >
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