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Old 05-08-2015, 06:26 AM   #1
ml439
Junior Member
 
Location: Cambridge

Join Date: May 2015
Posts: 9
Default problem running DEXSeq in parallel

Hi,

I'm trying to run DEXSeq in parallel in the server, but it returns the following error:

>library('parallel')
> dxd = testForDEU(dxd, nCores=16)
Error in testForDEU(dxd, nCores = 16) : unused argument (nCores = 16)

I also tried the following option, which I found in the DEXSeq vignette with no success either:

> BPPARAM= MultiCoreParam(workers=4)
Error: could not find function "MultiCoreParam"
> dxd = testForDEU(dxd, BPPARAM=BPPARAM)
Error in sort(rep(seq_len(BPPARAM$workers), length.out = nrow(object))) :

I would appreciate if anyone could help,

Thank you

>sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] DEXSeq_1.12.2 BiocParallel_1.0.3
[3] DESeq2_1.6.3 RcppArmadillo_0.5.100.1.0
[5] Rcpp_0.11.6 GenomicRanges_1.18.4
[7] GenomeInfoDb_1.2.5 IRanges_2.0.1
[9] S4Vectors_0.4.0 Biobase_2.26.0
[11] BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 annotate_1.44.0 AnnotationDbi_1.28.2
[4] base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9
[7] biomaRt_2.22.0 Biostrings_2.34.1 bitops_1.0-6
[10] brew_1.0-6 checkmate_1.5.2 cluster_2.0.1
[13] codetools_0.2-11 colorspace_1.2-6 DBI_0.3.1
[16] digest_0.6.8 fail_1.2 foreach_1.4.2
[19] foreign_0.8-63 Formula_1.2-1 genefilter_1.48.1
[22] geneplotter_1.44.0 ggplot2_1.0.1 grid_3.1.2
[25] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.16-0
[28] hwriter_1.3.2 iterators_1.0.7 lattice_0.20-31
[31] latticeExtra_0.6-26 locfit_1.5-9.1 magrittr_1.5
[34] MASS_7.3-40 munsell_0.4.2 nnet_7.3-9
[37] plyr_1.8.2 proto_0.3-10 RColorBrewer_1.1-2
[40] RCurl_1.95-4.6 reshape2_1.4.1 rpart_4.1-9
[43] Rsamtools_1.18.3 RSQLite_1.0.0 scales_0.2.4
[46] sendmailR_1.2-1 splines_3.1.2 statmod_1.4.21
[49] stringi_0.4-1 stringr_1.0.0 survival_2.38-1
[52] tools_3.1.2 XML_3.98-1.1 xtable_1.7-4
[55] XVector_0.6.0 zlibbioc_1.12.0
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Old 08-03-2015, 03:38 AM   #2
skdhanraj
Bioinformatician
 
Location: Norway

Join Date: May 2010
Posts: 4
Default

Use

BPPARAM= MulticoreParam(workers=4)

instead of

BPPARAM= MultiCoreParam(workers=4)

notice lowercase 'c'
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Old 12-03-2015, 01:23 AM   #3
gilh
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Location: Israel

Join Date: Nov 2015
Posts: 1
Default

Had this problem as well.
Thanks skdhanraj !
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Old 12-03-2015, 01:27 AM   #4
skdhanraj
Bioinformatician
 
Location: Norway

Join Date: May 2010
Posts: 4
Thumbs up

Nice. May be they should update the vignette as well.
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