Thanks Martin and Sean, found the culprit. It's DSS::DMLtest(). Looks
like it takes much longer under the new version. I should be able to
attenuate the vignette input considerably so hopefully it will now beat
the timeout.
For R/3.3.3, on a bsseq object with 5000 CpG sites, DMLtest() under
DSS_2.14.0 takes roughly 4 seconds:
> system.time(DSSres <- DMLtest(obj_bsseq, group1=sampnames[1:3],
group2=sampnames[4:6], smoothing=FALSE))
Estimating dispersion for each CpG site, this will take a while ...
user system elapsed
3.724 0.017 3.738
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] splines parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] DSS_2.14.0 bsseq_1.10.0
[3] limma_3.30.13 SummarizedExperiment_1.4.0
[5] Biobase_2.34.0 DMRcatedata_1.10.1
[7] GenomicRanges_1.26.4 GenomeInfoDb_1.10.3
[9] IRanges_2.8.2 S4Vectors_0.12.2
[11] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.11 XVector_0.14.1 zlibbioc_1.20.0 munsell_0.4.3
[5] colorspace_1.3-2 lattice_0.20-35 plyr_1.8.4 tools_3.3.3
[9] grid_3.3.3 data.table_1.10.4 R.oo_1.21.0 gtools_3.5.0
[13] matrixStats_0.52.2 permute_0.9-4 Matrix_1.2-10 R.utils_2.5.0
[17] bitops_1.0-6 RCurl_1.95-4.8 R.methodsS3_1.7.1 scales_0.4.1
[21] locfit_1.5-9.1
And under R/3.4.0 under DSS_2.16.0 it takes 108 seconds:
> system.time(DSSres <- DMLtest(obj_bsseq, group1=sampnames[1:3],
group2=sampnames[4:6], smoothing=FALSE))
Estimating dispersion for each CpG site, this will take a while ...
user system elapsed
108.305 0.184 108.596
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8
LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8
[6] LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8
LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines parallel stats4 stats graphics grDevices
utils datasets methods base
other attached packages:
[1] DSS_2.16.0 bsseq_1.12.1 SummarizedExperiment_1.6.2
DelayedArray_0.2.4 matrixStats_0.52.2
[6] Biobase_2.36.2 DMRcatedata_1.12.0
GenomicRanges_1.28.3 GenomeInfoDb_1.12.1 IRanges_2.10.2
[11] S4Vectors_0.14.2 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.11 XVector_0.16.0 zlibbioc_1.22.0
munsell_0.4.3 colorspace_1.3-2 lattice_0.20-35
[7] plyr_1.8.4 tools_3.4.0 grid_3.4.0
data.table_1.10.4 R.oo_1.21.0 gtools_3.5.0
[13] permute_0.9-4 Matrix_1.2-10 GenomeInfoDbData_0.99.0
R.utils_2.5.0 bitops_1.0-6 RCurl_1.95-4.8
[19] limma_3.32.2 compiler_3.4.0 R.methodsS3_1.7.1
scales_0.4.1 locfit_1.5-9.1
Thanks for your recommendations, I should be fine from here on.
Cheers,
Tim
On 31/05/17 21:36, Martin Morgan wrote:
On 05/31/2017 06:18 AM, Sean Davis wrote:
Hi, Tim. Have you tried building the vignette independently, separate from the package build process? Doing so might give you some hints about which code blocks are the culprits.
Also
Stangle("DMRcate.Rnw")
Writing to file DMRcate.R
source("DMRcate.R", echo=TRUE, max=Inf)
to generate the R code and process it. Martin
Sean On Wed, May 31, 2017 at 1:24 AM, Tim Peters <t.peters at garvan.org.au> wrote:
Hi bioc, Recently, under R/3.4.0, the newest version of DMRcate is taking 47mins to build on my local machine and I am getting TIMEOUTs on the build on the checkResults page http://master.bioconductor.org/checkResults/3.5/bioc- LATEST/DMRcate/malbec2-buildsrc.html. I have not made any changes to the attached data package or routines that warrant this increase in time. The vignette building in particular takes up the bulk of the time and this is where the build hangs. Building the same source on R/3.3.3 only takes 4mins 53secs by comparison. Screendump below. Can someone provide an insight into what they think is happening here? timpet at clark-lab:~/Documents$ time R CMD build DMRcate * checking for file ?DMRcate/DESCRIPTION? ... OK * preparing ?DMRcate?: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building ?DMRcate_1.12.1.tar.gz? real 47m33.472s user 46m55.023s sys 0m4.647s timpet at clark-lab:~/Documents$ R -e "sessionInfo()" R version 3.4.0 (2017-04-21) -- "You Stupid Darkness" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.0
Best,
Tim
--
Tim Peters, PhD
Bioinformatics Research Officer | Epigenetics Research Laboratory |
Genomics and Epigenetics Division
Garvan Institute of Medical Research
384 Victoria St., Darlinghurst, NSW, Australia 2010
Tel: +61 (2) 9295 8319
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