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.pet...@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@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@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 >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is prohibited. If > you have received this message in error, please notify the sender > immediately by e-mail and delete this email message from your > computer. Thank you. > -- 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel