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