[Bioc-devel] DMRcate: TIMEOUT

[Sean Davis]

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.

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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>
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-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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