[Bioc-devel] DMRcate: TIMEOUT

[Martin Morgan]

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
>>
>>
>>          [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
> 


This email message may contain legally privileged and/or...{{dropped:2}}