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
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