[Bioc-devel] proc.time error

[Martin Morgan]

On 05/08/2018 02:58 AM, Anand MT wrote:
> Hi Developers,
> 
> I maintain Bioconductor package maftools, which has been failing to build on WIndows platform since it the new release. Error seems to be originating while running examples with the below error.
> 
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")

The current build report shows release failing on 32-bit windows

 
http://bioconductor.org/checkResults/3.7/bioc-LATEST/maftools/tokay2-checksrc.html

because the example is too large. The solution, and better practice, is 
to use more modest computation in the example.

...
 > seg = system.file('extdata', 'TCGA.AB.3009.hg19.seg.txt', package = 
'maftools')
 > TCGA.AB.3009.clust <- inferHeterogeneity(maf = laml, tsb = 
'TCGA-AB-3009',
+ segFile = seg, vafCol = 'i_TumorVAF_WU')
Processing TCGA-AB-3009..
Error: cannot allocate vector of size 1.3 Gb
Execution halted

The devel build report

 
http://bioconductor.org/checkResults/3.8/bioc-LATEST/maftools/malbec1-buildsrc.html

shows all builds failing because of use of an undefined object in the 
vignette; this would appear to be a programming error.

Quitting from lines 269-270 (maftools.Rmd)
Error: processing vignette 'maftools.Rmd' failed with diagnostics:
object 'Cytoband' not found
Execution halted

Martin

> 
> I have googled the issue, many answers suggests to include examples within /dontrun{} to avoid errors. But this has never been the issue before and package has built successfully with the same examples. How do I solve this ?
> 
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