[Bioc-devel] proc.time error

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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