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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