Hi Shraddha,
Seems to be a BiocFileCache issue.
On my laptop the following code (taken from your
Predict_CaseControl_from_CNV.Rnw vignette):
require(BiocFileCache)
geneURL <- paste("http://download.baderlab.org/netDx/";,
"supporting_data/refGene.hg18.bed",sep="")
cache <- rappdirs::user_cache_dir(appname = "netDx")
bfc <- BiocFileCache::BiocFileCache(cache,ask=FALSE)
rid_rec <- bfcquery(bfc, "hg18_genes", "rname")
rid <- rid_rec$rid
returns only one rid:
> rid
[1] "BFC4"
whereas on malbec1 it returns two:
> rid
[1] "BFC6" "BFC11"
In both cases, I'm using the latest version of BiocFileCache (1.13.1).
I suspect this has to do with the cache being in different states on the
two machines.
The fact that 'rid' has a length of 2 causes the failure a few lines
later when bfcdownload() is called:
rid <- rid_rec$rid
if (!length(rid)) {
rid <- names(bfcadd(bfc, "hg18_genes", geneURL))
}
if (!isFALSE(bfcneedsupdate(bfc, rid))){
bfcdownload(bfc, rid,ask=FALSE)
}
I suggest that you open a BiocFileCache issue on GitHub.
Thanks,
H.
On 9/11/20 08:51, Shraddha Pai wrote:
> Hello BioC-devel team,
> Any idea why netDx 1.1.4 fails on the bioc devel build system?
>
> This is the error:
>
> --- re-building 'Predict_CaseControl_from_CNV.Rmd' using knitr
> Quitting from lines 173-195 (Predict_CaseControl_from_CNV.Rmd)
> Error: processing vignette 'Predict_CaseControl_from_CNV.Rmd' failed
> with diagnostics:
> length(url) == 1 is not TRUE
> --- failed re-building 'Predict_CaseControl_from_CNV.Rmd'
>
>
> I just set up the Bioc-devel docker, cloned the repo using
> git clone [email protected]:packages/netDx
> and ran the vignette, and it runs through successfully.
>
> However the build error occurs across all platforms so something needs to
> change.
>
> Thank you,
> Shraddha
>
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>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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