[Bioc-devel] "length(url) == 1 is not TRUE" error for vignette only on build system

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Fri Sep 11 19:22:19 CEST 2020

Hi Shraddha,

Seems to be a BiocFileCache issue.

On my laptop the following code (taken from your 
Predict_CaseControl_from_CNV.Rnw vignette):

   geneURL <- paste("http://download.baderlab.org/netDx/",
   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.


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 git using git.bioconductor.org: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
> 	[[alternative HTML version deleted]]
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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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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