Skip to content

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

3 messages · Shraddha Pai, Martin Morgan, Hervé Pagès

Original
Shraddha Pai
# 
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 at 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
Martin Morgan
# 
At the top of each build report page, e.g.,

 http://bioconductor.org/checkResults/3.12/bioc-LATEST/netDx/malbec1-buildsrc.html 

?there's a link with title 'following settings' describing build-system-specific settings. Does this help to reproduce the problem?

Martin
On 9/11/20, 11:52 AM, "Bioc-devel on behalf of Shraddha Pai" <bioc-devel-bounces at r-project.org on behalf of shraddha.pai at utoronto.ca> 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 at 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


    _______________________________________________
    Bioc-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hervé Pagès
# 
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: