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 g...@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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zwoVT5i-NLz7FqpRg0pSLIqNJBJiI_Ac8FigI43cwRc&s=YhavBW80Elhyr-R7RuyrA2bwYPfI08HAsraBEs2FRU0&e= > -- 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel