I'm not a BiocFileCache expert, sorry. You will probably get better help
by opening a BiocFileCache issue on GitHub.
Cheers,
H.
On 9/11/20 12:00, Shraddha Pai wrote:
> Hi Herve,
> Sorry - hit shortcut to "send" by mistake.
>
> This is the code snippet that got cut off:
> if (length(rid)>1) {
> x <- as.POSIXct(rid_rec$last_modified_time)
> y <- order(x,decreasing=TRUE)
> rid <- rid[y[1]]
> }
>
> Overkill? I could just take rid[1] but that would not be methodical.
>
> Will file issue once you confirm that the problem is that there should
> be a unique rid associated with each rname.
>
> Thanks again - appreciate it,
> Shraddha
>
> On Fri, Sep 11, 2020 at 2:57 PM Shraddha Pai <shraddha....@utoronto.ca
> <mailto:shraddha....@utoronto.ca>> wrote:
>
> Hi Herve,
> Thank you for pinpointing this.
> Just so I'm clear: rid should not have two IDs correct?
> For each rname, the cache should only have a unique ID, right? Or is
> that not the case?
>
> To get the package to build I will take the rid with the latest
> "last_modified_time".
> Looks like this can be achieved with:
> if (length(rid)>1) {
> x <- rid_rec$last_modified
>
> On Fri, Sep 11, 2020 at 1:22 PM Pages, Herve <hpa...@fredhutch.org
> <mailto:hpa...@fredhutch.org>> wrote:
>
> 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/
>
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__download.baderlab.org_netDx_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V-k2jGkEksU1mmcALiO9azNiQrGrVrfwlL4vMvJZwHQ&s=DG1UzWYSS8kbCIEYszKms6FBBQ-GZKWplwuOOOIf88c&e=>",
> "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 <mailto: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 <mailto:hpa...@fredhutch.org>
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
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
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