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

[Pages, Herve]

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$last_modified_time)
> y <- order(x,decreasing=TRUE)
> rid <- rid[y[1]]
> }
> 
> Overkill? I could just take rid[1] but that would not be methodical.
> 
> Will file issue once you confirm that the problem is that there should 
> be a unique rid associated with each rname.
> 
> Thanks again - appreciate it,
> Shraddha
> 
> On Fri, Sep 11, 2020 at 2:57 PM Shraddha Pai <shraddha.pai using utoronto.ca 
> <mailto:shraddha.pai using utoronto.ca>> wrote:
> 
>     Hi Herve,
>     Thank you for pinpointing this.
>     Just so I'm clear: rid should not have two IDs correct?
>     For each rname, the cache should only have a unique ID, right? Or is
>     that not the case?
> 
>     To get the package to build I will take the rid with the latest
>     "last_modified_time".
>     Looks like this can be achieved with:
>     if (length(rid)>1) {
>     x <- rid_rec$last_modified
> 
>     On Fri, Sep 11, 2020 at 1:22 PM Pages, Herve <hpages using fredhutch.org
>     <mailto:hpages using 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 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 <mailto:hpages using 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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319