[Bioc-devel] "length(url) == 1 is not TRUE" error for vignette only on build system
Shraddha Pai
@hr@ddh@@p@| @end|ng |rom utoronto@c@
Mon Sep 21 20:39:26 CEST 2020
Hi all,
I've updated the cache calls in netDx per Martin's suggestion above:
> bfc <- BiocFileCache()
> path <- bfcrpath(bfc, url)
The package now builds on netbbiolo but times out on malbec1 and tokay1,
and has an error on merida1.
I've never had a package timeout before. Is this because of the updated
cache calls?
A mix of outcomes on different platforms!
The error on the Windows machine (riesling) seems related to a message
Herve sent me, about java no longer being on the path.
Any guidance on how to resolve would be appreciated.
Thanks,Shraddha
On Mon, Sep 14, 2020 at 12:21 PM Shepherd, Lori <
Lori.Shepherd using roswellpark.org> wrote:
> To follow up on this:
>
> Please check the package code for adding/accessing resources in the netDx
> package. If the BiocFileCache options were used correctly there should not
> have been multiple entries added to the builders cache as Martin
> demonstrated below.
>
> Once the package has been updated to ensure duplicate entries will not be
> added, we can clean up the builders. The package code should be adjusted
> first to ensure that users will not encounter the same situation.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Martin
> Morgan <mtmorgan.bioc using gmail.com>
> *Sent:* Friday, September 11, 2020 6:22 PM
> *To:* Pages, Herve <hpages using fredhutch.org>; Shraddha Pai <
> shraddha.pai using utoronto.ca>
> *Cc:* bioc-devel using r-project.org <Bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] "length(url) == 1 is not TRUE" error for
> vignette only on build system
>
> bfcquery() just searches the cache, so if you've created two resources
> that match the name then you end up with two rids
>
> > xx = bfcnew(bfc, "foo")
> > bfcquery(bfc, "foo", "rname")
> # A tibble: 1 x 10
> rid rname create_time access_time rpath rtype fpath last_modified_t…
> etag
> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
> <chr>
> 1 BFC3 foo 2020-09-11… 2020-09-11… /Use… rela… 64ea… NA NA
> # … with 1 more variable: expires <dbl>
> > xx = bfcnew(bfc, "foo_bar")
> > bfcquery(bfc, "foo", "rname")
> # A tibble: 2 x 10
> rid rname create_time access_time rpath rtype fpath last_modified_t…
> etag
> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
> <chr>
> 1 BFC3 foo 2020-09-11… 2020-09-11… /Use… rela… 64ea… NA NA
> 2 BFC4 foo_… 2020-09-11… 2020-09-11… /Use… rela… 64ea… NA NA
> # … with 1 more variable: expires <dbl>
>
> and even
>
> > xx = bfcnew(bfc, "foo_bar")
> > bfcquery(bfc, "foo", "rname")
> # A tibble: 3 x 10
> rid rname create_time access_time rpath rtype fpath last_modified_t…
> etag
> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
> <chr>
> 1 BFC3 foo 2020-09-11… 2020-09-11… /Use… rela… 64ea… NA NA
> 2 BFC4 foo_… 2020-09-11… 2020-09-11… /Use… rela… 64ea… NA NA
> 3 BFC5 foo_… 2020-09-11… 2020-09-11… /Use… rela… 64ea… NA NA
> # … with 1 more variable: expires <dbl>
>
> If the cache is under netDx control, then you can be careful about
> creating new resources by checking first whether the resource exists, as
> outlined in
> http://secure-web.cisco.com/1t9-aFwD7wK-0S-MuqPB5uIzT5hQ2gyAD8KMGooS3HThd0k45RZ-frPKl-6Yl2EwZFFcmutTlgEODe0vTjmGHdvrtnhcf5beUQTSS3KiUAl4eWVWv4m3kjsTCUxTVQ2Ll5cGeus1QPlv2osdgHIycOGo6WKDjPqb6PoCxqWOMpEB_x8cSenUxF2N0OkDSEKuwlgJzHwqGjVOwqZQ_odXuqKEnKXz5moLlJO0XSz5XXkTj4kTGwtMAjqKAk_tR8DujPGfYr6Cc70ReKMZUWNVIOc4JgCOAmkILBW94Rp0x_3CX-8DEDeaRhlrgoM7MxkqHGyB0UxHyCXGepxXY196Uglz7WmH1uY02-XQsQ_6e8og/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fvignettes%2FBiocFileCache%2Finst%2Fdoc%2FBiocFileCache.html%23cache-to-manage-package-data
>
> If one is managing internet resources, just use bfcadd
>
> > bfc <- BiocFileCache()
> > path <- bfcrpath(bfc, url)
> adding rname '
> https://secure-web.cisco.com/1lUwUbgjSoXsv6f7JfdXhRG2f7_ISpNGSvQkNDjD3wQSEEMkTAVHfopgsowEo1GgsXrbByzyoKcAqYa3Kw2bxocuFRTwCIF5UxwWY7fw_FCeNByJcX4L4A9pGyPD1Il4OWJRoYewqI9SOxbFsK6XqqYQmOxhzALdAwDrJw1cOOpppzIIoz5unFJOO2Ihuca8QuIswQZGQqxSBXbeuu8WxSl9QoenolmV7PHovZu_sUMd1DYSflBtliuDz8hRJHSdp-N4wLsvl5GZXxTcJH4ZruhecvOJPR7aGrHCRLZln3wWoMKctL_Oc2xnUYu0ZYrCrVD5MQ8Wf7fgFEl7RPTt5RbTMxrbLO0zXxZZaEwhL5AU/https%3A%2F%2Fbioconductor.org%2Findex.html
> '
> |======================================================================|
> 100%
>
> > path <- bfcrpath(bfc, url)
> >
>
> where the first time 'url' is used (as a unique key) the resource is
> downloaded to the cache; the second time it is simply accessed from the
> cache.
>
> It might be necessary to manually 'clean up' the builders
>
> Martin
>
>
> On 9/11/20, 4:10 PM, "Bioc-devel on behalf of Pages, Herve" <
> bioc-devel-bounces using r-project.org on behalf of hpages using fredhutch.org> wrote:
>
> 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$last_modified_time)
> > y <- order(x,decreasing=TRUE)
> > rid <- rid[y[1]]
> > }
> >
> > Overkill? I could just take rid[1] but that would not be methodical.
> >
> > Will file issue once you confirm that the problem is that there
> should
> > be a unique rid associated with each rname.
> >
> > Thanks again - appreciate it,
> > Shraddha
> >
> > On Fri, Sep 11, 2020 at 2:57 PM Shraddha Pai <
> shraddha.pai using utoronto.ca
> > <mailto:shraddha.pai using utoronto.ca <shraddha.pai using utoronto.ca>>> wrote:
> >
> > Hi Herve,
> > Thank you for pinpointing this.
> > Just so I'm clear: rid should not have two IDs correct?
> > For each rname, the cache should only have a unique ID, right?
> Or is
> > that not the case?
> >
> > To get the package to build I will take the rid with the latest
> > "last_modified_time".
> > Looks like this can be achieved with:
> > if (length(rid)>1) {
> > x <- rid_rec$last_modified
> >
> > On Fri, Sep 11, 2020 at 1:22 PM Pages, Herve <
> hpages using fredhutch.org
> > <mailto:hpages using fredhutch.org <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://secure-web.cisco.com/1q6dletAEEmECRlpAh7w_w4AmdNAhzos1ijnImWIdzsuXHz3kMIav7Urj3RzYO0S8BzLMKG_0Zcp4ytMlPfA9Ht6IFyJIoCQY-9mRDq-BQDDX_zer8B-bkuIy0hvpOFRkd4a0lSKnviwzssrArVnDcHSCh7EQZsCSMgdEeFsojc3WO3wt8cG5GJztsLKILl9NFGnr2g19zjUcuvqtOBAyec62CVmCfonqPnOWy_VEUPd4WcDd2XwFUW7vEzrFcpC3V6K5pAc0bWjjqEz-3RLU0cWFYgNOGa7zIBwHCX8XMu1JcpLCVoXB-W_RXWMiOwtaHwy8vGei3fBckztfRFgZnA/http%3A%2F%2Fdownload.baderlab.org%2FnetDx%2F
> > <
> https://secure-web.cisco.com/1pBAaf568Sh8T9WwtZnai1icCdNVYUY8FRTQfjYtlK3gI5radqfCsKfzfJz-0BFk_9sTpehBBo60575Jx0MEnZeJRJIKZxiwx2eQ0X90O_CRwVziGst9BfByxNmW5LhvoYTWWSYm1G7ILPw13lka_Q4K2MiNJUX9s0gU6JDcCjBZ6000t2wqGJ_YEBcAGdt30Uv9ElTiYcAXps8tQzLNc9DGwx8ErTvnVmMjvbBVbBRQEBe3Gvo7OcE4-TS_nIEzsZhyvsT1V8xJ3KU9bTb_0J2S1AWC3ETe48ipc0WcJ_cA0OkCYMR7v5dIhE58VGsox/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__download.baderlab.org_netDx_%26d%3DDwMFaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DV-k2jGkEksU1mmcALiO9azNiQrGrVrfwlL4vMvJZwHQ%26s%3DDG1UzWYSS8kbCIEYszKms6FBBQ-GZKWplwuOOOIf88c%26e%3D
> >",
> > "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]]
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org
> <Bioc-devel using r-project.org>>
> > mailing list
> > >
> >
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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
> <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
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