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.sheph...@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-boun...@r-project.org> on behalf of Martin > Morgan <mtmorgan.b...@gmail.com> > *Sent:* Friday, September 11, 2020 6:22 PM > *To:* Pages, Herve <hpa...@fredhutch.org>; Shraddha Pai < > shraddha....@utoronto.ca> > *Cc:* bioc-devel@r-project.org <Bioc-devel@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-boun...@r-project.org on behalf of hpa...@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$last_modified_time) > > y <- order(x,decreasing=TRUE) > > rid <- rid[y[1]] > > } > > > > Overkill? I could just take rid[1] but that would not be methodical. > > > > Will file issue once you confirm that the problem is that there > should > > be a unique rid associated with each rname. > > > > Thanks again - appreciate it, > > Shraddha > > > > On Fri, Sep 11, 2020 at 2:57 PM Shraddha Pai < > shraddha....@utoronto.ca > > <mailto:shraddha....@utoronto.ca <shraddha....@utoronto.ca>>> wrote: > > > > Hi Herve, > > Thank you for pinpointing this. > > Just so I'm clear: rid should not have two IDs correct? > > For each rname, the cache should only have a unique ID, right? > Or is > > that not the case? > > > > To get the package to build I will take the rid with the latest > > "last_modified_time". > > Looks like this can be achieved with: > > if (length(rid)>1) { > > x <- rid_rec$last_modified > > > > On Fri, Sep 11, 2020 at 1:22 PM Pages, Herve < > hpa...@fredhutch.org > > <mailto:hpa...@fredhutch.org <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://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 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 > <Bioc-devel@r-project.org>> > > mailing list > > > > > > https://secure-web.cisco.com/1Q1gRqlh1AbjlYoYoW-Tao_IKz59ZWyREYyVSz_yAJWP75JqkTLfdvqwGnEwk-lQEa0GIswGLe7jTmscS0aE9zb844BYJvAdTWLUneOW1-5ZUjtTOWpbCs88HMYRlKLIrA9cP4HevAvVxueol9bqn0j0LHw-UZX-k72wAWe5tjjd54VbNWOM5kKAPNuti9OB4nxoSRxmrVXUKKx2oQB0wT_yROTrgBTc1EAjjJ1P3fI85SfYyYA2SwxLeltUGcEkWoxzDXL1y7atMucMCnMJ2fv8KN41qlhh0uuv8VaHXyIXcxcg76La78NT4MVLsfX2D/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DzwoVT5i-NLz7FqpRg0pSLIqNJBJiI_Ac8FigI43cwRc%26s%3DYhavBW80Elhyr-R7RuyrA2bwYPfI08HAsraBEs2FRU0%26e%3D > > > > > > > -- > > 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 > <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. 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