[Bioc-devel] Confusion on biocLite() with github and annotation data repo
James W. MacDonald
jmacdon at uw.edu
Tue Jun 28 17:41:13 CEST 2016
Sean did that. His original call was
biocLite('jmacdon/BiocAnno2016',dependencies=TRUE,build_vignettes=TRUE)
On Tue, Jun 28, 2016 at 11:24 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:
> I think you need to add the
>
> dependencies=TRUE
>
> argument which gets passed to devtools::install_github() and thence to
> devtools::install().
>
> Dan
>
>
> ----- Original Message -----
> > From: "Martin Morgan" <martin.morgan at roswellpark.org>
> > To: "James W. MacDonald" <jmacdon at u.washington.edu>, "Sean Davis" <
> sdavis2 at mail.nih.gov>
> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > Sent: Tuesday, June 28, 2016 8:11:26 AM
> > Subject: Re: [Bioc-devel] Confusion on biocLite() with github and
> annotation data repo
>
> > On 06/28/2016 10:56 AM, James W. MacDonald wrote:
> >> I had a similar experience, where the dependencies were not found upon
> >> installation. I didn't do anything to fix it - instead it seemed that
> just
> >> re-running biocLite after the initial failed install ended up working.
> >
> > Installing from github delegates to devtools::install_github, and that
> > the annotation repository is not found. So something like
> >
> > > options(repos=BiocInstaller::biocinstallRepos())
> > > biocLite("jmacdon/BiocAnno2016")
> >
> > I think the code is trying to do that, though
> >
> >
> https://github.com/Bioconductor-mirror/BiocInstaller/blob/master/R/biocLite.R#L72
> >
> > so don't really understand why it fails...
> >
> > Martin
> >
> >>
> >> Maybe the same will work for you?
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >>
> >> On Mon, Jun 27, 2016 at 5:03 PM, Davis, Sean (NIH/NCI) [E] <
> >> sdavis2 at mail.nih.gov> wrote:
> >>
> >>> I am trying to install from Jim’s annotation workflow from github (
> >>> https://github.com/jmacdon/BiocAnno2016), but biocLite() fails
> because it
> >>> cannot find annotation data packages. I *can* go back and install the
> >>> annotation data package with a separate call to biocLite(). Is this
> >>> expected behavior? If so, is it possible and desirable to install from
> >>> github and have it “do the right thing” to get Bioc dependencies?
> >>>
> >>> Thanks,
> >>> Sean
> >>>
> >>>
> >>>>
> biocLite('jmacdon/BiocAnno2016',dependencies=TRUE,build_vignettes=TRUE)
> >>> BioC_mirror: https://bioconductor.org
> >>> Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
> >>> Installing github package(s) ‘jmacdon/BiocAnno2016’
> >>> Downloading GitHub repo jmacdon/BiocAnno2016 at master
> >>> from URL
> https://api.github.com/repos/jmacdon/BiocAnno2016/zipball/master
> >>> Installing BiocAnno2016
> >>> Skipping 7 unavailable packages: BSgenome.Hsapiens.UCSC.hg19,
> >>> EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, Homo.sapiens,
> >>> hugene20sttranscriptcluster.db, org.Hs.eg.db,
> >>> TxDb.Hsapiens.UCSC.hg19.knownGene
> >>> Skipping 19 packages ahead of CRAN: AnnotationDbi, AnnotationHub,
> Biobase,
> >>> BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
> >>> GenomicAlignments, GenomicRanges, interactiveDisplayBase, IRanges,
> >>> rmarkdown, Rsamtools, rtracklayer, S4Vectors, SummarizedExperiment,
> >>> XVector, zlibbioc
> >>> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
> >>> --no-environ \
> >>> --no-save --no-restore --quiet CMD build \
> >>>
> >>>
> '/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnr0000gn/T/Rtmpq8yntE/devtools32fa3fcc4899/jmacdon-BiocAnno2016-7317126'
> >>> \
> >>> --no-resave-data --no-manual
> >>>
> >>> * checking for file
> >>>
> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnr0000gn/T/Rtmpq8yntE/devtools32fa3fcc4899/jmacdon-BiocAnno2016-7317126/DESCRIPTION’
> >>> ... OK
> >>> * preparing ‘BiocAnno2016’:
> >>> * checking DESCRIPTION meta-information ... OK
> >>> * installing the package to process help pages
> >>> -----------------------------------
> >>> ERROR: dependencies ‘EnsDb.Hsapiens.v79’, ‘Homo.sapiens’,
> >>> ‘EnsDb.Mmusculus.v79’ are not available for package ‘BiocAnno2016’
> >>> * removing
> >>>
> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnr0000gn/T/RtmpBduTCP/Rinst33cf24872f4e/BiocAnno2016’
> >>> -----------------------------------
> >>> ERROR: package installation failed
> >>> Error: Command failed (1)
> >>>> biocLite('Homo.sapiens')
> >>> BioC_mirror: https://bioconductor.org
> >>> Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
> >>> Installing package(s) ‘Homo.sapiens’
> >>> installing the source package ‘Homo.sapiens’
> >>>
> >>> trying URL '
> >>>
> https://bioconductor.org/packages/3.3/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz
> >>> '
> >>> Content type 'application/x-gzip' length 1617 bytes
> >>> ==================================================
> >>> downloaded 1617 bytes
> >>>
> >>> * installing *source* package ‘Homo.sapiens’ ...
> >>> ** R
> >>> ** data
> >>> ** preparing package for lazy loading
> >>> Warning: package ‘GenomicRanges’ was built under R version 3.3.1
> >>> ** help
> >>> *** installing help indices
> >>> ** building package indices
> >>> ** testing if installed package can be loaded
> >>> Warning: package ‘GenomicRanges’ was built under R version 3.3.1
> >>> * DONE (Homo.sapiens)
> >>>
> >>> The downloaded source packages are in
> >>>
> >>>
> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnr0000gn/T/Rtmpq8yntE/downloaded_packages’
> >>> Old packages: 'airway', 'BiocStyle', 'ComplexHeatmap', 'dendextend',
> >>> 'DESeq2',
> >>> 'devtools', 'docopt', 'dplyr', 'ensembldb', 'genefilter',
> >>> 'GenomicFeatures',
> >>> 'GEOquery', 'Gviz', 'h2o', 'HSMMSingleCell', 'lfa', 'limma',
> 'miRLAB',
> >>> 'monocle', 'nlme', 'oligo', 'pracma', 'purrr', 'RBGL',
> 'RcppArmadillo',
> >>> 'Rhtslib', 'robustbase', 'rstudioapi', 'rvest', 'sevenbridges',
> >>> 'SomaticCancerAlterations', 'survival', 'tidyr', 'tximport',
> >>> 'VariantAnnotation', 'vegan', 'VGAM', 'withr', 'XLConnect',
> >>> 'XLConnectJars',
> >>> 'xml2'
> >>> Update all/some/none? [a/s/n]: n
> >>>> sessionInfo()
> >>> R version 3.3.0 (2016-05-03)
> >>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> >>> Running under: OS X 10.11 (El Capitan)
> >>>
> >>> locale:
> >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>>
> >>> attached base packages:
> >>> [1] stats graphics grDevices utils datasets methods base
> >>>
> >>> other attached packages:
> >>> [1] BiocInstaller_1.22.3
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] httr_1.2.0 R6_2.1.2 tools_3.3.0 withr_1.0.1
> >>> [5] curl_0.9.7 memoise_1.0.0 knitr_1.13 git2r_0.15.0
> >>> [9] digest_0.6.9 devtools_1.11.1
> >>>
> >>
> >>
> >>
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:2}}
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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