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.
Maybe the same will work for you? Best, Jim On Mon, Jun 27, 2016 at 5:03 PM, Davis, Sean (NIH/NCI) [E] < sdav...@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@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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
