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
