[Bioc-devel] Confusion on biocLite() with github and annotation data repo

[Martin Morgan]

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
>>
>
>
>


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