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

2016-06-28 Thread Dan Tenenbaum 
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" 
> To: "James W. MacDonald" , "Sean Davis" 
> 
> Cc: "bioc-devel" 
> 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] <
>> 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_b1j5cp8qby0tnrgn/T/Rtmpq8yntE/devtools32fa3fcc4899/jmacdon-BiocAnno2016-7317126'
>>> \
>>>--no-resave-data --no-manual
>>>
>>> * checking for file
>>> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnrgn/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_b1j5cp8qby0tnrgn/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_b1j5cp8qby0tnrgn/T/Rtmpq8yntE/downloaded_packages’
>>> Old packages: 'airway', 'BiocStyle', 'ComplexHeatmap', 'dendextend',
>>> 'DESeq2',
>>>'devtools', 'docopt',

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

2016-06-28 Thread James W. MacDonald 
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_b1j5cp8qby0tnrgn/T/Rtmpq8yntE/devtools32fa3fcc4899/jmacdon-BiocAnno2016-7317126'
> \
>   --no-resave-data --no-manual
>
> * checking for file
> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnrgn/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_b1j5cp8qby0tnrgn/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_b1j5cp8qby0tnrgn/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_2.1.2tools_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_0.6.9devtools_1.11.1
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225