Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo
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
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"
> > To: "James W. MacDonald" , "Sean Davis" <
> sdav...@mail.nih.gov>
> > 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/BiocAnno201
Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo
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
>>> ==
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', '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
Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo
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 Rooseve
