[Bioc-devel] using BiocLite() on Ubuntu Xenial with its default R 3.2.3 release

[Martin Morgan]

On 07/20/2017 08:36 AM, Jack Howarth wrote:
> I am trying to use the BiocLite() feature of Bioconductor to install
> the R modules required by MetaboAnalyst 3.0 under Ubuntu Xenial
> 16.04LTS with its system R 3.2.3 release. I have added the repo for
> Micheal Rutter's cran2deb4ubuntu to provide the missing cran R modules
> but have avoided installing any of the r-bioc ones to keep the
> installation purely using those installed in /usr/local/lib/R by
> BiocLite(). Unfortunately, this is failing on
> 
> $ sudo R
> 
>> source("https://bioconductor.org/biocLite.R")
> 
>> biocLite("‘AnnotationDbi")
> 
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
> Installing package(s) ‘‘AnnotationDbi’
> Warning message:
> package ‘‘AnnotationDbi’ is not available (for R version 3.2.3)
>>
> 
> Certainly there must be a way to redirect BiocLite to a legacy release
> which fully supports the older R 3.2.3 in the current Ubuntu LTS
> release?

Unfortunately (?) this 'works for me' (the .5 Patched moniker should 
really be of no consequence)

 > biocLite("AnnotationDbi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.5 Patched (2016-05-05
   r72327).
Installing package(s) ‘AnnotationDbi’
trying URL 
'https://bioconductor.org/packages/3.2/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz'
Content type 'application/x-gzip' length 4268480 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in 
package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package 
‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationDbi)

The downloaded source packages are in
	‘/tmp/Rtmpbyzs5c/downloaded_packages’

The message about 'package not available' could have a number of 
interpretations; it's R's way of saying that it doesn't know where to 
find the package, but that could be, e.g., because R can't access the 
web site where the package is. To trouble shoot, you could try

 > BiocInstaller::biocinstallRepos()
                                                BioCsoft
            "https://bioconductor.org/packages/3.2/bioc"
                                                 BioCann
"https://bioconductor.org/packages/3.2/data/annotation"
                                                 BioCexp
"https://bioconductor.org/packages/3.2/data/experiment"
                                               BioCextra
           "https://bioconductor.org/packages/3.2/extra"
                                                    CRAN
                              "https://cran.rstudio.com"


AnnotationDbi should be listed in

 > url = paste0(contrib.url(BiocInstaller::biocinstallRepos())[1], 
"/PACKAGES")
 > url
[1] "https://bioconductor.org/packages/3.2/bioc/src/contrib/PACKAGES"

and you should be able read that file, e.g.,

 > txt = readLines(url)
 > length(txt)
[1] 10581
 > grep("Package: AnnotationDbi", txt)
[1] 390

You should also be able to download the package

 > download.packages("AnnotationDbi", tempdir(), repos=biocinstallRepos())
trying URL 
'https://bioconductor.org/packages/3.2/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz'
Content type 'application/x-gzip' length 4268480 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

      [,1]            [,2]
[1,] "AnnotationDbi" "/tmp/Rtmpbyzs5c/AnnotationDbi_1.32.3.tar.gz"

I'm not sure if that helps...

Martin

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