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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