I would like to install older version AnnotationHub_2.4.2 under R version 3.3.0 or R version 3.3.3.
But package ‘AnnotationHub_2.4.2’ is not available (for R version 3.3.0).
Now AnnotationHub_2.6.4 is installed.
How can I install older version of AnnotationHub ?
Bioconductor packages are tightly associated with the R version. If you want to use an older version of any package, you have to use the correct version of R. Unfortunately, R is released yearly and Bioc is semi-annually, so you are asking for a version of AnnotationHub that corresponds to Bioc 3.3, which was the first version of Bioconductor for R-3.3.x. Simply installing R-3.3.0 and using biocLite will get you AnnotationHub 2.6.4, as you have noted. So we have to be a bit tricky.
You can either uninstall BiocInstaller (using remove.packages), or just install a clean version of R-3.3.0, and install BiocInstaller by hand (here I am using my Windows box. You need to point to the correct version of the package for your OS).
> install.packages("http://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/BiocInstaller_1.22.3.zip", repos=NULL)
trying URL 'http://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/BiocInstaller_1.22.3.zip'
Content type 'application/zip' length 119756 bytes (116 KB)
downloaded 116 KB
package ‘BiocInstaller’ successfully unpacked and MD5 sums checked
> library(BiocInstaller)
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
> biocLite("AnnotationHub")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘AnnotationHub’
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/AnnotationHub_2.4.2.zip'
Thank you for replying my question.
I used Yosemite macOS10.10.5.
>install.packages("http://bioconductor.org/packages/3.3/bioc/bin/macosx/yosemite/contrib/3.3/BiocInstaller_1.22.3.zip", repos=NULL)
downloaded 0 bytes
Warning in install.packages :
URL 'http://bioconductor.org/packages/3.3/bioc/bin/macosx/yosemite/contrib/3.3/BiocInstaller_1.22.3.zip': status was '404 Not Found'
Error in download.file(p, destfile, method, mode = "wb", ...) :
cannot download all files
Error in install.packages : type == "both" cannot be used with 'repos = NULL'
I tried mavericks instead of yosemite, but failed.
How should I do to solve this problem?
Make sure you have removed all versions of BiocInstaller
R --vanilla
> remove.packages("BiocInstaller") # repeat until R says "there is no pacakge called 'BiocInstaller'
Start a new R session and install the default BiocInstaller
R --vanilla
> source("http://bioconductor.org/biocLite.R")
Downgrade BiocInstaller
> BiocInstaller::useDevel(FALSE)
You'll now have BiocInstaller 1.22.3.
> BiocInstaller::biocLite("AnnotationHub")
will install the version of AnnnotationHub you are looking for.
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version 2.3.6
Why do you need an older version? Perhaps AnnotationHub::snapshotDate() will help, or perhaps the resource that you are after is simply no longer available?