Running old packages on Mac
Entering edit mode
Last seen 19 months ago

Hi all!

I would like to run some bioconductor packages on a really old (but still powerful) MacPro (OS X 10.8.5) with R 3.1.3 (I cannot install newer R versions on this machine). Now I installed an old distribution of ShortRead using biocLite(). But when I run


it tells me that the required BiocParallel could not load. Hence I run


which produces the warning:

'Error in readRDS(pfile):

cannot read workspace version 3 written by R 3.6.2; need R 3.5.0 or newer.'

So package load for BiocParallel fails. I understand that this is because of the old R version used. However, loading the Biostrings package, for instance, works fine, so I was wondering if there is a trick to make ANY bioconductor package load properly (i.e., circumvent this readRDS error issue).

Thanks a lot, Daniel

ShortRead • 709 views
Entering edit mode

Some of the technical members more familiar with the package builds, etc., may respond, but I think that a solution via conda would work here? That is, create a new conda environment for R 3.1.3, and then also install packages outside R via conda. In this way, all package versions should function 'harmoniously', unless a particular package was never available for R 3.1.3

Entering edit mode
Last seen 13 days ago
United States

I don't think you want to trick an old R into loading new packages. Instead, arrange for old R to have access to old packages.

Do this by creating a directory for the old packages.

mkdir ~/R-3.1.3-library

In R, set the library path so that this is in the first position

.libPaths()  # confirm set correctly

If possible, set the CRAN repository to an appropriate snapshot date, e.g,. in the Microsoft 'time machine' . Looks like for R 3.1.3 you might have been using Bioc 3.0, and from it looks like the last date of that release was sometime around October 14, 2014. It would be great to install CRAN packages from that date, but I think the best you can do is a snapshot from 2015-01-01. So set

options(repos = c(CRAN = ""))

Use biocLite (if that's appropriate) to install packages -- during the installation, you should see (a) the packages from the correct Bioconductor and CRAN repositories and (b) they are installed into the correct library path.

This is only a 'shot in the dark' so you might need to do some additional work -- it will be useful to do this with a small number of packages (Biobase?) to work out the bugs. I'm not sure, for instance, whether that old version of R supports https on Windows, or conversely whether the Microsoft time machine is listening on http.

But this is a very old release; are you really sure you want to go through these steps?


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