Question: Install Bioconductor package locally/temporarily
0
gravatar for ariel
8 months ago by
ariel0
ariel0 wrote:

It is possible to install regular R packages so that they are deleted after the current session, and better yet, don't touch current packages.

You can use install.packags(destdir="...") as well as other methods

Is there a way to do this with bioconductor packages? I am working on a project that involves a large number of bioconductor packages. I'm running into installation conflicts. The best method I've found is to use a conda environment that gets me all but a two of the packages I need. I'd like to be able to install them without touching the conda environment.

ADD COMMENTlink modified 8 months ago by Martin Morgan ♦♦ 23k • written 8 months ago by ariel0
Answer: Install Bioconductor package locally/temporarily
0
gravatar for Martin Morgan
8 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

use BiocInstaller::biocinstallRepos() to get the correct repositories to be used with standard R package installation commands. (bio)conda expects all packages to be installed by bioconda; if there are packages not available from bioconda or if a recent distribution is important then personally I think your best bet is to forgo using conda. The alternative is I think like Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH, where conda-installed system dependencies are not found by standard R installation commands. 

ADD COMMENTlink written 8 months ago by Martin Morgan ♦♦ 23k
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