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geneplotter is installed but BiocManager::install function will still try to download and install, how to change such behave? Because my connetion is very bad.
> packageVersion("geneplotter")
[1] ‘1.64.0’
> BiocManager::install("GSVA")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'GSVA'
also installing the dependencies ‘geneplotter’, ‘shinythemes’
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz'
Content type 'application/x-gzip' length 1431450 bytes (1.4 MB)
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Here:
I have many anaconda environments for different project.
I also have only one package library path and I cannot reproduce this problem. So, this is then likely to be associated with your specific installation setup, such as what you mention about having different anaconda environments. Unfortunately, I have no experience with those and cannot give further advice. In any case, this does not look as a Bioconductor specific problem. If nobody else here gives you any further hint, you may have better luck asking in some anaconda specific forum or some other more general support site such as biostars or stackoverflow. If you end up following that path, please link to this post to let people know where you've already asked about this.
I think the recommended advice is that if you've installed R via conda then you also want to use conda to install packages, rather than using BiocManager.