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installing bioconductor packages downgrades R #135

Closed kcivkulis closed 3 years ago

kcivkulis commented 3 years ago

Hello,

I can successfully setup my conda and bioinfo environment following How to install conda and How to install software on Linux system. R is installed, and which R shows /home/kristaps/miniconda3/envs/bioinfo/bin/R, and R --version starts with R version 4.0.3 (2020-10-10).

Later following https://www.biostarhandbook.com/bio-statistics.html I try to setup bioconductor. Since R is installed from conda, I run conda install -y bioconductor-deseq bioconductor-deseq2 bioconductor-edger r-gplots.

Conda shows

The following packages will be SUPERSEDED by a higher-priority channel:

  r-base               conda-forge::r-base-4.0.3-ha43b4e8_3 --> pkgs/r::r-base-3.2.2-0

After installation I can't run R anymore. When I launch R it shows /home/kristaps/miniconda3/envs/bioinfo/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory.

As a side note, conda installs 4.0.2 version of R if I install the bioconductor packages first and only then install packages mentioned in How to install software. What a strange behavior. Still, I would like to keep the freshest 4.0.3 version.

ialbert commented 3 years ago

Apologies, looks like I have forgotten to remove the link to that page. It has been reworked.

The bioconductor-deseq has been deprecated and should not be installed. The proper installation for statistical methods is on the following page:

https://www.biostarhandbook.com/books/rnaseq/rnaseq-statistics.html

ialbert commented 3 years ago

In this case you should rerun the environment setup starting with:

conda create --name bioinfo python=3.6

https://www.biostarhandbook.com/install-software.html

Again apologies for leaving that in, unfortunately conda is unable to handle it graciously.

ialbert commented 3 years ago

The outdated installation instructions have been removed from the book.