rnaseq role fails to install bioconductor packages

[johnbradley]

The error is as follows:

   googlecompute: TASK [rnaseq : Install bioconductor packages for R] ****************************
    googlecompute: fatal: [127.0.0.1]: FAILED! => {"changed": true, "cmd": ["/usr/bin/Rscript", "-e", "install.packages('BiocManager', repos = 'http://cran.us.r-project.org'); 
BiocManager::install('DESeq2');"], "delta": "0:00:02.859477", "end": "2020-02-21 
15:58:03.128996", "msg": "non-zero return code", "rc": 1, "start": "2020-02-21 15:58:00.269519", "stderr": "Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
  cannot open URL 
'http://cran.us.r-project.org/src/contrib/PACKAGES'
Warning message:
package ‘BiocManager’ is not available (for R version 3.6.0) 
Error in loadNamespace(name) : there is no package called ‘BiocManager’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted", "stderr_lines": ["Installing package into ‘/usr/lib64/R/library’", "(as ‘lib’ is unspecified)", "Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:", "  cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES'", "Warning message:", "package ‘BiocManager’ is not available (for R version 3.6.0) ", "Error in loadNamespace(name) : there is no package called ‘BiocManager’", "Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart", "Execution halted"], "stdout": "", "stdout_lines": []}

Currently the http://cran.us.r-project.org URL redirects to http://cran.revolutionanalytics.com/ and fails to connect to that server.

Relevant code:

gcb-ansible-roles/rnaseq/tasks/main.yml

Line 56 in c4b8af5

command: /usr/bin/Rscript -e "install.packages('BiocManager', repos = 'http://cran.us.r-project.org'); BiocManager::install('DESeq2');"