rJava issue in topanat

[fbastian]

In GitLab by @smoretti on Nov 26, 2018, 15:40

Weird issue with TopAnat

...
Error:Loading required package: rJava
Error:Error: package or namespace load failed for ‘rJava’:
Error: .onLoad failed in loadNamespace() for 'rJava', details:
Error:  call: dyn.load(file, DLLpath = DLLpath, ...)
Error:  error: unable to load shared object '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
Error:  libjvm.so: cannot open shared object file: No such file or directory
Error:Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
Error:A newer version of Bioconductor is available for this version of R,
Error:  ?BiocUpgrade for help
Error:BioC_mirror: https://bioconductor.org
Error:Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Error:Installing package(s) ‘rJava’
Error:Warning in install.packages(pkgs = doing, lib = lib, ...) :
Error:  'lib = "/usr/local/lib/R/site-library"' is not writable
Error:Error in install.packages(pkgs = doing, lib = lib, ...) : 
Error:  unable to install packages
Error:Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages
Error:Execution halted