We get the following error sometimes when running SomaticRunSVCircos:
Error in file(con, "w") : cannot open the connection
Calls: <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
In addition: Warning messages:
1: In grSoftVersion() :
unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
libXt.so.6: cannot open shared object file: No such file or directory
2: In file(con, "w") :
cannot open file 'biocircos.knit.md': Permission denied
Execution halted
We found that it's because of how rmarkdown::render works. unless intermediates_dir is defined when calling the function intermediate files are written to the same directory as the input file (the .Rmd file). Because the .Rmd file is symlinked from the code repo, the function is attempting to write intermediate files not in the work directory but in the code repo, even though it is later cleaned up. To fix, we should set intermediates_dir to the current directory or to a temp directory.
We get the following error sometimes when running
SomaticRunSVCircos:We found that it's because of how rmarkdown::render works. unless
intermediates_diris defined when calling the function intermediate files are written to the same directory as the input file (the .Rmd file). Because the .Rmd file is symlinked from the code repo, the function is attempting to write intermediate files not in the work directory but in the code repo, even though it is later cleaned up. To fix, we should setintermediates_dirto the current directory or to a temp directory.