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markziemann / mitch

An R package for multi-dimensional pathway enrichment analysis
https://bioconductor.org/packages/mitch
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mitch_report fails if an absoulte path is given as outfile #13

Closed Christian-Heyer closed 4 years ago

Christian-Heyer commented 4 years ago

When I attempt to run mitch_report using an absolute path for outfile, it will fail with an error message like:

> data(resExample)
> mitch_report(resExample, '/desktop-home/heyer/outres2.html')
Error in file(file, "wb") : cannot open the connection
In addition: Warning message:
In file(file, "wb") :
  cannot open file '/tmp/Rtmpv71mKa//desktop-home/heyer/outres2.RDataTmp': No such file or directory
Warning message:
In file.remove(outfile) :
  cannot remove file '/tmp/Rtmpv71mKa//desktop-home/heyer/outres2.RDataTmp', reason 'No such file or directory'

I guess this is somehow related to how the temporary file paths are created from the outfile in the mitch_report function. I don't know if this is somehow related to #10, but after installing the package from GitHub directly i still ran into this issue.

markziemann commented 4 years ago

@Christian-Heyer Thanks for raising this issue. I can reproduce it, so I will start work on a patch.

markziemann commented 4 years ago

Hi Christian, I've pushed a patch, could you install from GitHub and give it a try? Thanks

Christian-Heyer commented 4 years ago

Hi Mark, sorry for the delay, but I was able to try out the new version and the bug is fixed. Thanks for the quick fix.