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cbielow / PTXQC

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
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Error pandoc #89

Closed DaliJarboui closed 10 months ago

DaliJarboui commented 3 years ago

Dear developer, I followed your installation steps to the word for windows, however when trying to use PTXQC, I receive an error that pandoc.exe is missing, I installed pandoc for windows (pandoc-2.11.1.1-windows-x86_64.msi) and retrieved the doc containing pandoc copied it as you detailed, and still I receive an error about pandoc missing. is there a dependency to a specific version of pandoc ??. appreciate your help regards

cbielow commented 3 years ago

The pandoc installer should(?) have made pandoc available within R. Well... seems that did not work.

Some ideas to fix this: 1) make sure pandoc.exe is found globally in a commandline/console/terminal, i.e.

c:\>where pandoc

should give something like

C:\Program Files\RStudio\bin\pandoc\pandoc.exe

If that is not the case, then add the path to pandoc.exe (in my case C:\Program Files\RStudio\bin\pandoc to your $PATH variable) and make sure to restart the console or any other application afterwards so they use the updated PATH.

2) within R, try

> rmarkdown::pandoc_available()
[1] TRUE

this should return TRUE. If it does, then PTXQC should also run fine. Do this is the same R session, that is used for PTXQC, in particular not in RStudio (which is a wrapper around a plain R console because it adds more enviroment variables, which might make pandoc available, even though it would be missing in a plain R console).

Hope this helps. Let me know if this fixes it. Good luck :)