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csoneson / alevinQC

Create QC and summary reports for Alevin output
https://csoneson.github.io/alevinQC/
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suggestion to update ignorePandoc argument #19

Closed LisaHagenau closed 3 years ago

LisaHagenau commented 3 years ago

I had a problem generating the report with alevinQCReport(), with the error message "pandoc-citeproc is not available! The final report will not be generated.". I tried installing pandoc-citeproc with brew on MacOS Catalina, but this gave an error as well. Apparently, pandoc-citeproc is deprecated since pandoc version 2.11 (https://github.com/jgm/pandoc/releases/tag/2.11). Removing the .checkPandoc function and the ignorePandoc arguments in alevinQCReport.R and re-installing from source got rid of the error message and output the report. A better solution might be to update the .checkPandoc function: check the pandoc version and only checking for pandoc-citeproc for versions <2.11.

Thanks!

csoneson commented 3 years ago

Thanks for the report! You are correct - I'll fix this.

LisaHagenau commented 3 years ago

Great, thank you!

csoneson commented 3 years ago

Sorry for the delay - would you be able to try the fix that I just pushed to the master branch of this repository, to see if that solves the problem for you?

LisaHagenau commented 3 years ago

Yes, it works fine now. Thank you!