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I have a LaTeX file ThesisFinal.tex that I compile with arara. The file starts with the following lines:

% arara: clean: { extensions: [aux, bbl, bcf, blg, glg, glo, gls, idx, ilg, ind, ist, log, out, run.xml, slnc, tex~, toc] }
% arara: lualatex
% arara: biber
% arara: makeglossaries
% arara: lualatex
% arara: makeglossaries
% arara: lualatex

When I run the command arara ThesisFinal, the compilation stops on the biber call with the following error message:

(Biber) The Biber reference management software ......... FAILURE

If I then run biber ThesisFinal the execution seems to run error-free, here's the complete output:

INFO - This is Biber 2.16
INFO - Logfile is 'ThesisFinal.blg'
INFO - Reading 'ThesisFinal.bcf'
INFO - Found 10 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'Bibliography.bib' for section 0
INFO - LaTeX decoding ...
INFO - Found BibTeX data source 'Bibliography.bib'

How can I find the problem, and fix it?

EDIT: I've just checked out the entire folder to the state it was in yesterday when everything compiled successfully, but now the compilation fails on Biber, as above.

Evan Aad
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    unrelated to biber, but your document needs two runs of makeglossaries and only needs three runs of latex to converge? Both seem unusual. – David Carlisle Aug 16 '21 at 07:45
  • @DavidCarlisle: Is one run of makeglossaries usually enough? – Evan Aad Aug 16 '21 at 07:46
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    well unless you have glossaries entries in generated content that does not appear until later eg nested entries – David Carlisle Aug 16 '21 at 07:48
  • @DavidCarlisle: What does 'nested entries' mean? Can you give me an example of a nested entry? – Evan Aad Aug 16 '21 at 07:50
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    a glossary enty with a definition text using a glossary term not used elsewhere so the first run of makeglossaries generates a new entry that would appear on the second. – David Carlisle Aug 16 '21 at 08:00
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    It could be that Biber's cache is corrupted. (The biber ThesisFinal run shows no error, but is also not complete and it is possible that the return code of this run is non-zero.) See https://tex.stackexchange.com/q/543837/35864. Try deleting the cache as described in https://tex.stackexchange.com/q/140814/35864. Then rerun Biber. That Biber run will take much longer than usual, because it unpacks the cache again: Do not abort the Biber run. Wait for it to complete. – moewe Aug 16 '21 at 08:33
  • @moewe: Yes, this was the problem. Thank you very much! – Evan Aad Aug 16 '21 at 09:10
  • I'd like to clarify the solution to the problem, since I've had to deal with it more than once. All that needs to be done is run the following command from the console: rm -rf `biber --cache` This clears the Biber cache. Once the cache has been cleared, the problem is solved. This solution as well as the explanation for it are described in this answer, which was suggested above by moewe. – Evan Aad Dec 03 '21 at 07:35

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