Biber suddenly unstable

Question

Suddenly biber (under bibtex) has become unstable in the sense that it occasionally doesn't compile citekeys into references. In practice this means that in the pdf, instead of the reference, the citekey is printed.

When manually running Tools -> Commands -> Biber it works again ... for some time.

Any suggestions on how to fix that?

The problem occurred again (after several successful compilations). I have added the log file (is there better way to add it?):

'firstinits' option is deprecated, use 'giveninits' instead.
Upgrade package 'polyglossia' to >v1.42.0 recommended.
'babel/polyglossia' detected but 'csquotes' missing.
Conflicting options.
Not defining \perthousand.
Not defining \micro.
Overfull \hbox (5.69069pt too wide) in alignment
Font shape `OMS/LiberationSerif(0)/bx/n' undefined(Font) using `OMS/cmsy/m/n' instead
Font shape `OMS/LiberationSerif(0)/m/n' undefined(Font) using `OMS/cmsy/m/n' instead
Underfull \hbox (badness 10000) in paragraph
Citation 'bahn2015' on page 6 undefined
Citation 'bahn2016' on page 6 undefined
Citation 'bahn2016a' on page 6 undefined
Citation 'bahn2017a' on page 6 undefined
Citation 'bahn2017b' on page 6 undefined
Citation 'bahn2017c' on page 6 undefined
Citation 'bahn2017d' on page 6 undefined
Citation 'bahn2017e' on page 6 undefined
Citation 'clivaz2017' on page 6 undefined
Citation 'bahn2018' on page 6 undefined
Citation 'winslow2018' on page 6 undefined
Citation 'bahn2018a' on page 6 undefined
Citation 'bahn2009' on page 7 undefined
Citation 'allerup2012' on page 7 undefined
Citation 'allerup2012' on page 7 undefined
Citation 'allerup2012' on page 7 undefined
Citation 'sorensen2014' on page 7 undefined
Citation 'niss2002' on page 7 undefined
Citation 'niss2006' on page 7 undefined
Citation 'jespersen2013' on page 7 undefined
Overfull \hbox (10.5564pt too wide) in paragraph
Citation 'artigue2013' on page 8 undefined
Citation 'rocard2007' on page 8 undefined
Citation 'q-model' on page 8 undefined
Citation 'artigue2012' on page 8 undefined
Citation 'rocard2007' on page 8 undefined
Citation 'mogensen2011' on page 8 undefined
Citation 'niss2006' on page 8 undefined
Citation 'rocard2007' on page 8 undefined
Citation 'lindhart2007' on page 8 undefined
Citation 'rocard2007' on page 8 undefined
Citation 'artigue2013' on page 8 undefined
Citation 'bruce2008' on page 8 undefined
Citation 'jackson2009a' on page 8 undefined
Citation 'seidel2011' on page 8 undefined
Citation 'tripp2012' on page 8 undefined
Citation 'stigler1999' on page 8 undefined
Citation 'isoda2007' on page 8 undefined
Citation 'makinae2010' on page 8 undefined
Citation 'becker1997' on page 8 undefined
Citation 'nohda1995' on page 8 undefined
Citation 'nohda2000' on page 8 undefined
Citation 'stigler1999' on page 8 undefined
Citation 'isoda2015a' on page 8 undefined
Overfull \hbox (8.00838pt too wide) in paragraph
Citation 'isoda2007' on page 8 undefined
Citation 'fernandez2004' on page 8 undefined
Citation 'stigler2016' on page 8 undefined
Citation 'bahn2018' on page 9 undefined
Citation 'lewis2016' on page 9 undefined
Citation 'murata2011' on page 9 undefined
Citation 'miyakawa2009' on page 9 undefined
Citation 'miyakawa2017' on page 9 undefined
Overfull \hbox (28.85829pt too wide) in paragraph
Citation 'isoda2007' on page 10 undefined
Citation 'makinae2010' on page 10 undefined
Citation 'makinae2010' on page 10 undefined
Citation 'makinae2010' on page 10 undefined
Citation 'makinae2010' on page 10 undefined
Overfull \hbox (11.70674pt too wide) in paragraph
Citation 'fernandez2004' on page 10 undefined
Citation 'fernandez2004' on page 10 undefined
Citation 'lewis2009' on page 10 undefined
Citation 'stigler1999' on page 10 undefined
Citation 'fujii2016a' on page 10 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'fujii2014' on page 10 undefined
Citation 'takahashi2016' on page 10 undefined
Citation 'murata2011' on page 10 undefined
Citation 'takahashi2016' on page 10 undefined
Citation 'winslow2018' on page 10 undefined
Citation 'winslow2018' on page 10 undefined
Citation 'fujii2016a' on page 10 undefined
Citation 'fujii2016a' on page 10 undefined
Citation 'miyakawa2013' on page 10 undefined
Citation 'miyakawa2009' on page 11 undefined
Citation 'watanabe2008' on page 11 undefined
Citation 'takahashi2011a' on page 11 undefined
Citation 'takahashi2011a' on page 11 undefined
Citation 'fujii2014' on page 11 undefined
Citation 'fujii2014' on page 11 undefined
Citation 'isoda2015a' on page 11 undefined
Citation 'watanabe2008' on page 11 undefined
Citation 'fujii2016' on page 11 undefined
Citation 'hino2007' on page 11 undefined
Citation 'miyakawa2017' on page 11 undefined
Citation 'lewis2016' on page 11 undefined
Citation 'miyakawa2017' on page 11 undefined
Citation 'fujii2016a' on page 11 undefined
Citation 'takahashi2014' on page 11 undefined
Citation 'takahashi2014' on page 11 undefined
Citation 'takahashi2014' on page 11 undefined
Citation 'takahashi2014' on page 11 undefined
Citation 'takahashi2011a' on page 11 undefined
Citation 'takahashi2011a' on page 11 undefined
Citation 'lewis2016a' on page 12 undefined
Citation 'lewis2016a' on page 12 undefined
Citation 'lewis2016a' on page 12 undefined
Citation 'lewis2011a' on page 12 undefined
Citation 'inoue2011' on page 12 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'winslow2018' on page 12 undefined
Citation 'winslow2018' on page 12 undefined
Citation 'murata2011' on page 12 undefined
Citation 'murata2011' on page 13 undefined
Citation 'takahashi2016' on page 13 undefined
Citation 'fujii2014' on page 13 undefined
Citation 'murata2011' on page 13 undefined
Citation 'isoda2015a' on page 13 undefined
Overfull \hbox (4.26518pt too wide) in paragraph
Citation 'fujii2014' on page 13 undefined
Citation 'fujii2014' on page 13 undefined
Citation 'fujii2014' on page 13 undefined
Citation 'hart2011a' on page 13 undefined
Citation 'quaresma2018' on page 13 undefined
Citation 'fernandez2004' on page 13 undefined
Citation 'hino2007' on page 13 undefined
Citation 'ermeling2014' on page 13 undefined
Citation 'takahashi2016' on page 13 undefined
Citation 'winslow2004' on page 13 undefined
Citation 'winslow2004' on page 13 undefined
Citation 'winslow2006' on page 13 undefined
Citation 'miyakawa2009' on page 13 undefined
Citation 'miyakawa2013' on page 13 undefined
Citation 'miyakawa2017' on page 13 undefined
Citation 'winslow2012a' on page 13 undefined
Citation 'mogensen2011' on page 14 undefined
Citation 'rasmussen2016a' on page 14 undefined
Citation 'ostergaard2016' on page 14 undefined
Citation 'becker1997' on page 14 undefined
Citation 'becker1997' on page 14 undefined
Citation 'isoda2007' on page 14 undefined
Citation 'nohda2000' on page 14 undefined
Citation 'becker1997' on page 14 undefined
Citation 'hino2007' on page 14 undefined
Citation 'stigler1999' on page 14 undefined
Citation 'hino2007' on page 14 undefined
Citation 'isoda2015a' on page 14 undefined
Citation 'nohda2000' on page 14 undefined
Citation 'isoda2015a' on page 14 undefined
Citation 'nohda2000' on page 14 undefined
Citation 'nohda1995' on page 14 undefined
Citation 'nohda2000' on page 14 undefined
Citation 'nohda2000' on page 14 undefined
Citation 'nohda1995' on page 14 undefined
Citation 'becker1997' on page 14 undefined
Citation 'becker1997' on page 15 undefined
Citation 'nohda1995' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'becker1997' on page 15 undefined
Citation 'nohda1995' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'isoda2015a' on page 15 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'nohda2000' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'nohda2000' on page 15 undefined
Citation 'miyakawa2009' on page 15 undefined
Citation 'miyakawa2009' on page 15 undefined
Citation 'miyakawa2009' on page 15 undefined
Citation 'miyakawa2009' on page 15 undefined
Citation 'miyakawa2009' on page 15 undefined
Citation 'nohda2000' on page 16 undefined
Citation 'nohda2000' on page 16 undefined
Citation 'nohda2000' on page 16 undefined
Underfull \hbox (badness 4403) in paragraph
Citation 'nohda2000' on page 16 undefined
Citation 'nohda2000' on page 16 undefined
Citation 'nohda2000' on page 16 undefined
Underfull \hbox (badness 10000) in paragraph
Underfull \hbox (badness 10000) in paragraph
Citation 'nohda1995' on page 16 undefined
Citation 'becker1997' on page 16 undefined
Citation 'becker1997' on page 16 undefined
Citation 'nohda2000' on page 16 undefined
Citation 'nohda2000' on page 16 undefined
Citation 'chevallard1988' on page 16 undefined
Citation 'brousseau1997' on page 17 undefined
Citation 'hersant2005' on page 17 undefined
Citation 'miyakawa2015' on page 17 undefined
Citation 'miyakawa2009' on page 17 undefined
Citation 'margolinas2005' on page 17 undefined
Citation 'clivaz2016' on page 17 undefined
Citation 'clivaz2015' on page 17 undefined
Citation 'clivaz2018a' on page 17 undefined
Citation 'winslow2018' on page 17 undefined
Citation 'masoval2011' on page 18 undefined
Citation 'warfield2013' on page 18 undefined
Citation 'brousseau1997' on page 18 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'brousseau1997' on page 18 undefined
Citation 'brousseau1997' on page 18 undefined
Citation 'perrin-glorian2008' on page 18 undefined
Citation 'brousseau1997' on page 21 undefined
Citation 'brousseau1997' on page 21 undefined
Citation 'brousseau1997' on page 21 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'brousseau1997' on page 21 undefined
Citation 'hersant2005' on page 21 undefined
Citation 'bahn2017c' on page 21 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'winslow2018' on page 22 undefined
Citation 'winslow2018' on page 22 undefined
Citation 'winslow2018' on page 23 undefined
Citation 'winslow2018' on page 23 undefined
Underfull \hbox (badness 10000) in paragraph
Underfull \hbox (badness 10000) in paragraph
Underfull \hbox (badness 10000) in paragraph
Underfull \hbox (badness 10000) in paragraph
Underfull \hbox (badness 10000) in paragraph
Reference `fig:T-DS' on page 24 undefined
Citation 'fujii2016a' on page 24 undefined
Citation 'takahashi2011a' on page 24 undefined
Citation 'winslow2018' on page 25 undefined
Citation 'winslow2018' on page 25 undefined
Citation 'winslow2018' on page 25 undefined
Citation 'winslow2018' on page 25 undefined
Underfull \hbox (badness 10000) in paragraph
Citation 'winslow2012a' on page 25 undefined
Citation 'hart2011' on page 35 undefined
Citation 'clivaz2018' on page 35 undefined
Citation 'clivaz2018' on page 35 undefined
Citation 'clivaz2018' on page 35 undefined
Citation 'takahashi2011a' on page 35 undefined
Underfull \hbox (badness 10000) in paragraph
Underfull \hbox (badness 10000) in paragraph
Overfull \hbox (6.30957pt too wide) in paragraph
Overfull \hbox (13.91507pt too wide) in paragraph
Overfull \hbox (6.30957pt too wide) in paragraph
Overfull \hbox (13.624pt too wide) in paragraph
Overfull \hbox (6.30957pt too wide) in paragraph
Overfull \hbox (13.624pt too wide) in paragraph
Underfull \hbox (badness 10000) in paragraph
Citation 'clivaz2015' on page 41 undefined
Citation 'miyakawa2009' on page 41 undefined
Citation 'lewis2002a' on page 43 undefined
Empty bibliography
Underfull \hbox (badness 2970) in paragraph
Underfull \hbox (badness 2744) in paragraph
Some font shapes were not available, defaults substituted.
There were undefined references.
Please (re)run Biber on the file:(biblatex) Inquiry_based_mathematics_education_and_lesson_study(biblatex) and rerun LaTeX afterwards.

if there is an error in your bib file (or citation reference) biber may fail to generate a bibliography in which case biblatex will act as it acts on the first run, and show the key. There is no generic solution to avoiding errors, if you show the log file or source with an error someone could suggest a fix. — David Carlisle, Jul 19 '18 at 12:31
@DavidCarlisle, thanks for pointing that out. I should of course have pasted the log file. I'll do that when it occurs again. — jbahn, Jul 19 '18 at 12:34
How are you normally compiling? If Tools -> Commands -> Biber this sounds like whatever tool you use for compiling, it might not always run biber — samcarter_is_at_topanswers.xyz, Jul 19 '18 at 12:51
You mean under biblatex and not under BibTeX, right? If you apply changes to your .bib file or change bibliography-sensitive bits of your document, LaTeX will prompt you for a Biber-(re-)run in the .log file/warnings. You should then run Biber. If your editor does not automatically run Biber for you on each compilation that means you have to 'manually' initiate the Biber run. If the Biber run finished successfully everything is fine, if you get warnings or errors from Biber (in the .blg file), you must fix these before you can continue. It is not clear to me what exactly you are doing — moewe, Jul 19 '18 at 13:10
... Can you give more details? Did you instruct your editor to run Biber at all times automatically for you or do you have to call it manually? When or how does the output become unstable? Are all citations affected or only new (updated, changed) ones? — moewe, Jul 19 '18 at 13:11
@DavidCarlisle, as it most of the time runs fine, I don't think there is an error in the bib file — jbahn, Jul 20 '18 at 07:09
@samcarter, I usually just compile! I mean, until this problem occurred, I would just press F6 and voila... — jbahn, Jul 20 '18 at 07:10
Can you upload the complete .log file (maybe to a text sharing website such as pastebin, GitHub Gists, GitLab snippets, ...) This seems to be the digested (and pruned log) that your editor produces, it does not contain all the information LaTeX gives us. — moewe, Jul 20 '18 at 07:13
@moewe, I can not account for what I may have done that case this situation in detail. As described here: https://tex.stackexchange.com/questions/442213/restoring-default-color-scheme-of-texstudio I did delete the texstudio.ini file in order to restore the color scheme of the editor. After deletion and restart of texstudio (which recreates the .ini file), biber compiled perfectly for some time, until this problem occurred. I believe I did nothing other than writing and compiling inbetween. — jbahn, Jul 20 '18 at 07:15
A few things: Your TeX system is a bit dated by now (TeX live 2015, biblatex from 2016). That need to necessarily be a bad thing, but some packages like biblatex (and Biber) are actively developed, so you can't use new features and won't get the bug fixes. You don't have to update and an update is always always brings the risk of incompatibilities after an update, but keep that in mind. — moewe, Jul 20 '18 at 07:23
Furthermore, the log shows a few warnings, you should try to get rid of: 'firstinits' option is deprecated, use 'giveninits' instead. 'giveninits' conflicts with 'uniquename=full'. Setting 'uniquename=init'. Lastly LaTeX asks you to re-run Biber, you should do that. The citations should work when you have done that. — moewe, Jul 20 '18 at 07:27
@moewe, as stated in the OP, re-running biber does in fact solve the problem - for a while. — jbahn, Jul 20 '18 at 09:29
@moewe, I have now changed firstinits to giveninits and will see if that helps. I apparently don't use the uniguename command. — jbahn, Jul 20 '18 at 09:31
As stated in my answer: That is expected. In certain situations you need to (re-)run Biber to obtain correct citations. That is a fact. If LaTeX prompts you to do that, it will have its reasons. We don't know enough about your situation to be able to say more. But it could be that from time to time your editor decides to clean auxiliary files, which would mean that Biber needs to run again. Maybe your editor sometimes gets confused and runs BibTeX instead of Biber - you would need to run Biber after that to clean up the mess as well. ... — moewe, Jul 20 '18 at 10:02
... As long as you are not prompted to run Biber every time and you can not reproduce a situation in which you are asked to re-run Biber when it is not (should not be) necessary, I'm going to assume that things are working as intended. You are indeed not using uniquename, but you should load uniquename=init with your settings (or uniquename=false if you prefer, check out uniquename in the documentation). Neither uniquename nor giveninits should have an impact on the problem, but you should still use the correct settings. — moewe, Jul 20 '18 at 10:03

score 1 · Answer 1 · answered Jul 19 '18 at 16:03

Usually Biber does not become occasionally unstable. Biber might be more sensitive than BibTeX in some regards, but usually that should not result in erratic occasional problems, but in clear cut errors that are always reproducible (I remember one elusive SIGSEGV with weird name formats a while ago, but that is about it).

There are a few possible explanations for your problems. To understand what is going on, we first need to understand what Biber does for the bibliography. Paul Stanley explains that much better than I ever could in Question mark or bold citation key instead of citation number and you should definitely read his answer (completely!, note in particular that what he says about BibTeX is roughly also applicable to Biber, Biber is biblatex's BibTeX replacement) before you continue here. Just to recap:

LaTeX logs the entries you cite and the order in which you cite them in an external auxiliary file (with biblatex and Biber that is the .bcf, otherwise the .aux file).
Biber reads the .bcf and gets the requested entries from the .bib file.
- Biber parses the relevant entries into a format that LaTeX or rather biblatex can understand.
- Then Biber sorts the citations and writes the sorted list of citations into an auxiliary file (the .bbl) in a format that biblatex can easily digest.
LaTeX then reads the entries from the auxiliary .bbl file and uses the data to construct the citations and the bibliography.

That means that you at least need to compile your document (mydoc.tex, say) with LaTeX, Biber, LaTeX to be sure to obtain a complete bibliography, in particular

LaTeX: pdflatex mydoc (of course you can also use any other flavour of LaTeX, for example xelatex or lualatex)
Biber: biber mydoc
LaTeX: pdflatex mydoc
LaTeX: pdflatex mydoc

often - but not always - the last LaTeX run is required at the end to get page numbers and cross references right, but that need not concern us here.

The bibliography data is only available and usable for LaTeX after a Biber run. Naturally only the data collected at the point of the Biber run is available. If you change the contents of your .bib file after the Biber run, these changes will only propagate to the output of your document after a new Biber and subsequent LaTeX run.

LaTeX will usually prompt you to run Biber or LaTeX again in the .log files if it can detect that a new run is required. That message is usually classified as a warning, so that your editor should show it quite prominently if it parses the log output for you. But LaTeX can not detect all cases in which a Biber re-run is required, it does for example not monitor your .bib file for changes. An automatic tool like latexmk can help you there.

In general you do not need to call Biber every time you call LaTeX. If you just added a bit of text, a new Biber run is often not necessary. But you need to run Biber in the following cases, the reasons marked with an asterisk are normally detected automatically, so that LaTeX reminds you to run Biber if you happen to forget it.

An entries cited in the document is modified in the .bib file.
*An entry that was not cited before is cited (the new entry needs to be added).
*The order of citations is changed (depending on the sorting scheme and other settings).
*An entry that was cited before is not cited any more (and needs to be removed).

If you notice certain citations missing or misbehaving it can be a good idea to run Biber (and then LaTeX again).

When LaTeX can not find the data for a specific entry in the .bbl file, it just prints the key of the entry in bold and issues a warning. There are several possible causes for such a warning

There is a typo in the entry key, i.e. sigfridson instead of sigfridsson.
The entry is not present in the .bib file.
The entry is 'new' (either in the .bib file or the .tex file) and was not present when the Biber was called the last time.

At the moment what you are describing suggests that your editor does not run Biber for you all the time. That is, as outlined above, not a bad decision, since a Biber run takes a bit of time and is not always required. That means, however, that you need to initiate the Biber run explicitly when it is called for.

Call Biber whenever you change something bibliography-related in your document or .bib file.
Call Biber when LaTeX issues a warning to that effect.
Call Biber when you notice that your citations appear off or broken.

If the full compilation circle LaTeX, Biber, LaTeX, LaTeX does not help to resolve the bad output, you may want to try to delete the temporary files (.aux, .bbl, .bcf, ...) and recompile with LaTeX, Biber, LaTeX, LaTeX from scratch.

If you get any errors on the first (clean) LaTeX run, these must be fixed before you continue. You can ignore warnings about missing citations and references, but all other warnings should ideally also be fixed before you continue. Errors and warnings on the Biber run should also be fixed. On the second LaTeX run you should not get any new errors and warnings. If you get errors even though the first LaTeX run did not cause errors, the cause for your errors lives in your .bib file. On the last LaTeX run you should obtain a error- and warning-free document with correct citations and complete bibliography.

You can find further hints for troubleshooting Biber in Troubleshooting for biber

Biber suddenly unstable

1 Answers1