Lyx-2.2.0 fails on Biblatex/natbib

ExecutorElassus · Post by **ExecutorElassus** » Fri Jun 03, 2016 12:17 pm

So, I downgraded Lyx to 2.1.4, and now it won't start. The error is:

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 $ lyx
Warning: Could not read configuration file
----------------------------------------
Error while reading the configuration file
preferences.
Please check your installation.
 
 
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Where would that file be?

Also, when I previously clicked "show output anyway" it shows a document, but the bibliography entries are not compiled (it just prints the entry IDs).

Cheers,

EE

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ExecutorElassus · Post by **ExecutorElassus** » Fri Jun 03, 2016 12:27 pm

In the meantime, here's the LyX file I was using:

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#LyX 2.2 created this file. For more info see http://www.lyx.org/
\lyxformat 508
\begin_document
\begin_header
\save_transient_properties true
\origin unavailable
\textclass scrbook
\begin_preamble
\usepackage{polyglossia}
\setdefaultlanguage{usenglish}
\usepackage[notes,natbib,backend=biber,alldates=iso8601,idemtracker=context,ibidtracker=context,dateabbrev=false,language=american]{biblatex-chicago}
\renewcommand\citet{\autocite}
\bibliography{/[$HOME]/bookbib}
\addbibresource{/[$HOME]/bookbib.bib}
\errorcontextlines=10
\end_preamble
\use_default_options true
\begin_modules
biblatex
\end_modules
\maintain_unincluded_children false
\begin_local_layout
Format 60
Provides natbib 1
\end_local_layout
\language american
\language_package auto
\inputencoding default
\fontencoding global
\font_roman "default" "Linux Libertine O"
\font_sans "default" "Linux Biolinum O"
\font_typewriter "default" "default"
\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts true
\font_sc false
\font_osf true
\font_sf_scale 100 100
\font_tt_scale 100 100
\graphics default
\default_output_format default
 
 
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I'm uploading the bib file. Also, where do I find the compile log?

Cheers,

EE

PS- Addendum: I moved the 'preferences' file to a backup, and now 2.1.4 started. However, all of the files I've been using were modified by 2.2.0, so 2.1.4 can't open them. I made a new file, which still doesn't work in 2.1.4 (which should not be the case). Now I suspect the .bib file has a problem. I use jabref as my editor. Do you see anything in the .bib file that looks odd? There may be some utf-8 stuff in there, or odd characters. Let me know if you find something.

PPS- Second Addendum: Also, I notice that the Lyx wiki has removed the section about modifying the preamble to configure for Xetex with polyglossia (previously you had to set the language manually if using polyglossia). Is that no longer necessary?

ExecutorElassus · Post by **ExecutorElassus** » Fri Jun 03, 2016 4:14 pm

Also, here's the biblatex log:

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[0] Config.pm:340> INFO - This is Biber 2.4
[0] Config.pm:343> INFO - Logfile is 'bibliography_tester.blg'
[56] biber:286> INFO - === Fr Jun  3, 2016, 13:40:16
[79] Biber.pm:347> INFO - Reading 'bibliography_tester.bcf'
[223] Utils.pm:147> WARN - Warning: Found biblatex control file version 3.1, expected version 3.0
[225] Biber.pm:741> INFO - Found 1 citekeys in bib section 0
[236] Biber.pm:3150> INFO - Processing section 0
[295] Biber.pm:3307> INFO - Looking for bibtex format file '/[$HOME]/bookbib.bib' for section 0
[367] bibtex.pm:1111> INFO - Decoding LaTeX character macros into UTF-8
[431] bibtex.pm:972> INFO - Found BibTeX data source '/[$HOME]/bookbib.bib'
[567] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
[567] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
[567] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'level = 4' with 'level = 2'
[567] Biber.pm:3027> INFO - Sorting list 'cms/global/' of type 'entry' with scheme 'cms' and locale 'en-US'
[567] Biber.pm:3031> INFO - No sort tailoring available for locale 'en-US'
[599] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
[599] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
[599] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'level = 4' with 'level = 2'
[599] Biber.pm:3027> INFO - Sorting list 'cms/global' of type 'entry' with scheme 'cms' and locale 'en-US'
[599] Biber.pm:3031> INFO - No sort tailoring available for locale 'en-US'
[602] bbl.pm:519> INFO - Writing 'bibliography_tester.bbl' with encoding 'UTF-8'
[603] bbl.pm:615> INFO - Output to bibliography_tester.bbl
[603] Biber.pm:108> INFO - WARNINGS: 1
 
 
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And here's the Latex log:

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This is XeTeX, Version 3.14159265-2.6-0.99992 (TeX Live 2015) (preloaded format=xelatex 2016.5.24)  3 JUN 2016 13:40
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**bibliography_tester.tex
(./bibliography_tester.tex
LaTeX2e <2015/01/01> patch level 2
Babel <3.9l> and hyphenation patterns for 19 languages loaded.
(/usr/share/texmf-dist/tex/latex/koma-script/scrbook.cls
Document Class: scrbook 2015/07/02 v3.18 KOMA-Script document class (book)
(/usr/share/texmf-dist/tex/latex/koma-script/scrkbase.sty
Package: scrkbase 2015/07/02 v3.18 KOMA-Script package (KOMA-Script-dependent b
asics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrbase.sty
Package: scrbase 2015/07/02 v3.18 KOMA-Script package (KOMA-Script-independent 
basics and keyval usage)
(/usr/share/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks14
) (/usr/share/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package: scrlfile 2015/07/02 v3.18 KOMA-Script package (loading files)
Package scrlfile, 2015/07/02 v3.18 KOMA-Script package (loading files)
                  Copyright (C) Markus Kohm
))) (/usr/share/texmf-dist/tex/latex/koma-script/tocbasic.sty
Package: tocbasic 2015/07/02 v3.18 KOMA-Script package (handling toc-files)
)
Package tocbasic Info: omitting babel extension for `toc'
(tocbasic)             because of feature `nobabel' available
(tocbasic)             for `toc' on input line 125.
Package tocbasic Info: omitting babel extension for `lof'
(tocbasic)             because of feature `nobabel' available
(tocbasic)             for `lof' on input line 126.
Package tocbasic Info: omitting babel extension for `lot'
(tocbasic)             because of feature `nobabel' available
(tocbasic)             for `lot' on input line 127.
Package tocbasic Info: defining new hook before heading of `' on input line 157
8.
Package scrbook Info: You've used standard option `12pt'.
(scrbook)             This is correct!
 
 
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Post by **scottkosty** » Sat Jun 04, 2016 4:25 am

The LyX wiki pages regarding biblatex have been updated. Apparently the way in LyX 2.2.0 is different than before:

https://wiki.lyx.org/BibTeX/Biblatex

If you want to go back to 2.1.4, exit LyX, move the folder ~/.lyx somewhere else. Then start LyX again.

PhilipPirrip · Post by **PhilipPirrip** » Wed Jun 08, 2016 3:40 pm

Have you checked if the "two simple examples" from https://wiki.lyx.org/BibTeX/Biblatex work?
You're using some absolute paths, but what exactly do you have for [Home]?
I don't think this is the right way of redefining \renewcommand\citet{\autocite} as well.

ExecutorElassus · Post by **ExecutorElassus** » Thu Jun 09, 2016 2:45 pm

In the simple examples, it doesn't work with biber, but does print titles and dates in the proper style with bibtex8.

So, it seems like my biber installation is broken?

Also, to answer your question about the [$HOME] path. It's the same in every case: a subdirectory residing on another partition. It starts "/home/[username]/…" and finishes at the proper location (it has to, or else citations wouldn't work).

ExecutorElassus · Post by **ExecutorElassus** » Thu Jun 09, 2016 3:24 pm

Also, here is the bibtex log from the simple example:

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[0] Config.pm:340> INFO - This is Biber 2.4
[0] Config.pm:343> INFO - Logfile is 'bibliography-biblatex-biber.blg'
[57] biber:286> INFO - === Do Jun  9, 2016, 15:09:25
[78] Biber.pm:347> INFO - Reading 'bibliography-biblatex-biber.bcf'
[226] Utils.pm:147> WARN - Warning: Found biblatex control file version 3.1, expected version 3.0
[229] Biber.pm:738> INFO - Using all citekeys in bib section 0
[240] Biber.pm:3150> INFO - Processing section 0
[299] Biber.pm:3307> INFO - Looking for bibtex format file 'bibliography.bib' for section 0
[355] bibtex.pm:1111> INFO - Decoding LaTeX character macros into UTF-8
[357] bibtex.pm:972> INFO - Found BibTeX data source '/[$HOME-DOCS]/bibtext tests/Bibliography-BibLaTeX-LyX220/bibliography.bib'
[509] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
[510] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
[510] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'level = 4' with 'level = 2'
[510] Biber.pm:3027> INFO - Sorting list 'cms/global/' of type 'entry' with scheme 'cms' and locale 'en-US'
[510] Biber.pm:3031> INFO - No sort tailoring available for locale 'en-US'
[578] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
[578] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
[578] UCollate.pm:65> INFO - Overriding locale 'en-US' defaults 'level = 4' with 'level = 2'
[578] Biber.pm:3027> INFO - Sorting list 'cms/global' of type 'entry' with scheme 'cms' and locale 'en-US'
[579] Biber.pm:3031> INFO - No sort tailoring available for locale 'en-US'
[585] bbl.pm:519> INFO - Writing 'bibliography-biblatex-biber.bbl' with encoding 'UTF-8'
[586] bbl.pm:615> INFO - Output to bibliography-biblatex-biber.bbl
[586] Biber.pm:108> INFO - WARNINGS: 1
 
 
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ExecutorElassus · Post by **ExecutorElassus** » Thu Jun 09, 2016 6:00 pm

Another thing: when I tell jabref (the binary for v3.3) to "check integrity" on the .bib file, I get a lot of warnings about the entries. Almost all of them are about capital letters not being inside curly braces, but also page number ranges being invalid (I think I was typing "--" in the entries, as this would typeset to an en-dash), and the occasional "abbreviation detected."

How urgent are these warnings, and might they be causing biber to fail to process the bibtex file?

Post by **Johannes_B** » Thu Jun 09, 2016 8:44 pm

You need to do an update for pacages biblatex and biber.

PhilipPirrip · Post by **PhilipPirrip** » Thu Jun 09, 2016 8:45 pm

Why don't you try your MWE with the .bib file from "two simple examples". Debugging is hard with so many entries. Biber+biblatex is probably broken (don't know why), so you might need to stick to bibtex8.
Btw. if your .bib file is in the same directory as your main document, biblatex in LyX 2.2 should work without specifying the absolute path. You'll appreciate this once you have to move your files.

LaTeX.org

LyX ⇒ Lyx-2.2.0 fails on Biblatex/natbib