LyX ⇒ Lyx-2.2.0 fails on Biblatex/natbib

[ExecutorElassus]

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.

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

[ExecutorElassus]

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
\output_sync 0
\bibtex_command biber
\index_command default
\paperfontsize 12
\spacing single
\use_hyperref false
\papersize a4paper
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
\use_package cancel 0
\use_package esint 1
\use_package mathdots 1
\use_package mathtools 0
\use_package mhchem 1
\use_package stackrel 0
\use_package stmaryrd 0
\use_package undertilde 0
\cite_engine natbib
\cite_engine_type authoryear
\biblio_style \use_bibtopic false
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification false
\use_refstyle 1
\index Index
\shortcut idx
\color #008000
\end_index
\paperwidth 200mm
\paperheight 287mm
\leftmargin 2cm
\topmargin 2cm
\rightmargin 3cm
\bottommargin 2cm
\secnumdepth 3
\tocdepth 1
\paragraph_separation skip
\defskip smallskip
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle fancy
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header

\begin_body

\begin_layout Standard
blah 
\begin_inset CommandInset citation
LatexCommand citet
key "aarseth1994nonlinearity"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Note Note
status collapsed

\begin_layout Plain Layout
\begin_inset CommandInset bibtex
LatexCommand bibtex
bibfiles "/[$HOME]/bookbib"
options "bibtotoc,plainnat"

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
printbibliography
\end_layout

\end_inset


\end_layout

\end_body
\end_document

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]

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

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.

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. 
. * 'small caps' with NFSS spec.:
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. and font adjustment code:
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. 
. * 'bold' with NFSS spec.:
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. 
. * 'bold small caps' with NFSS spec.:
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. and font adjustment code:
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. 
. * 'small caps' with NFSS spec.:
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. and font adjustment code:
. 
. 
. * 'bold italic' with NFSS spec.:
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. 
. * 'bold small caps' with NFSS spec.:
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cp;"
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. and font adjustment code:
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. 
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. 
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. and font adjustment code:
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. and font adjustment code:
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* \topskip=12.0pt
* \footskip=50.75pt
* \marginparwidth=49.79233pt
* \marginparsep=12.8401pt
* \columnsep=10.0pt
* \skip\footins=10.8pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

Package biblatex Info: XeTeX detected.
(biblatex)             Assuming input encoding 'utf8'.
Package biblatex Info: Automatic encoding selection.
(biblatex)             Assuming data encoding 'utf8'.
\openout4 = `bibliography_tester.bcf'.

Package biblatex Info: Trying to load bibliographic data...

Package biblatex Warning: File 'bibliography_tester.bbl' is wrong format versio
n - expected 2.7.

Package biblatex Info: ... file 'bibliography_tester.bbl' found.
(./bibliography_tester.bbl)
Package biblatex Info: Reference section=0 on input line 33.
Package biblatex Info: Reference segment=0 on input line 33.
Package polyglossia Info: Option: english variant=american.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <12> on input line 34.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <8> on input line 34.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <6> on input line 34.

LaTeX Warning: Citation 'aarseth1994nonlinearity' on page 1 undefined on input 
line 34.


LaTeX Warning: Empty bibliography on input line 36.


Class scrbook Warning: Usage of deprecated font command `\sl'!
(scrbook)              You should note, that in 1994 font command `\sl' has
(scrbook)              been defined for compatiblitiy to Script 2.0 only.
(scrbook)              Now, after two decades of LaTeX2e and NFSS2, you
(scrbook)              shouldn't use such commands any longer and within
(scrbook)              KOMA-Script usage of `\sl' is definitely deprecated.
(scrbook)              See `fntguide.pdf' for more information about
(scrbook)              recommended font commands.
(scrbook)              Note also, that KOMA-Script will remove the definition
(scrbook)              of `\sl' anytime until release of about version 3.20.
(scrbook)              But for now, KOMA-Script will replace deprecated `\sl'
(scrbook)              by `\normalfont \slshape ' on input line 37.

LaTeX Font Info:    Font shape `EU1/LinuxLibertineO(0)/m/sl' in size <12> not a
vailable
(Font)              Font shape `EU1/LinuxLibertineO(0)/m/it' tried instead on i
nput line 37.

Class scrbook Warning: Usage of deprecated font command `\sl'!
(scrbook)              You should note, that in 1994 font command `\sl' has
(scrbook)              been defined for compatiblitiy to Script 2.0 only.
(scrbook)              Now, after two decades of LaTeX2e and NFSS2, you
(scrbook)              shouldn't use such commands any longer and within
(scrbook)              KOMA-Script usage of `\sl' is definitely deprecated.
(scrbook)              See `fntguide.pdf' for more information about
(scrbook)              recommended font commands.
(scrbook)              Note also, that KOMA-Script will remove the definition
(scrbook)              of `\sl' anytime until release of about version 3.20.
(scrbook)              But for now, KOMA-Script will replace deprecated `\sl'
(scrbook)              by `\normalfont \slshape ' on input line 37.


Class scrbook Warning: Usage of deprecated font command `\rm'!
(scrbook)              You should note, that in 1994 font command `\rm' has
(scrbook)              been defined for compatiblitiy to Script 2.0 only.
(scrbook)              Now, after two decades of LaTeX2e and NFSS2, you
(scrbook)              shouldn't use such commands any longer and within
(scrbook)              KOMA-Script usage of `\rm' is definitely deprecated.
(scrbook)              See `fntguide.pdf' for more information about
(scrbook)              recommended font commands.
(scrbook)              Note also, that KOMA-Script will remove the definition
(scrbook)              of `\rm' anytime until release of about version 3.20.
(scrbook)              But for now, KOMA-Script will replace deprecated `\rm'
(scrbook)              by `\normalfont \rmfamily ' on input line 37.

[1

] (./bibliography_tester.aux)

LaTeX Warning: There were undefined references.


Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)                bibliography_tester
(biblatex)                and rerun LaTeX afterwards.

Package logreq Info: Writing requests to 'bibliography_tester.run.xml'.
\openout1 = `bibliography_tester.run.xml'.

 ) 
Here is how much of TeX's memory you used:
 23620 strings out of 495438
 470222 string characters out of 6181911
 1015571 words of memory out of 5000000
 26678 multiletter control sequences out of 15000+600000
 6886 words of font info for 44 fonts, out of 8000000 for 9000
 76 hyphenation exceptions out of 8191
 58i,10n,70p,10436b,3367s stack positions out of 5000i,500n,10000p,200000b,80000s

Output written on bibliography_tester.pdf (1 page).

[scottkosty]

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]

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]

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]

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

Code: Select all

[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

[ExecutorElassus]

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?

[Johannes_B]

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

[PhilipPirrip]

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.