Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[KIM Musak]

Hi,

Still does not work for me. I found these in my log files:

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\blx-dm.def)

Package biblatex Info: Trying to load biblatex style data model...

Package biblatex Info: ... file 'authoryear.dbx' not found.

Package biblatex Info: Trying to load biblatex custom data model...

Package biblatex Info: ... file 'biblatex-dm.cfg' not found.


and also


Package biblatex Warning: Please (re)run Biber on the file:

(biblatex) testing-natbib

(biblatex) and rerun LaTeX afterwards.


I wonder if MikTex is the culprit?


Thanks


Kamarul


On Mon, Jan 13, 2014 at 11:01 PM, stefano franchi stefano.fran...@gmail.com
 wrote:




 On Mon, Jan 13, 2014 at 3:52 AM, Wolfgang Engelmann 
 engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 18:03:52 stefano franchi wrote:

  On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 

 

  engelm...@uni-tuebingen.de wrote:

   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:

 On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

for biber type

   

biber --version

  

   it is 1.6

  

for biblatex, the easier way is to look at the latex log. Whn

biblatex

   

is loaded (at the beginning of the log) it will tell you the version

  

   biblatex 2013/05/01 v2.6

 

  You're all right then---biblatex 2.6 wants biber 1.6, so everything is

  fine on that front.

 

  I still think you may have path-related issues in the preamble.

 

  Do check the capitalization of your home directory (WE vs we) as per my

  previous message.



 Did take care of that, Stefano,



 Your example is working.



 However, if I try my document, I get on the terminal output under the
 biber part this:



 ###

 Scanning input file PB-Biber.nlodone (150 entries accepted, 0
 rejected).

 Sorting entriesdone (1163 comparisons).

 Generating output file PB-Biber.nlsdone (298 lines written, 0
 warnings).

 Output written in PB-Biber.nls.

 Transcript written in PB-Biber.ilg.



 Running: pdflatex PB-Biber.tex  /dev/null

 This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)

 restricted \write18 enabled.

 entering extended mode

 (./PB-Biber.tex

 LaTeX2e 2011/06/27

 Babel 3.9f and hyphenation patterns for 78 languages loaded.



 Running: xdg-open PB-Biber.pdf

 



 and as a result a pdf file with all citation included, but no
 Bibliography at the end, listing my references.




 That does not look like the output from biber. Are you sure you are
 looking at the latex log in lyx, and selected the bibtex option from the
 drop down menu?




 I wonder what

 Running: xdg-open PB-Biber.pdf

 means.


 xdg-open is just the program that will try to find a suitable program to
 open the pdf file, in your case that will most likely be okular (or
 acroread, depending on your setup).

 S.

 --
 __
 Stefano Franchi
 Associate Research Professor
 Department of Hispanic StudiesPh:   +1 (979) 845-2125
 Texas AM University  Fax:  +1 (979) 845-6421
 College Station, Texas, USA

 stef...@tamu.edu
 http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[KIM Musak]

Hi,

Still does not work for me. I found these in my log files:

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\blx-dm.def)

Package biblatex Info: Trying to load biblatex style data model...

Package biblatex Info: ... file 'authoryear.dbx' not found.

Package biblatex Info: Trying to load biblatex custom data model...

Package biblatex Info: ... file 'biblatex-dm.cfg' not found.


and also


Package biblatex Warning: Please (re)run Biber on the file:

(biblatex) testing-natbib

(biblatex) and rerun LaTeX afterwards.


I wonder if MikTex is the culprit?


Thanks


Kamarul


On Mon, Jan 13, 2014 at 11:01 PM, stefano franchi stefano.fran...@gmail.com
 wrote:




 On Mon, Jan 13, 2014 at 3:52 AM, Wolfgang Engelmann 
 engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 18:03:52 stefano franchi wrote:

  On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 

 

  engelm...@uni-tuebingen.de wrote:

   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:

 On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

for biber type

   

biber --version

  

   it is 1.6

  

for biblatex, the easier way is to look at the latex log. Whn

biblatex

   

is loaded (at the beginning of the log) it will tell you the version

  

   biblatex 2013/05/01 v2.6

 

  You're all right then---biblatex 2.6 wants biber 1.6, so everything is

  fine on that front.

 

  I still think you may have path-related issues in the preamble.

 

  Do check the capitalization of your home directory (WE vs we) as per my

  previous message.



 Did take care of that, Stefano,



 Your example is working.



 However, if I try my document, I get on the terminal output under the
 biber part this:



 ###

 Scanning input file PB-Biber.nlodone (150 entries accepted, 0
 rejected).

 Sorting entriesdone (1163 comparisons).

 Generating output file PB-Biber.nlsdone (298 lines written, 0
 warnings).

 Output written in PB-Biber.nls.

 Transcript written in PB-Biber.ilg.



 Running: pdflatex PB-Biber.tex  /dev/null

 This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)

 restricted \write18 enabled.

 entering extended mode

 (./PB-Biber.tex

 LaTeX2e 2011/06/27

 Babel 3.9f and hyphenation patterns for 78 languages loaded.



 Running: xdg-open PB-Biber.pdf

 



 and as a result a pdf file with all citation included, but no
 Bibliography at the end, listing my references.




 That does not look like the output from biber. Are you sure you are
 looking at the latex log in lyx, and selected the bibtex option from the
 drop down menu?




 I wonder what

 Running: xdg-open PB-Biber.pdf

 means.


 xdg-open is just the program that will try to find a suitable program to
 open the pdf file, in your case that will most likely be okular (or
 acroread, depending on your setup).

 S.

 --
 __
 Stefano Franchi
 Associate Research Professor
 Department of Hispanic StudiesPh:   +1 (979) 845-2125
 Texas AM University  Fax:  +1 (979) 845-6421
 College Station, Texas, USA

 stef...@tamu.edu
 http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[KIM Musak]

Hi,

Still does not work for me. I found these in my log files:

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\blx-dm.def")

Package biblatex Info: Trying to load biblatex style data model...

Package biblatex Info: ... file 'authoryear.dbx' not found.

Package biblatex Info: Trying to load biblatex custom data model...

Package biblatex Info: ... file 'biblatex-dm.cfg' not found.


and also


Package biblatex Warning: Please (re)run Biber on the file:

(biblatex) testing-natbib

(biblatex) and rerun LaTeX afterwards.


I wonder if MikTex is the culprit?


Thanks


Kamarul


On Mon, Jan 13, 2014 at 11:01 PM, stefano franchi  wrote:

>
>
>
> On Mon, Jan 13, 2014 at 3:52 AM, Wolfgang Engelmann <
> engelm...@uni-tuebingen.de> wrote:
>
>>  On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
>>
>> > On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann <
>>
>> >
>>
>> > engelm...@uni-tuebingen.de> wrote:
>>
>> > > On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
>>
>> > > > > On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
>>
>> > > > for biber type
>>
>> > > >
>>
>> > > > biber --version
>>
>> > >
>>
>> > > it is 1.6
>>
>> > >
>>
>> > > > for biblatex, the easier way is to look at the latex log. Whn
>>
>> > > > biblatex
>>
>> > > >
>>
>> > > > is loaded (at the beginning of the log) it will tell you the version
>>
>> > >
>>
>> > > biblatex 2013/05/01 v2.6
>>
>> >
>>
>> > You're all right then---biblatex 2.6 wants biber 1.6, so everything is
>>
>> > fine on that front.
>>
>> >
>>
>> > I still think you may have path-related issues in the preamble.
>>
>> >
>>
>> > Do check the capitalization of your home directory (WE vs we) as per my
>>
>> > previous message.
>>
>>
>>
>> Did take care of that, Stefano,
>>
>>
>>
>> Your example is working.
>>
>>
>>
>> However, if I try my document, I get on the terminal output under the
>> biber part this:
>>
>>
>>
>> ###
>>
>> Scanning input file PB-Biber.nlodone (150 entries accepted, 0
>> rejected).
>>
>> Sorting entriesdone (1163 comparisons).
>>
>> Generating output file PB-Biber.nlsdone (298 lines written, 0
>> warnings).
>>
>> Output written in PB-Biber.nls.
>>
>> Transcript written in PB-Biber.ilg.
>>
>>
>>
>> Running: pdflatex "PB-Biber.tex" > /dev/null
>>
>> This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
>>
>> restricted \write18 enabled.
>>
>> entering extended mode
>>
>> (./PB-Biber.tex
>>
>> LaTeX2e <2011/06/27>
>>
>> Babel <3.9f> and hyphenation patterns for 78 languages loaded.
>>
>>
>>
>> Running: xdg-open "PB-Biber.pdf"
>>
>> 
>>
>>
>>
>> and as a result a pdf file with all citation included, but no
>> Bibliography at the end, listing my references.
>>
>>
>>
>
> That does not look like the output from biber. Are you sure you are
> looking at the latex log in lyx, and selected the "bibtex" option from the
> drop down menu?
>
>
>
>
>> I wonder what
>>
>> Running: xdg-open "PB-Biber.pdf"
>>
>> means.
>>
>>
> xdg-open is just the program that will try to find a suitable program to
> open the pdf file, in your case that will most likely be okular (or
> acroread, depending on your setup).
>
> S.
>
> --
> __
> Stefano Franchi
> Associate Research Professor
> Department of Hispanic StudiesPh:   +1 (979) 845-2125
> Texas A University  Fax:  +1 (979) 845-6421
> College Station, Texas, USA
>
> stef...@tamu.edu
> http://stefano.cleinias.org
>

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
 On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 
 
 engelm...@uni-tuebingen.de wrote:
   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
   for biber type
   
   biber --version
  
  it is 1.6
  
   for biblatex, the easier way is to look at the latex log. Whn
   biblatex
   
   is loaded (at the beginning of the log) it will tell you the version
  
  biblatex 2013/05/01 v2.6
 
 You're all right then---biblatex 2.6 wants biber 1.6, so everything is
 fine on that front.
 
 I still think you may have path-related  issues in the preamble.
 
 Do check the capitalization of your home directory (WE vs we) as per my
 previous message.

Did take care of that, Stefano,

Your example is working.

However, if I try my document, I get on the terminal output under the biber 
part this:

###
Scanning input file PB-Biber.nlodone (150 entries accepted, 0 rejected).
Sorting entriesdone (1163 comparisons).
Generating output file PB-Biber.nlsdone (298 lines written, 0 warnings).
Output written in PB-Biber.nls.
Transcript written in PB-Biber.ilg.

Running: pdflatex  PB-Biber.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./PB-Biber.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.

Running: xdg-open PB-Biber.pdf


and as a result a pdf file with all citation included, but no Bibliography 
at the end, listing my references.

I wonder what 
Running: xdg-open PB-Biber.pdf
means.

I guess I have to experiment with Stefanos example, which works, adding bit 
by bit the essentials of my document and see where and why it fails, unless 
somebody sees already from the output above what went wrong.

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
 On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 
 
 engelm...@uni-tuebingen.de wrote:
   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
   for biber type
   
   biber --version
  
  it is 1.6
  
   for biblatex, the easier way is to look at the latex log. Whn
   biblatex
   
   is loaded (at the beginning of the log) it will tell you the version
  
  biblatex 2013/05/01 v2.6
 
 You're all right then---biblatex 2.6 wants biber 1.6, so everything is
 fine on that front.
 
 I still think you may have path-related  issues in the preamble.
 
 Do check the capitalization of your home directory (WE vs we) as per my
 previous message.
 
 
 Cheers,
 
 S.


we@wolfgang:~$ 
Running: xdg-open testing-biblatexE.pdf



Running: xdg-open testing-biblatexE.pdf


Running: xdg-open testing-biblatexC.pdf

Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: biber testing-biblatexD
INFO - This is Biber 1.6
INFO - Logfile is 'testing-biblatexD.blg'
INFO - Reading 'testing-biblatexD.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file '/tmp/lisp.bib' for section 0
INFO - Found BibTeX data source '/tmp/lisp.bib'
INFO - Overriding locale 'de_DE.UTF-8' default tailoring 'variable = 
shifted' with 'variable = non-ignorable'
INFO - Sorting 'entry' list 'nyt' keys
INFO - No sort tailoring available for locale 'de_DE.UTF-8'
INFO - Writing 'testing-biblatexD.bbl' with encoding 'ascii'
INFO - Output to testing-biblatexD.bbl

Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: xdg-open testing-biblatexD.pdf

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

...
Did take care of that, Stefano,
nbsp;
Your example is working.
nbsp;
However, if I try my document, I get on the terminal output under the biber 
part this:
nbsp;
###
Scanning input file PB-Biber.nlodone (150 entries accepted, 0 rejected).
Sorting entriesdone (1163 comparisons).
Generating output file PB-Biber.nlsdone (298 lines written, 0 warnings).
Output written in PB-Biber.nls.

Hello:

If Stephano's  example file is working it might be that your bib file causes 
the problem.

What I suggest is:

1. Copy your bib file to the same place where you have the working example file.
2. If it still doesn't work, try to remove parts from your bib file step by 
step (first make a backup of the original bib file), and check if it works. 
This may help find the lines of the bib file that causes the problem. 

bcsikos

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Mon, Jan 13, 2014 at 3:52 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 18:03:52 stefano franchi wrote:

  On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 

 

  engelm...@uni-tuebingen.de wrote:

   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:

 On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

for biber type

   

biber --version

  

   it is 1.6

  

for biblatex, the easier way is to look at the latex log. Whn

biblatex

   

is loaded (at the beginning of the log) it will tell you the version

  

   biblatex 2013/05/01 v2.6

 

  You're all right then---biblatex 2.6 wants biber 1.6, so everything is

  fine on that front.

 

  I still think you may have path-related issues in the preamble.

 

  Do check the capitalization of your home directory (WE vs we) as per my

  previous message.



 Did take care of that, Stefano,



 Your example is working.



 However, if I try my document, I get on the terminal output under the
 biber part this:



 ###

 Scanning input file PB-Biber.nlodone (150 entries accepted, 0
 rejected).

 Sorting entriesdone (1163 comparisons).

 Generating output file PB-Biber.nlsdone (298 lines written, 0
 warnings).

 Output written in PB-Biber.nls.

 Transcript written in PB-Biber.ilg.



 Running: pdflatex PB-Biber.tex  /dev/null

 This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)

 restricted \write18 enabled.

 entering extended mode

 (./PB-Biber.tex

 LaTeX2e 2011/06/27

 Babel 3.9f and hyphenation patterns for 78 languages loaded.



 Running: xdg-open PB-Biber.pdf

 



 and as a result a pdf file with all citation included, but no Bibliography
 at the end, listing my references.




That does not look like the output from biber. Are you sure you are looking
at the latex log in lyx, and selected the bibtex option from the drop
down menu?




 I wonder what

 Running: xdg-open PB-Biber.pdf

 means.


xdg-open is just the program that will try to find a suitable program to
open the pdf file, in your case that will most likely be okular (or
acroread, depending on your setup).

S.

-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Stefano Franchi]

On Sun, Jan 12, 2014 at 7:33 PM, KIM Musak kim2u4...@gmail.com wrote:

 Dear Wolgang, Stefano

 I have followed your suggestion. I copied and pasted the files into the
 tmp folders in my windows. still got errors and these are the log files ---
 it is long. But I could see some potential problems as shown by the log
 file - BOLD by me. I know it will take time, but someone will able to find
 the problems there.



Skipping to the bold section:


 Package biblatex Info: Trying to load biblatex default data model...

 Package biblatex Info: ... file 'blx-dm.def' found.

 (C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\blx-dm.def)

 *Package biblatex Info: Trying to load biblatex style data model...*

 *Package biblatex Info: ... file 'authoryear.dbx' not found.*

 *Package biblatex Info: Trying to load biblatex custom data model...*

 *Package biblatex Info: ... file 'biblatex-dm.cfg' not found.*



This should be okay. You are not using a custom data model, and authoryear
using the default, not its own datamodel. So no problems there.

*Package biblatex Info: No input encoding detected.*

 *(biblatex) Assuming 'ascii'.*

 *Package biblatex Info: Automatic encoding selection.*

 *(biblatex) Assuming data encoding 'ascii'.*

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

 *Package biblatex Info: ... file 'testing-natbib.bbl' not found.*


This means that biber failed to produce your bibbliography references (they
would have ended up in a .bbl file, which now biblatex is looking for and
not finding.



 *No file testing-natbib.bbl.*

 *Package biblatex Info: Reference section=0 on input line 18.*

 *Package biblatex Info: Reference segment=0 on input line 18.*


  *LaTeX Warning: Citation '808387' on page 1 undefined on input line 21.*



 *LaTeX Warning: Citation '808387' on page 1 undefined on input line 22.*



  *LaTeX Warning: Empty bibliography on input line 26.*


  *[1*



More of the above. No bbl found, hence your referennces are all undefined.




 BIBTEX


 [0] Config.pm:361 INFO - This is Biber 1.5

 [1] Config.pm:364 INFO - Logfile is 'testing-natbib.blg'

 [85] biber-MSWIN:190 INFO - === %a %b %e, %Y, %H:%M:%S

 [86] Biber.pm:327 INFO - Reading 'testing-natbib.bcf'

 [162] Utils.pm:167 WARN - Warning: Found biblatex control file version
 2.5, expected version 2.3

 [163] Biber.pm:619 INFO - Found 1 citekeys in bib section 0

 [187] Biber.pm:2976 INFO - Processing section 0

 [209] Biber.pm:3086 INFO - Looking for bibtex format file 'lisp.bib' for
 section 0

 *[356] Utils.pm:183 ERROR - Cannot find 'lisp.bib'!*

 *[356] Biber.pm:107 INFO - WARNINGS: 1*

 *[356] Biber.pm:111 INFO - ERRORS: 1*




Here is the main issue: biber cannot find your bib file (lisp.bib).
Notice that I had (wrongly) assumed you were working, like Wolfgang, on a
linux system. But you are on Windows and the /tmp directory makes no sense
in that context. There is no standard /tmp directory in windows. And
slashes are reversed, as far as I remember. So you should modify my test
file:

- copy the lisp.bib file to a local directory you own (perhaps the same
directory you put my text lyx file in)

- insert the exact pathname of the file in your preamble in the
\addbibresource command. I actually do not know how to do that in
Windows--Windows users on the list may be able to help. Assuming you put
your lisp.bib file I would try something like
\addbibresource{C:\Users\YOURHOMEDIR\Documents\lisp.bib}
or
\addbibresource{\Users\YOURHOMEDIR\Documents\lisp.bib}


Cheers,

Stefano

-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
 On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 
 
 engelm...@uni-tuebingen.de wrote:
   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
   for biber type
   
   biber --version
  
  it is 1.6
  
   for biblatex, the easier way is to look at the latex log. Whn
   biblatex
   
   is loaded (at the beginning of the log) it will tell you the version
  
  biblatex 2013/05/01 v2.6
 
 You're all right then---biblatex 2.6 wants biber 1.6, so everything is
 fine on that front.
 
 I still think you may have path-related  issues in the preamble.
 
 Do check the capitalization of your home directory (WE vs we) as per my
 previous message.

Did take care of that, Stefano,

Your example is working.

However, if I try my document, I get on the terminal output under the biber 
part this:

###
Scanning input file PB-Biber.nlodone (150 entries accepted, 0 rejected).
Sorting entriesdone (1163 comparisons).
Generating output file PB-Biber.nlsdone (298 lines written, 0 warnings).
Output written in PB-Biber.nls.
Transcript written in PB-Biber.ilg.

Running: pdflatex  PB-Biber.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./PB-Biber.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.

Running: xdg-open PB-Biber.pdf


and as a result a pdf file with all citation included, but no Bibliography 
at the end, listing my references.

I wonder what 
Running: xdg-open PB-Biber.pdf
means.

I guess I have to experiment with Stefanos example, which works, adding bit 
by bit the essentials of my document and see where and why it fails, unless 
somebody sees already from the output above what went wrong.

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
 On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 
 
 engelm...@uni-tuebingen.de wrote:
   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
   for biber type
   
   biber --version
  
  it is 1.6
  
   for biblatex, the easier way is to look at the latex log. Whn
   biblatex
   
   is loaded (at the beginning of the log) it will tell you the version
  
  biblatex 2013/05/01 v2.6
 
 You're all right then---biblatex 2.6 wants biber 1.6, so everything is
 fine on that front.
 
 I still think you may have path-related  issues in the preamble.
 
 Do check the capitalization of your home directory (WE vs we) as per my
 previous message.
 
 
 Cheers,
 
 S.


we@wolfgang:~$ 
Running: xdg-open testing-biblatexE.pdf



Running: xdg-open testing-biblatexE.pdf


Running: xdg-open testing-biblatexC.pdf

Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: biber testing-biblatexD
INFO - This is Biber 1.6
INFO - Logfile is 'testing-biblatexD.blg'
INFO - Reading 'testing-biblatexD.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file '/tmp/lisp.bib' for section 0
INFO - Found BibTeX data source '/tmp/lisp.bib'
INFO - Overriding locale 'de_DE.UTF-8' default tailoring 'variable = 
shifted' with 'variable = non-ignorable'
INFO - Sorting 'entry' list 'nyt' keys
INFO - No sort tailoring available for locale 'de_DE.UTF-8'
INFO - Writing 'testing-biblatexD.bbl' with encoding 'ascii'
INFO - Output to testing-biblatexD.bbl

Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: pdflatex  testing-biblatexD.tex  /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e 2011/06/27
Babel 3.9f and hyphenation patterns for 78 languages loaded.


Running: xdg-open testing-biblatexD.pdf

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

...
Did take care of that, Stefano,
nbsp;
Your example is working.
nbsp;
However, if I try my document, I get on the terminal output under the biber 
part this:
nbsp;
###
Scanning input file PB-Biber.nlodone (150 entries accepted, 0 rejected).
Sorting entriesdone (1163 comparisons).
Generating output file PB-Biber.nlsdone (298 lines written, 0 warnings).
Output written in PB-Biber.nls.

Hello:

If Stephano's  example file is working it might be that your bib file causes 
the problem.

What I suggest is:

1. Copy your bib file to the same place where you have the working example file.
2. If it still doesn't work, try to remove parts from your bib file step by 
step (first make a backup of the original bib file), and check if it works. 
This may help find the lines of the bib file that causes the problem. 

bcsikos

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Mon, Jan 13, 2014 at 3:52 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 18:03:52 stefano franchi wrote:

  On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 

 

  engelm...@uni-tuebingen.de wrote:

   On Saturday 11 January 2014 16:23:41 stefano franchi wrote:

 On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

for biber type

   

biber --version

  

   it is 1.6

  

for biblatex, the easier way is to look at the latex log. Whn

biblatex

   

is loaded (at the beginning of the log) it will tell you the version

  

   biblatex 2013/05/01 v2.6

 

  You're all right then---biblatex 2.6 wants biber 1.6, so everything is

  fine on that front.

 

  I still think you may have path-related issues in the preamble.

 

  Do check the capitalization of your home directory (WE vs we) as per my

  previous message.



 Did take care of that, Stefano,



 Your example is working.



 However, if I try my document, I get on the terminal output under the
 biber part this:



 ###

 Scanning input file PB-Biber.nlodone (150 entries accepted, 0
 rejected).

 Sorting entriesdone (1163 comparisons).

 Generating output file PB-Biber.nlsdone (298 lines written, 0
 warnings).

 Output written in PB-Biber.nls.

 Transcript written in PB-Biber.ilg.



 Running: pdflatex PB-Biber.tex  /dev/null

 This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)

 restricted \write18 enabled.

 entering extended mode

 (./PB-Biber.tex

 LaTeX2e 2011/06/27

 Babel 3.9f and hyphenation patterns for 78 languages loaded.



 Running: xdg-open PB-Biber.pdf

 



 and as a result a pdf file with all citation included, but no Bibliography
 at the end, listing my references.




That does not look like the output from biber. Are you sure you are looking
at the latex log in lyx, and selected the bibtex option from the drop
down menu?




 I wonder what

 Running: xdg-open PB-Biber.pdf

 means.


xdg-open is just the program that will try to find a suitable program to
open the pdf file, in your case that will most likely be okular (or
acroread, depending on your setup).

S.

-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Stefano Franchi]

On Sun, Jan 12, 2014 at 7:33 PM, KIM Musak kim2u4...@gmail.com wrote:

 Dear Wolgang, Stefano

 I have followed your suggestion. I copied and pasted the files into the
 tmp folders in my windows. still got errors and these are the log files ---
 it is long. But I could see some potential problems as shown by the log
 file - BOLD by me. I know it will take time, but someone will able to find
 the problems there.



Skipping to the bold section:


 Package biblatex Info: Trying to load biblatex default data model...

 Package biblatex Info: ... file 'blx-dm.def' found.

 (C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\blx-dm.def)

 *Package biblatex Info: Trying to load biblatex style data model...*

 *Package biblatex Info: ... file 'authoryear.dbx' not found.*

 *Package biblatex Info: Trying to load biblatex custom data model...*

 *Package biblatex Info: ... file 'biblatex-dm.cfg' not found.*



This should be okay. You are not using a custom data model, and authoryear
using the default, not its own datamodel. So no problems there.

*Package biblatex Info: No input encoding detected.*

 *(biblatex) Assuming 'ascii'.*

 *Package biblatex Info: Automatic encoding selection.*

 *(biblatex) Assuming data encoding 'ascii'.*

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

 *Package biblatex Info: ... file 'testing-natbib.bbl' not found.*


This means that biber failed to produce your bibbliography references (they
would have ended up in a .bbl file, which now biblatex is looking for and
not finding.



 *No file testing-natbib.bbl.*

 *Package biblatex Info: Reference section=0 on input line 18.*

 *Package biblatex Info: Reference segment=0 on input line 18.*


  *LaTeX Warning: Citation '808387' on page 1 undefined on input line 21.*



 *LaTeX Warning: Citation '808387' on page 1 undefined on input line 22.*



  *LaTeX Warning: Empty bibliography on input line 26.*


  *[1*



More of the above. No bbl found, hence your referennces are all undefined.




 BIBTEX


 [0] Config.pm:361 INFO - This is Biber 1.5

 [1] Config.pm:364 INFO - Logfile is 'testing-natbib.blg'

 [85] biber-MSWIN:190 INFO - === %a %b %e, %Y, %H:%M:%S

 [86] Biber.pm:327 INFO - Reading 'testing-natbib.bcf'

 [162] Utils.pm:167 WARN - Warning: Found biblatex control file version
 2.5, expected version 2.3

 [163] Biber.pm:619 INFO - Found 1 citekeys in bib section 0

 [187] Biber.pm:2976 INFO - Processing section 0

 [209] Biber.pm:3086 INFO - Looking for bibtex format file 'lisp.bib' for
 section 0

 *[356] Utils.pm:183 ERROR - Cannot find 'lisp.bib'!*

 *[356] Biber.pm:107 INFO - WARNINGS: 1*

 *[356] Biber.pm:111 INFO - ERRORS: 1*




Here is the main issue: biber cannot find your bib file (lisp.bib).
Notice that I had (wrongly) assumed you were working, like Wolfgang, on a
linux system. But you are on Windows and the /tmp directory makes no sense
in that context. There is no standard /tmp directory in windows. And
slashes are reversed, as far as I remember. So you should modify my test
file:

- copy the lisp.bib file to a local directory you own (perhaps the same
directory you put my text lyx file in)

- insert the exact pathname of the file in your preamble in the
\addbibresource command. I actually do not know how to do that in
Windows--Windows users on the list may be able to help. Assuming you put
your lisp.bib file I would try something like
\addbibresource{C:\Users\YOURHOMEDIR\Documents\lisp.bib}
or
\addbibresource{\Users\YOURHOMEDIR\Documents\lisp.bib}


Cheers,

Stefano

-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
> On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann <
> 
> engelm...@uni-tuebingen.de> wrote:
> >  On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
> > > > On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
> > > for biber type
> > > 
> > > biber --version
> > 
> > it is 1.6
> > 
> > > for biblatex, the easier way is to look at the latex log. Whn
> > > biblatex
> > > 
> > > is loaded (at the beginning of the log) it will tell you the version
> > 
> > biblatex 2013/05/01 v2.6
> 
> You're all right then---biblatex 2.6 wants biber 1.6, so everything is
> fine on that front.
> 
> I still think you may have path-related  issues in the preamble.
> 
> Do check the capitalization of your home directory (WE vs we) as per my
> previous message.

Did take care of that, Stefano,

Your example is working.

However, if I try my document, I get on the terminal output under the biber 
part this:

###
Scanning input file PB-Biber.nlodone (150 entries accepted, 0 rejected).
Sorting entriesdone (1163 comparisons).
Generating output file PB-Biber.nlsdone (298 lines written, 0 warnings).
Output written in PB-Biber.nls.
Transcript written in PB-Biber.ilg.

Running: pdflatex  "PB-Biber.tex" > /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./PB-Biber.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.

Running: xdg-open "PB-Biber.pdf"


and as a result a pdf file with all citation included, but no Bibliography 
at the end, listing my references.

I wonder what 
Running: xdg-open "PB-Biber.pdf"
means.

I guess I have to experiment with Stefanos example, which works, adding bit 
by bit the essentials of my document and see where and why it fails, unless 
somebody sees already from the output above what went wrong.

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
> On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann <
> 
> engelm...@uni-tuebingen.de> wrote:
> >  On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
> > > > On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
> > > for biber type
> > > 
> > > biber --version
> > 
> > it is 1.6
> > 
> > > for biblatex, the easier way is to look at the latex log. Whn
> > > biblatex
> > > 
> > > is loaded (at the beginning of the log) it will tell you the version
> > 
> > biblatex 2013/05/01 v2.6
> 
> You're all right then---biblatex 2.6 wants biber 1.6, so everything is
> fine on that front.
> 
> I still think you may have path-related  issues in the preamble.
> 
> Do check the capitalization of your home directory (WE vs we) as per my
> previous message.
> 
> 
> Cheers,
> 
> S.


we@wolfgang:~$ 
Running: xdg-open "testing-biblatexE.pdf"



Running: xdg-open "testing-biblatexE.pdf"


Running: xdg-open "testing-biblatexC.pdf"

Running: pdflatex  "testing-biblatexD.tex" > /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.


Running: biber "testing-biblatexD"
INFO - This is Biber 1.6
INFO - Logfile is 'testing-biblatexD.blg'
INFO - Reading 'testing-biblatexD.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file '/tmp/lisp.bib' for section 0
INFO - Found BibTeX data source '/tmp/lisp.bib'
INFO - Overriding locale 'de_DE.UTF-8' default tailoring 'variable = 
shifted' with 'variable = non-ignorable'
INFO - Sorting 'entry' list 'nyt' keys
INFO - No sort tailoring available for locale 'de_DE.UTF-8'
INFO - Writing 'testing-biblatexD.bbl' with encoding 'ascii'
INFO - Output to testing-biblatexD.bbl

Running: pdflatex  "testing-biblatexD.tex" > /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.


Running: pdflatex  "testing-biblatexD.tex" > /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.


Running: pdflatex  "testing-biblatexD.tex" > /dev/null
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./testing-biblatexD.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.


Running: xdg-open "testing-biblatexD.pdf"

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Csikos Bela]

Wolfgang Engelmann  írta:

...
>Did take care of that, Stefano,
>
>Your example is working.
>
>However, if I try my document, I get on the terminal output under the biber 
>part this:
>
>###
>Scanning input file PB-Biber.nlodone (150 entries accepted, 0 rejected).
>Sorting entriesdone (1163 comparisons).
>Generating output file PB-Biber.nlsdone (298 lines written, 0 warnings).
>Output written in PB-Biber.nls.

Hello:

If Stephano's  example file is working it might be that your bib file causes 
the problem.

What I suggest is:

1. Copy your bib file to the same place where you have the working example file.
2. If it still doesn't work, try to remove parts from your bib file step by 
step (first make a backup of the original bib file), and check if it works. 
This may help find the lines of the bib file that causes the problem. 

bcsikos

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Mon, Jan 13, 2014 at 3:52 AM, Wolfgang Engelmann <
engelm...@uni-tuebingen.de> wrote:

>  On Saturday 11 January 2014 18:03:52 stefano franchi wrote:
>
> > On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann <
>
> >
>
> > engelm...@uni-tuebingen.de> wrote:
>
> > > On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
>
> > > > > On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
>
> > > > for biber type
>
> > > >
>
> > > > biber --version
>
> > >
>
> > > it is 1.6
>
> > >
>
> > > > for biblatex, the easier way is to look at the latex log. Whn
>
> > > > biblatex
>
> > > >
>
> > > > is loaded (at the beginning of the log) it will tell you the version
>
> > >
>
> > > biblatex 2013/05/01 v2.6
>
> >
>
> > You're all right then---biblatex 2.6 wants biber 1.6, so everything is
>
> > fine on that front.
>
> >
>
> > I still think you may have path-related issues in the preamble.
>
> >
>
> > Do check the capitalization of your home directory (WE vs we) as per my
>
> > previous message.
>
>
>
> Did take care of that, Stefano,
>
>
>
> Your example is working.
>
>
>
> However, if I try my document, I get on the terminal output under the
> biber part this:
>
>
>
> ###
>
> Scanning input file PB-Biber.nlodone (150 entries accepted, 0
> rejected).
>
> Sorting entriesdone (1163 comparisons).
>
> Generating output file PB-Biber.nlsdone (298 lines written, 0
> warnings).
>
> Output written in PB-Biber.nls.
>
> Transcript written in PB-Biber.ilg.
>
>
>
> Running: pdflatex "PB-Biber.tex" > /dev/null
>
> This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
>
> restricted \write18 enabled.
>
> entering extended mode
>
> (./PB-Biber.tex
>
> LaTeX2e <2011/06/27>
>
> Babel <3.9f> and hyphenation patterns for 78 languages loaded.
>
>
>
> Running: xdg-open "PB-Biber.pdf"
>
> 
>
>
>
> and as a result a pdf file with all citation included, but no Bibliography
> at the end, listing my references.
>
>
>

That does not look like the output from biber. Are you sure you are looking
at the latex log in lyx, and selected the "bibtex" option from the drop
down menu?




> I wonder what
>
> Running: xdg-open "PB-Biber.pdf"
>
> means.
>
>
xdg-open is just the program that will try to find a suitable program to
open the pdf file, in your case that will most likely be okular (or
acroread, depending on your setup).

S.

-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Stefano Franchi]

On Sun, Jan 12, 2014 at 7:33 PM, KIM Musak  wrote:

> Dear Wolgang, Stefano
>
> I have followed your suggestion. I copied and pasted the files into the
> tmp folders in my windows. still got errors and these are the log files ---
> it is long. But I could see some potential problems as shown by the log
> file - BOLD by me. I know it will take time, but someone will able to find
> the problems there.
>


Skipping to the bold section:


> Package biblatex Info: Trying to load biblatex default data model...
>
> Package biblatex Info: ... file 'blx-dm.def' found.
>
> ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\blx-dm.def")
>
> *Package biblatex Info: Trying to load biblatex style data model...*
>
> *Package biblatex Info: ... file 'authoryear.dbx' not found.*
>
> *Package biblatex Info: Trying to load biblatex custom data model...*
>
> *Package biblatex Info: ... file 'biblatex-dm.cfg' not found.*
>


This should be okay. You are not using a custom data model, and authoryear
using the default, not its own datamodel. So no problems there.

*Package biblatex Info: No input encoding detected.*

> *(biblatex) Assuming 'ascii'.*
>
> *Package biblatex Info: Automatic encoding selection.*
>
> *(biblatex) Assuming data encoding 'ascii'.*
>
> *Package biblatex Info: Trying to load bibliographic data...*
>
> *Package biblatex Info: ... file 'testing-natbib.bbl' not found.*
>
>
This means that biber failed to produce your bibbliography references (they
would have ended up in a .bbl file, which now biblatex is looking for and
not finding.



> *No file testing-natbib.bbl.*
>
> *Package biblatex Info: Reference section=0 on input line 18.*
>
> *Package biblatex Info: Reference segment=0 on input line 18.*
>
>
>  *LaTeX Warning: Citation '808387' on page 1 undefined on input line 21.*
>
>
>
> *LaTeX Warning: Citation '808387' on page 1 undefined on input line 22.*
>
>
>
>  *LaTeX Warning: Empty bibliography on input line 26.*
>
>
>  *[1*
>
>
>
More of the above. No bbl found, hence your referennces are all undefined.



>
> BIBTEX
>
>
> [0] Config.pm:361> INFO - This is Biber 1.5
>
> [1] Config.pm:364> INFO - Logfile is 'testing-natbib.blg'
>
> [85] biber-MSWIN:190> INFO - === %a %b %e, %Y, %H:%M:%S
>
> [86] Biber.pm:327> INFO - Reading 'testing-natbib.bcf'
>
> [162] Utils.pm:167> WARN - Warning: Found biblatex control file version
> 2.5, expected version 2.3
>
> [163] Biber.pm:619> INFO - Found 1 citekeys in bib section 0
>
> [187] Biber.pm:2976> INFO - Processing section 0
>
> [209] Biber.pm:3086> INFO - Looking for bibtex format file 'lisp.bib' for
> section 0
>
> *[356] Utils.pm:183> ERROR - Cannot find 'lisp.bib'!*
>
> *[356] Biber.pm:107> INFO - WARNINGS: 1*
>
> *[356] Biber.pm:111> INFO - ERRORS: 1*
>
>
>
>
Here is the main issue: biber cannot find your bib file (lisp.bib).
Notice that I had (wrongly) assumed you were working, like Wolfgang, on a
linux system. But you are on Windows and the /tmp directory makes no sense
in that context. There is no standard /tmp directory in windows. And
slashes are reversed, as far as I remember. So you should modify my test
file:

- copy the lisp.bib file to a local directory you own (perhaps the same
directory you put my text lyx file in)

- insert the exact pathname of the file in your preamble in the
\addbibresource command. I actually do not know how to do that in
Windows--Windows users on the list may be able to help. Assuming you put
your lisp.bib file I would try something like
\addbibresource{"C:\Users\YOURHOMEDIR\Documents\lisp.bib"}
or
\addbibresource{\Users\YOURHOMEDIR\Documents\lisp.bib}


Cheers,

Stefano

-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[KIM Musak]

Dear Wolgang, Stefano

I have followed your suggestion. I copied and pasted the files into the tmp
folders in my windows. still got errors and these are the log files --- it
is long. But I could see some potential problems as shown by the log file -
BOLD by me. I know it will take time, but someone will able to find the
problems there.

Regards,

kamarul




LATEX:


This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9) (preloaded
format=pdflatex 2013.11.8) 13 JAN 2014 08:42

entering extended mode

**testing-natbib.tex


(C:\Users\kim\AppData\Local\Temp\lyx_tmpdir.Hp8364\lyx_tmpbuf2\testing-natbib.t

ex

LaTeX2e 2011/06/27

Babel v3.8m and hyphenation patterns for english, afrikaans,
ancientgreek, ar

abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan,
coptic,

croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish,
french, ga

lician, german, german-x-2012-05-30, greek, gujarati, hindi, hungarian,
iceland

ic, indonesian, interlingua, irish, italian, kannada, kurmanji, latin,
latvian,

lithuanian, malayalam, marathi, mongolian, mongolianlmc, monogreek,
ngerman, n

german-x-2012-05-30, nynorsk, oriya, panjabi, pinyin, polish, portuguese,
roman

ian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish,
swissgerm

an, tamil, telugu, turkish, turkmen, ukenglish, ukrainian, uppersorbian,
usengl

ishmax, welsh, loaded.


(C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\article.cls

Document Class: article 2007/10/19 v1.4h Standard LaTeX document class

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\size11.clo

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\c@subparagraph=\count84

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(C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\t1enc.def

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Package: setspace 2011/12/19 v6.7a set line spacing

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Package: biblatex 2013/11/25 v2.8a programmable bibliographies (PK/JW/AB)

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\biblatex2.sty

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(PK/JW/

AB)

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Package: etoolbox 2011/01/03 v2.1 e-TeX tools for LaTeX

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\misc\etex.sty

Package: etex 1998/03/26 v2.0 eTeX basic definition package (PEB)

\et@xins=\count87

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\etb@tempcnta=\count88

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Package: keyval 1999/03/16 v1.13 key=value parser (DPC)

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(C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\ltxcmds.sty

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) (C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\kvsetkeys.sty

Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)

(C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\infwarerr.sty

Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages
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) (C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\etexcmds.sty

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(C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\ifluatex.sty

Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)

Package ifluatex Info: LuaTeX not detected.

)

Package etexcmds Info: Could not find \expanded.

(etexcmds) That can mean that you are not using pdfTeX 1.50 or

(etexcmds) that some package has redefined \expanded.

(etexcmds) In the latter case, load this package earlier.

))) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\logreq\logreq.sty

Package: logreq 2010/08/04 v1.0 xml request logger

\lrq@indent=\count89

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\logreq\logreq.def

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Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)

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\Urlmuskip=\muskip10

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)

\c@tabx@nest=\count90

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\c@liststop=\count94

\c@citecount=\count95

\c@citetotal=\count96

\c@multicitecount=\count97

\c@multicitetotal=\count98

Re: Author-year in Lyx

[KIM Musak]

Dear Wolgang, Stefano

I have followed your suggestion. I copied and pasted the files into the tmp
folders in my windows. still got errors and these are the log files --- it
is long. But I could see some potential problems as shown by the log file -
BOLD by me. I know it will take time, but someone will able to find the
problems there.

Regards,

kamarul




LATEX:


This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9) (preloaded
format=pdflatex 2013.11.8) 13 JAN 2014 08:42

entering extended mode

**testing-natbib.tex


(C:\Users\kim\AppData\Local\Temp\lyx_tmpdir.Hp8364\lyx_tmpbuf2\testing-natbib.t

ex

LaTeX2e 2011/06/27

Babel v3.8m and hyphenation patterns for english, afrikaans,
ancientgreek, ar

abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan,
coptic,

croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish,
french, ga

lician, german, german-x-2012-05-30, greek, gujarati, hindi, hungarian,
iceland

ic, indonesian, interlingua, irish, italian, kannada, kurmanji, latin,
latvian,

lithuanian, malayalam, marathi, mongolian, mongolianlmc, monogreek,
ngerman, n

german-x-2012-05-30, nynorsk, oriya, panjabi, pinyin, polish, portuguese,
roman

ian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish,
swissgerm

an, tamil, telugu, turkish, turkmen, ukenglish, ukrainian, uppersorbian,
usengl

ishmax, welsh, loaded.


(C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\article.cls

Document Class: article 2007/10/19 v1.4h Standard LaTeX document class

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\size11.clo

File: size11.clo 2007/10/19 v1.4h Standard LaTeX file (size option)

)

\c@part=\count79

\c@section=\count80

\c@subsection=\count81

\c@subsubsection=\count82

\c@paragraph=\count83

\c@subparagraph=\count84

\c@figure=\count85

\c@table=\count86

\abovecaptionskip=\skip41

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\bibindent=\dimen102

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Package: fontenc 2005/09/27 v1.99g Standard LaTeX package

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\t1enc.def

File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file

LaTeX Font Info: Redeclaring font encoding T1 on input line 43.

)) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\setspace\setspace.sty

Package: setspace 2011/12/19 v6.7a set line spacing

) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\biblatex.sty

Package: biblatex 2013/11/25 v2.8a programmable bibliographies (PK/JW/AB)

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\biblatex2.sty

Package: biblatex2 2013/11/25 v2.8a programmable bibliographies (biber)
(PK/JW/

AB)

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\etoolbox\etoolbox.sty

Package: etoolbox 2011/01/03 v2.1 e-TeX tools for LaTeX

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\misc\etex.sty

Package: etex 1998/03/26 v2.0 eTeX basic definition package (PEB)

\et@xins=\count87

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\etb@tempcnta=\count88

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Package: keyval 1999/03/16 v1.13 key=value parser (DPC)

\KV@toks@=\toks14

) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\oberdiek\kvoptions.sty

Package: kvoptions 2011/06/30 v3.11 Key value format for package options
(HO)

(C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\ltxcmds.sty

Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)

) (C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\kvsetkeys.sty

Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)

(C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\infwarerr.sty

Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages
(HO)

) (C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\etexcmds.sty

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(HO)

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Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)

Package ifluatex Info: LuaTeX not detected.

)

Package etexcmds Info: Could not find \expanded.

(etexcmds) That can mean that you are not using pdfTeX 1.50 or

(etexcmds) that some package has redefined \expanded.

(etexcmds) In the latter case, load this package earlier.

))) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\logreq\logreq.sty

Package: logreq 2010/08/04 v1.0 xml request logger

\lrq@indent=\count89

(C:\Program Files (x86)\MiKTeX2.9\tex\latex\logreq\logreq.def

File: logreq.def 2010/08/04 v1.0 logreq spec v1.0

)) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\ifthen.sty

Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)

) (C:\Program Files (x86)\MiKTeX2.9\tex\latex\ltxmisc\url.sty

\Urlmuskip=\muskip10

Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc.

)

\c@tabx@nest=\count90

\c@listtotal=\count91

\c@listcount=\count92

\c@liststart=\count93

\c@liststop=\count94

\c@citecount=\count95

\c@citetotal=\count96

\c@multicitecount=\count97

\c@multicitetotal=\count98

Re: Author-year in Lyx

[KIM Musak]

Dear Wolgang, Stefano

I have followed your suggestion. I copied and pasted the files into the tmp
folders in my windows. still got errors and these are the log files --- it
is long. But I could see some potential problems as shown by the log file -
BOLD by me. I know it will take time, but someone will able to find the
problems there.

Regards,

kamarul




LATEX:


This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9) (preloaded
format=pdflatex 2013.11.8) 13 JAN 2014 08:42

entering extended mode

**testing-natbib.tex


(C:\Users\kim\AppData\Local\Temp\lyx_tmpdir.Hp8364\lyx_tmpbuf2\testing-natbib.t

ex

LaTeX2e <2011/06/27>

Babel  and hyphenation patterns for english, afrikaans,
ancientgreek, ar

abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan,
coptic,

croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish,
french, ga

lician, german, german-x-2012-05-30, greek, gujarati, hindi, hungarian,
iceland

ic, indonesian, interlingua, irish, italian, kannada, kurmanji, latin,
latvian,

lithuanian, malayalam, marathi, mongolian, mongolianlmc, monogreek,
ngerman, n

german-x-2012-05-30, nynorsk, oriya, panjabi, pinyin, polish, portuguese,
roman

ian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish,
swissgerm

an, tamil, telugu, turkish, turkmen, ukenglish, ukrainian, uppersorbian,
usengl

ishmax, welsh, loaded.


("C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\article.cls"

Document Class: article 2007/10/19 v1.4h Standard LaTeX document class

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\size11.clo"

File: size11.clo 2007/10/19 v1.4h Standard LaTeX file (size option)

)

\c@part=\count79

\c@section=\count80

\c@subsection=\count81

\c@subsubsection=\count82

\c@paragraph=\count83

\c@subparagraph=\count84

\c@figure=\count85

\c@table=\count86

\abovecaptionskip=\skip41

\belowcaptionskip=\skip42

\bibindent=\dimen102

) ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\fontenc.sty"

Package: fontenc 2005/09/27 v1.99g Standard LaTeX package

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\t1enc.def"

File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file

LaTeX Font Info: Redeclaring font encoding T1 on input line 43.

)) ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\setspace\setspace.sty"

Package: setspace 2011/12/19 v6.7a set line spacing

) ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\biblatex.sty"

Package: biblatex 2013/11/25 v2.8a programmable bibliographies (PK/JW/AB)

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\biblatex\biblatex2.sty"

Package: biblatex2 2013/11/25 v2.8a programmable bibliographies (biber)
(PK/JW/

AB)

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\etoolbox\etoolbox.sty"

Package: etoolbox 2011/01/03 v2.1 e-TeX tools for LaTeX

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\misc\etex.sty"

Package: etex 1998/03/26 v2.0 eTeX basic definition package (PEB)

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\etb@tempcnta=\count88

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Package: keyval 1999/03/16 v1.13 key=value parser (DPC)

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("C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\ltxcmds.sty"

Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)

) ("C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\kvsetkeys.sty"

Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)

("C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\infwarerr.sty"

Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages
(HO)

) ("C:\Program Files (x86)\MiKTeX2.9\tex\generic\oberdiek\etexcmds.sty"

Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands
(HO)

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Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)

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)

Package etexcmds Info: Could not find \expanded.

(etexcmds) That can mean that you are not using pdfTeX 1.50 or

(etexcmds) that some package has redefined \expanded.

(etexcmds) In the latter case, load this package earlier.

))) ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\logreq\logreq.sty"

Package: logreq 2010/08/04 v1.0 xml request logger

\lrq@indent=\count89

("C:\Program Files (x86)\MiKTeX2.9\tex\latex\logreq\logreq.def"

File: logreq.def 2010/08/04 v1.0 logreq spec v1.0

)) ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\base\ifthen.sty"

Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)

) ("C:\Program Files (x86)\MiKTeX2.9\tex\latex\ltxmisc\url.sty"

\Urlmuskip=\muskip10

Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc.

)

\c@tabx@nest=\count90

\c@listtotal=\count91

\c@listcount=\count92

\c@liststart=\count93

\c@liststop=\count94

\c@citecount=\count95

\c@citetotal=\count96

\c@multicitecount=\count97

Re: Author-year in Lyx

[KIM Musak]

Dear Stefano, unfortunately I still can't get lyx to
1) show Author-Year , instead the bibtexkey shown
2) no bibliography listed at the end of the text

I am pretty sure the problem happens during generation of the PDF file. The
reasons being, I could see all the reference in my Lyx document, I could
cite the selected reference. They are nicely shown in lyx file, and nicely
shown as Author-Year.  The only problem is when I click preview, the PDF
only shows the citation but only in bibtexkey and no bibliography printed.
Anything to do with the module? or Windows 8? or probably with Lyx 2.0.6?

--, what have I done wrong? still clueless ---

Regards,

Kamarul


On Sat, Jan 11, 2014 at 1:30 AM, Stefano Franchi stef...@tamu.edu wrote:




 On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com wrote:

 Dear Stefano and all,

 Coming back to setting Lyx to work with biblatex, I am not so sure how to
 make it works in my Lyx. I have tried the steps listed at
 http://wiki.lyx.org/BibTeX/Biblatex , which includes
 1) Put the file biblatex.module in the layouts folder

 2) Reconfigure Lyx - then restart



 3) Setting the Preamble with
 a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}


 you should really use biber instead of bibtex with bibblatex. It is not
 mandatory but I strongly recommend it. Many biblatex features only wotk
 with biber. So replace your line with:

 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

 (actually biber is the default, so you clould eliminate the backend clause
 completely, but just for clarity)

 b) \usepackage[style=numeric,backend=bibtex]{biblatex}


 This is wrong. You should only load biblatex once, with the style you
 want. So either load it with style=authoryear, or with style=numeric, but
 do not load it twice

 Stefano, yes, I used only
 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

c) \addbibresource{name of bib-file with .bib-extension}


 You should have the complete path from root here, otherwise biblatex won't
 find you bib file. This is actually  lyx's problem, not biblatex's. The
 problem is that when you instruct lix to typeset your file into a a pdf,
 lyx first copies your lyx-converted tex  file to a temp directory, then it
 runs (pdf)latex and biber/bibtex on it. At that point, the relative path
 you had inserted in the preamble becomes meaningless since you are no
 longer in the original location.
 IN SHORT: always use absolute paths in your \addbibresource commands in
 the preamble.


Stefano, i did use the complete the path and also the file name only




 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
 LyX note or comment

 good


I can confirmed that I did this



 5) enter \printbibliography in ERT

 good


I can confirm that i did this


 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
 change the bibtex

 good


I can confirm I did this


 7) pass the option backend=biber

 see comment to point 3a above


I did add this and without this



 When I inserted the citation, Lyx managed to find it.
 But when I previewed it, the citation is not in author-year and no
 bibliography printed

 Did I miss any steps? I am using Lyx 2.0.6




 Let me know if it works.

 Cheers,
 Stefano
 --
 __
 Stefano Franchi
 Associate Research Professor
 Department of Hispanic StudiesPh:   +1 (979) 845-2125
 Texas AM University  Fax:  +1 (979) 845-6421
 College Station, Texas, USA

 stef...@tamu.edu
 http://stefano.cleinias.org

Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

 Thanks, Stefano. 

Here again what I followed up or tried:

1) Put the file biblatex.module in the layouts folder
I guess the /.lyx/layouts/  is meant ?
 or is it documentsmoduleBiblatex-citation-styles  
 I have selected this and added to 'chosen' in right box
 or both, which I tried ??
 2) toolsreconfigure
  restart lyx
 3) documentsSettingsBibliography
  citation style: standard
  Processor: biber
 3) preamble
 \usepackage[style=authoryear,natbib=true]{biblatex}
 \addbibresource{name of bib-file with .bib-extension}
  in my case \addbibresource{PBRef.bib}
  tried also  
   \addbibresource{/home/we/Photobiology2013/PBRFigFinal/PBRef.bib}

 4) InsertList/TOCBibTeX Bibliography...
  in my case PBRef
  style: plain
  and put it in LyX note (turns yellow)
 5)  \printbibliography in ERT 
inserted after the yellow BibTeX Bibliography note
 6) ToolsSettingsOutputLaTeX
 processor: biber

 I did all this including reconfigure, the terminal says
Running: biber PB-Biber
INFO - This is Biber 1.6
INFO - Logfile is 'PB-Biber.blg'
INFO - Reading 'PB-Biber.bcf'
INFO - Found 748 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 
'/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib' for section 0
ERROR - Cannot find '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib'!
INFO - ERRORS: 1
support/Systemcall.cpp (273): Systemcall: 'biber PB-Biber' finished with 
exit code 2

However, the PBRef.bib is there:
 so you can make up your own command by typing the following
 at a prompt, to get the complete path of file  myfilename.bib
 
 $ls $PWD/myfilename.bib
Dolphin tells me:
/home/we/Photobiology2013/PBRFigFinal
and your proposal:
we@wolfgang:~/Photobiology2013/PBRFigFinal$ $ls $PWD/PBRef.bib
bash: /home/we/Photobiology2013/PBRFigFinal/PBRef.bib: Keine Berechtigung 
(no admission)
I changed the permission to include group, but still no change in output

 
 Ok, this is confusing. Are you getting the references in your pdf files?
 If so, it means that biber has found your bib file and has processed it
 correctly. If you are not getting the References section at the end,
 however, you may have forgotten and/or mispelled the /printbibliography
 command. Or latex may have choked on it due to some error in the bbl
 file.
 
 Can you confirm that:
 
 1. You are getting the correct citations in the pdf file
yes, I do
 2. You have entered \printbibliography in ERT at the end of your
 document 
yes, I did
 3. You do not see a corresponding  References or Works
 cited section with your full references at the end of your pdf file
No, I don't

I should perhaps add, that I use Koma script (book)
I tried with the normal book style,
but get an error 
Der Absatzstil `Publishers' wurde nicht gefunden.
(paragraph style  `Publishers' was not found
The same with other book styles except Koma

I have taken out all entrances in the preamble except 

 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
%could also be
% \usepackage[style=authoryear,natbib=true]{biblatex}
\addbibresource{/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib}

but still no Bibliography output in the pdf
although the references are cited in the pdf output

I tried furthermore ps output, same problem: citations alright, but no 
Bibliography output.

I tried also a (almost) minimal example with no success either. 
May I include this example and the bib file going with it? It is quite short 
and might help you in finding out what I do wrong.

Thanks for all the help for and patience with me 


Wolfgang
% This file was created with JabRef 2.7b.
% Encoding: ISO8859_1

@ARTICLE{Hennessey1991,
  author = {Hennessey, T. L. and Field, C. B.},
  title = {Circadian rhythms in photosynthesis},
  journal = {Plant Physiol},
  year = {1991},
  volume = {96},
  pages = {831--836},
  owner = {wolfgang},
  timestamp = {2012.02.25}
}

@comment{jabref-meta: selector_publisher:}

@comment{jabref-meta: selector_author:}

@comment{jabref-meta: selector_journal:}

@comment{jabref-meta: selector_keywords:}



PB-BiberXX.lyx
Description: application/lyx

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 09:34:17 KIM Musak wrote:

Just saw this; its the same issue I have posted just now under
Biblatex and LyX issue #was: Re: Author-year in Lyx

Wolfgang

 Dear Stefano, unfortunately I still can't get lyx to
 1) show Author-Year , instead the bibtexkey shown
 2) no bibliography listed at the end of the text
 
 I am pretty sure the problem happens during generation of the PDF file.
 The reasons being, I could see all the reference in my Lyx document, I
 could cite the selected reference. They are nicely shown in lyx file,
 and nicely shown as Author-Year.  The only problem is when I click
 preview, the PDF only shows the citation but only in bibtexkey and no
 bibliography printed. Anything to do with the module? or Windows 8? or
 probably with Lyx 2.0.6?
 
 --, what have I done wrong? still clueless ---
 
 Regards,
 
 Kamarul
 
 On Sat, Jan 11, 2014 at 1:30 AM, Stefano Franchi stef...@tamu.edu 
wrote:
  On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com 
wrote:
  Dear Stefano and all,
  
  Coming back to setting Lyx to work with biblatex, I am not so sure
  how to make it works in my Lyx. I have tried the steps listed at
  http://wiki.lyx.org/BibTeX/Biblatex , which includes
  1) Put the file biblatex.module in the layouts folder
  
  2) Reconfigure Lyx - then restart
  
  3) Setting the Preamble with
  a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
  
  you should really use biber instead of bibtex with bibblatex. It is
  not mandatory but I strongly recommend it. Many biblatex features
  only wotk with biber. So replace your line with:
  
  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
  
  (actually biber is the default, so you clould eliminate the backend
  clause completely, but just for clarity)
  
  b) \usepackage[style=numeric,backend=bibtex]{biblatex}
  
  This is wrong. You should only load biblatex once, with the style you
  want. So either load it with style=authoryear, or with style=numeric,
  but do not load it twice
  
  Stefano, yes, I used only
 
  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
 
 c) \addbibresource{name of bib-file with .bib-extension}
 
  You should have the complete path from root here, otherwise biblatex
  won't find you bib file. This is actually  lyx's problem, not
  biblatex's. The problem is that when you instruct lix to typeset your
  file into a a pdf, lyx first copies your lyx-converted tex  file to a
  temp directory, then it runs (pdf)latex and biber/bibtex on it. At
  that point, the relative path you had inserted in the preamble
  becomes meaningless since you are no longer in the original location.
  IN SHORT: always use absolute paths in your \addbibresource commands
  in the preamble.
 
 Stefano, i did use the complete the path and also the file name only
 
  4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
  in a LyX note or comment
  
  good
 
 I can confirmed that I did this
 
  5) enter \printbibliography in ERT
  
  good
 
 I can confirm that i did this
 
  6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
  
  change the bibtex
  
  good
 
 I can confirm I did this
 
  7) pass the option backend=biber
  
  see comment to point 3a above
 
 I did add this and without this
 
  When I inserted the citation, Lyx managed to find it.
  But when I previewed it, the citation is not in author-year and no
  bibliography printed
  
  Did I miss any steps? I am using Lyx 2.0.6
  
  Let me know if it works.
  
  Cheers,
  Stefano
  --
  __
  Stefano Franchi
  Associate Research Professor
  Department of Hispanic StudiesPh:   +1 (979) 845-2125
  Texas AM University  Fax:  +1 (979) 845-6421
  College Station, Texas, USA
  
  stef...@tamu.edu
  http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

Wolfgang,

your file had an error in the preamble. You had

\addbibresource{/home/stefano/Desktop/PBRef.bib}


but the file you enclosed is called PBReffXX.bib


Once I fixed the filename to PBRefXX.bib the file compiled fine, and the
references and bibliography appeared in the pdf output (I also had to
change the directory, of course).


Stefano


On Sat, Jan 11, 2014 at 4:25 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

   Thanks, Stefano.



 Here again what I followed up or tried:



 1) Put the file biblatex.module in the layouts folder

 I guess the /.lyx/layouts/ is meant ?

 or is it documentsmoduleBiblatex-citation-styles

 I have selected this and added to 'chosen' in right box

 or both, which I tried ??

 2) toolsreconfigure

 restart lyx

 3) documentsSettingsBibliography

 citation style: standard

 Processor: biber

 3) preamble

 \usepackage[style=authoryear,natbib=true]{biblatex}

 \addbibresource{name of bib-file with .bib-extension}

 in my case \addbibresource{PBRef.bib}

 tried also

 \addbibresource{/home/we/Photobiology2013/PBRFigFinal/PBRef.bib}



 4) InsertList/TOCBibTeX Bibliography...

 in my case PBRef

 style: plain

 and put it in LyX note (turns yellow)

 5) \printbibliography in ERT

 inserted after the yellow BibTeX Bibliography note

 6) ToolsSettingsOutputLaTeX

 processor: biber



 I did all this including reconfigure, the terminal says

 Running: biber PB-Biber

 INFO - This is Biber 1.6

 INFO - Logfile is 'PB-Biber.blg'

 INFO - Reading 'PB-Biber.bcf'

 INFO - Found 748 citekeys in bib section 0

 INFO - Processing section 0

 INFO - Looking for bibtex format file
 '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib' for section 0

 ERROR - Cannot find '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib'!

 INFO - ERRORS: 1

 support/Systemcall.cpp (273): Systemcall: 'biber PB-Biber' finished with
 exit code 2



 However, the PBRef.bib is there:

  so you can make up your own command by typing the following

  at a prompt, to get the complete path of file myfilename.bib

 

  $ls $PWD/myfilename.bib

 Dolphin tells me:

 /home/we/Photobiology2013/PBRFigFinal

 and your proposal:

 we@wolfgang:~/Photobiology2013/PBRFigFinal$ $ls $PWD/PBRef.bib

 bash: /home/we/Photobiology2013/PBRFigFinal/PBRef.bib: Keine Berechtigung

 (no admission)

 I changed the permission to include group, but still no change in output



 

  Ok, this is confusing. Are you getting the references in your pdf files?

  If so, it means that biber has found your bib file and has processed it

  correctly. If you are not getting the References section at the end,

  however, you may have forgotten and/or mispelled the /printbibliography

  command. Or latex may have choked on it due to some error in the bbl

  file.

 

  Can you confirm that:

 

  1. You are getting the correct citations in the pdf file

 yes, I do

  2. You have entered \printbibliography in ERT at the end of your

  document

 yes, I did

  3. You do not see a corresponding References or Works

  cited section with your full references at the end of your pdf file

 No, I don't



 I should perhaps add, that I use Koma script (book)

 I tried with the normal book style,

 but get an error

 Der Absatzstil `Publishers' wurde nicht gefunden.

 (paragraph style `Publishers' was not found

 The same with other book styles except Koma



 I have taken out all entrances in the preamble except



 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

 %could also be

 % \usepackage[style=authoryear,natbib=true]{biblatex}

 \addbibresource{/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib}



 but still no Bibliography output in the pdf

 although the references are cited in the pdf output



 I tried furthermore ps output, same problem: citations alright, but no
 Bibliography output.



 I tried also a (almost) minimal example with no success either.

 May I include this example and the bib file going with it? It is quite
 short and might help you in finding out what I do wrong.



 Thanks for all the help for and patience with me





 Wolfgang




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

I wonder whether my and Kim's difficulties with biber has to do with the 
versions of biber and biblatex.
According to the biber handbook (Kime, UK) the latest are
Biber version 1.8
Biblatex version 2.8
If I check via synaptic (debian)
I have 0.9.9+release-1 for Biber
and 1.7-1 for biblatex.

Since I have installed texlive 2013
I searched for biber and found it to be in 
/usr/local/texlive/2013/bin/x86-64-linux/
/usr/local/texlive/2013/texmf-dist/doc/bibtex/
/usr/local/texlive/2013/texmf-dist/source/bibtex/

and biblatex in
/usr/local/texlive/2013/texmf-dist/doc/latex/
/usr/local/texlive/2013/texmf-dist/bibtex/csf/
/usr/local/texlive/2013/texmf-dist/bibtex/bst/
/usr/local/texlive/2013/texmf-dist/tex/latex/
/usr/local/texlive/2013/texmf-dist/bibtex/bib/biblatex/

Two questions:

How can I find out the version of these?
How can I find out, that they are used by lyx

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Sat, Jan 11, 2014 at 9:10 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:



 I wonder whether my and Kim's difficulties with biber has to do with the
 versions of biber and biblatex.

 According to the biber handbook (Kime, UK) the latest are

 Biber version 1.8

 Biblatex version 2.8

 If I check via synaptic (debian)

 I have 0.9.9+release-1 for Biber

 and 1.7-1 for biblatex.




Thos are very old version. I would not recommend using biblatex 2


 Since I have installed texlive 2013

 I searched for biber and found it to be in

 /usr/local/texlive/2013/bin/x86-64-linux/

 /usr/local/texlive/2013/texmf-dist/doc/bibtex/

 /usr/local/texlive/2013/texmf-dist/source/bibtex/





 and biblatex in

 /usr/local/texlive/2013/texmf-dist/doc/latex/

 /usr/local/texlive/2013/texmf-dist/bibtex/csf/

 /usr/local/texlive/2013/texmf-dist/bibtex/bst/

 /usr/local/texlive/2013/texmf-dist/tex/latex/

 /usr/local/texlive/2013/texmf-dist/bibtex/bib/biblatex/



 Two questions:



 How can I find out the version of these?


for biber type
biber --version
at a prompt

for biblatex, the easier way is to look at the latex log. Whn biblatex is
loaded (at the beginning of the log) it will tell you the version

How can I find out, that they are used by lyx


If you have multiple versions of biber, it may get complicated. It all
depends on your PATH variable, but there are additional complications if
you start lyx from  the GUI. If you start lyx from the command line
(recommended), then lyx will find the biber program whose version you saw
with biber --version and which is located in the output of which biber.
If you start it from the GUI (double-clicking on a lyx file, using the F2
shortcut in Kde, etcetera), it all depends on how you set up KDE. I never
got the hang of it, to be frank, so I always start it from the command line.

Cheers,

Stefano




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 15:54:44 stefano franchi wrote:
 Wolfgang, Kamarul,
 
 my guess is that you have the same problem. Namely, biber cannot find
 the bib file. Or perhaps biber is not launched at all.
 
 Try looking at the latex log (DocumentLaTeX log), and check out both
 the latex log proper and the bibtex log (the two choices in  the
 dropdown menu). You should get an idea of what is going wrong. If biber
 cannot find the file, you should see something like the following in
 the bibtex log:
 
 [181] Biber.pm:3190 INFO - Looking for bibtex format file '[YOUR BIB
 FILENAME HERE]' for section 0
 [252] Utils.pm:185 ERROR - Cannot find '[YOUR BIB FILENAME HERE]'!
 [253] Biber.pm:109 INFO - ERRORS: 1
 
 To sort out if there is something wrong with your installation, try out
 the enclosed files:
 1. first, copy the lisp.bb file to /tmp (that is the tmp directory
 directly under root, not in your home folder. It is generally writable
 on linux systems).
 2. then try typesetting the lyx file from within lyx
 3. If your result is identical to the pdf file I am enclosing we'll know
 your installation is all right and we can focus on what is wrong with
 your lyx files
 
Doing 1 and 2 gives me in the pdf file:

Testing biber and biblatex
Here is a reference to McCarthy’s history of lisp (808387 ), followed by
the same reference in traditional author-year-format (808387 ).

compared to your pdf file:

Testing biber and biblatex
Here is a reference to McCarthy’s history of lisp (1978), followed by the
same reference in traditional author-year-format (McCarthy, 1978).
References
McCarthy, John (1978). “History of LISP”. In: SIGPLAN Not. 13.8, pp. 217–
223. issn: 0362-1340. doi: http : / / doi . acm . org / 10 . 1145 / 960118 
.
808387.

That means, my installation is not working properly.
Perhaps what I mentioned in my EMail Today 16:10:42?
(old versions of biber and biblatex)

So I should first find out which versions are in Texlive2013 (see my EMail 
Today 16:10:42

How to?

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
   On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
  
  
  Two questions:
  
  
  
  How can I find out the version of these?
 
 for biber type
 biber --version

it is 1.6


 at a prompt
 
 for biblatex, the easier way is to look at the latex log. Whn biblatex
 is loaded (at the beginning of the log) it will tell you the version

 biblatex 2013/05/01 v2.6

 
 How can I find out, that they are used by lyx
 
 
 If you have multiple versions of biber, it may get complicated. It all
 depends on your PATH variable, but there are additional complications if
 you start lyx from  the GUI. If you start lyx from the command line
 (recommended), then lyx will find the biber program whose version you
 saw with biber --version and which is located in the output of which
 biber. If you start it from the GUI (double-clicking on a lyx file,
 using the F2 shortcut in Kde, etcetera), it all depends on how you set
 up KDE. I never got the hang of it, to be frank, so I always start it
 from the command line.
so do I


Thanks, Stefano, will try later.

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 16:23:41 stefano franchi wrote:

   On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
  for biber type

  biber --version



 it is 1.6


  for biblatex, the easier way is to look at the latex log. Whn biblatex

  is loaded (at the beginning of the log) it will tell you the version



 biblatex 2013/05/01 v2.6


You're all right then---biblatex 2.6 wants biber 1.6, so everything is fine
on that front.

I still think you may have path-related  issues in the preamble.

Do check the capitalization of your home directory (WE vs we) as per my
previous message.


Cheers,

S.
-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[KIM Musak]

Dear Stefano, unfortunately I still can't get lyx to
1) show Author-Year , instead the bibtexkey shown
2) no bibliography listed at the end of the text

I am pretty sure the problem happens during generation of the PDF file. The
reasons being, I could see all the reference in my Lyx document, I could
cite the selected reference. They are nicely shown in lyx file, and nicely
shown as Author-Year.  The only problem is when I click preview, the PDF
only shows the citation but only in bibtexkey and no bibliography printed.
Anything to do with the module? or Windows 8? or probably with Lyx 2.0.6?

--, what have I done wrong? still clueless ---

Regards,

Kamarul


On Sat, Jan 11, 2014 at 1:30 AM, Stefano Franchi stef...@tamu.edu wrote:




 On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com wrote:

 Dear Stefano and all,

 Coming back to setting Lyx to work with biblatex, I am not so sure how to
 make it works in my Lyx. I have tried the steps listed at
 http://wiki.lyx.org/BibTeX/Biblatex , which includes
 1) Put the file biblatex.module in the layouts folder

 2) Reconfigure Lyx - then restart



 3) Setting the Preamble with
 a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}


 you should really use biber instead of bibtex with bibblatex. It is not
 mandatory but I strongly recommend it. Many biblatex features only wotk
 with biber. So replace your line with:

 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

 (actually biber is the default, so you clould eliminate the backend clause
 completely, but just for clarity)

 b) \usepackage[style=numeric,backend=bibtex]{biblatex}


 This is wrong. You should only load biblatex once, with the style you
 want. So either load it with style=authoryear, or with style=numeric, but
 do not load it twice

 Stefano, yes, I used only
 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

c) \addbibresource{name of bib-file with .bib-extension}


 You should have the complete path from root here, otherwise biblatex won't
 find you bib file. This is actually  lyx's problem, not biblatex's. The
 problem is that when you instruct lix to typeset your file into a a pdf,
 lyx first copies your lyx-converted tex  file to a temp directory, then it
 runs (pdf)latex and biber/bibtex on it. At that point, the relative path
 you had inserted in the preamble becomes meaningless since you are no
 longer in the original location.
 IN SHORT: always use absolute paths in your \addbibresource commands in
 the preamble.


Stefano, i did use the complete the path and also the file name only




 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
 LyX note or comment

 good


I can confirmed that I did this



 5) enter \printbibliography in ERT

 good


I can confirm that i did this


 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
 change the bibtex

 good


I can confirm I did this


 7) pass the option backend=biber

 see comment to point 3a above


I did add this and without this



 When I inserted the citation, Lyx managed to find it.
 But when I previewed it, the citation is not in author-year and no
 bibliography printed

 Did I miss any steps? I am using Lyx 2.0.6




 Let me know if it works.

 Cheers,
 Stefano
 --
 __
 Stefano Franchi
 Associate Research Professor
 Department of Hispanic StudiesPh:   +1 (979) 845-2125
 Texas AM University  Fax:  +1 (979) 845-6421
 College Station, Texas, USA

 stef...@tamu.edu
 http://stefano.cleinias.org

Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

 Thanks, Stefano. 

Here again what I followed up or tried:

1) Put the file biblatex.module in the layouts folder
I guess the /.lyx/layouts/  is meant ?
 or is it documentsmoduleBiblatex-citation-styles  
 I have selected this and added to 'chosen' in right box
 or both, which I tried ??
 2) toolsreconfigure
  restart lyx
 3) documentsSettingsBibliography
  citation style: standard
  Processor: biber
 3) preamble
 \usepackage[style=authoryear,natbib=true]{biblatex}
 \addbibresource{name of bib-file with .bib-extension}
  in my case \addbibresource{PBRef.bib}
  tried also  
   \addbibresource{/home/we/Photobiology2013/PBRFigFinal/PBRef.bib}

 4) InsertList/TOCBibTeX Bibliography...
  in my case PBRef
  style: plain
  and put it in LyX note (turns yellow)
 5)  \printbibliography in ERT 
inserted after the yellow BibTeX Bibliography note
 6) ToolsSettingsOutputLaTeX
 processor: biber

 I did all this including reconfigure, the terminal says
Running: biber PB-Biber
INFO - This is Biber 1.6
INFO - Logfile is 'PB-Biber.blg'
INFO - Reading 'PB-Biber.bcf'
INFO - Found 748 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 
'/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib' for section 0
ERROR - Cannot find '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib'!
INFO - ERRORS: 1
support/Systemcall.cpp (273): Systemcall: 'biber PB-Biber' finished with 
exit code 2

However, the PBRef.bib is there:
 so you can make up your own command by typing the following
 at a prompt, to get the complete path of file  myfilename.bib
 
 $ls $PWD/myfilename.bib
Dolphin tells me:
/home/we/Photobiology2013/PBRFigFinal
and your proposal:
we@wolfgang:~/Photobiology2013/PBRFigFinal$ $ls $PWD/PBRef.bib
bash: /home/we/Photobiology2013/PBRFigFinal/PBRef.bib: Keine Berechtigung 
(no admission)
I changed the permission to include group, but still no change in output

 
 Ok, this is confusing. Are you getting the references in your pdf files?
 If so, it means that biber has found your bib file and has processed it
 correctly. If you are not getting the References section at the end,
 however, you may have forgotten and/or mispelled the /printbibliography
 command. Or latex may have choked on it due to some error in the bbl
 file.
 
 Can you confirm that:
 
 1. You are getting the correct citations in the pdf file
yes, I do
 2. You have entered \printbibliography in ERT at the end of your
 document 
yes, I did
 3. You do not see a corresponding  References or Works
 cited section with your full references at the end of your pdf file
No, I don't

I should perhaps add, that I use Koma script (book)
I tried with the normal book style,
but get an error 
Der Absatzstil `Publishers' wurde nicht gefunden.
(paragraph style  `Publishers' was not found
The same with other book styles except Koma

I have taken out all entrances in the preamble except 

 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
%could also be
% \usepackage[style=authoryear,natbib=true]{biblatex}
\addbibresource{/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib}

but still no Bibliography output in the pdf
although the references are cited in the pdf output

I tried furthermore ps output, same problem: citations alright, but no 
Bibliography output.

I tried also a (almost) minimal example with no success either. 
May I include this example and the bib file going with it? It is quite short 
and might help you in finding out what I do wrong.

Thanks for all the help for and patience with me 


Wolfgang
% This file was created with JabRef 2.7b.
% Encoding: ISO8859_1

@ARTICLE{Hennessey1991,
  author = {Hennessey, T. L. and Field, C. B.},
  title = {Circadian rhythms in photosynthesis},
  journal = {Plant Physiol},
  year = {1991},
  volume = {96},
  pages = {831--836},
  owner = {wolfgang},
  timestamp = {2012.02.25}
}

@comment{jabref-meta: selector_publisher:}

@comment{jabref-meta: selector_author:}

@comment{jabref-meta: selector_journal:}

@comment{jabref-meta: selector_keywords:}



PB-BiberXX.lyx
Description: application/lyx

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 09:34:17 KIM Musak wrote:

Just saw this; its the same issue I have posted just now under
Biblatex and LyX issue #was: Re: Author-year in Lyx

Wolfgang

 Dear Stefano, unfortunately I still can't get lyx to
 1) show Author-Year , instead the bibtexkey shown
 2) no bibliography listed at the end of the text
 
 I am pretty sure the problem happens during generation of the PDF file.
 The reasons being, I could see all the reference in my Lyx document, I
 could cite the selected reference. They are nicely shown in lyx file,
 and nicely shown as Author-Year.  The only problem is when I click
 preview, the PDF only shows the citation but only in bibtexkey and no
 bibliography printed. Anything to do with the module? or Windows 8? or
 probably with Lyx 2.0.6?
 
 --, what have I done wrong? still clueless ---
 
 Regards,
 
 Kamarul
 
 On Sat, Jan 11, 2014 at 1:30 AM, Stefano Franchi stef...@tamu.edu 
wrote:
  On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com 
wrote:
  Dear Stefano and all,
  
  Coming back to setting Lyx to work with biblatex, I am not so sure
  how to make it works in my Lyx. I have tried the steps listed at
  http://wiki.lyx.org/BibTeX/Biblatex , which includes
  1) Put the file biblatex.module in the layouts folder
  
  2) Reconfigure Lyx - then restart
  
  3) Setting the Preamble with
  a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
  
  you should really use biber instead of bibtex with bibblatex. It is
  not mandatory but I strongly recommend it. Many biblatex features
  only wotk with biber. So replace your line with:
  
  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
  
  (actually biber is the default, so you clould eliminate the backend
  clause completely, but just for clarity)
  
  b) \usepackage[style=numeric,backend=bibtex]{biblatex}
  
  This is wrong. You should only load biblatex once, with the style you
  want. So either load it with style=authoryear, or with style=numeric,
  but do not load it twice
  
  Stefano, yes, I used only
 
  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
 
 c) \addbibresource{name of bib-file with .bib-extension}
 
  You should have the complete path from root here, otherwise biblatex
  won't find you bib file. This is actually  lyx's problem, not
  biblatex's. The problem is that when you instruct lix to typeset your
  file into a a pdf, lyx first copies your lyx-converted tex  file to a
  temp directory, then it runs (pdf)latex and biber/bibtex on it. At
  that point, the relative path you had inserted in the preamble
  becomes meaningless since you are no longer in the original location.
  IN SHORT: always use absolute paths in your \addbibresource commands
  in the preamble.
 
 Stefano, i did use the complete the path and also the file name only
 
  4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
  in a LyX note or comment
  
  good
 
 I can confirmed that I did this
 
  5) enter \printbibliography in ERT
  
  good
 
 I can confirm that i did this
 
  6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
  
  change the bibtex
  
  good
 
 I can confirm I did this
 
  7) pass the option backend=biber
  
  see comment to point 3a above
 
 I did add this and without this
 
  When I inserted the citation, Lyx managed to find it.
  But when I previewed it, the citation is not in author-year and no
  bibliography printed
  
  Did I miss any steps? I am using Lyx 2.0.6
  
  Let me know if it works.
  
  Cheers,
  Stefano
  --
  __
  Stefano Franchi
  Associate Research Professor
  Department of Hispanic StudiesPh:   +1 (979) 845-2125
  Texas AM University  Fax:  +1 (979) 845-6421
  College Station, Texas, USA
  
  stef...@tamu.edu
  http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

Wolfgang,

your file had an error in the preamble. You had

\addbibresource{/home/stefano/Desktop/PBRef.bib}


but the file you enclosed is called PBReffXX.bib


Once I fixed the filename to PBRefXX.bib the file compiled fine, and the
references and bibliography appeared in the pdf output (I also had to
change the directory, of course).


Stefano


On Sat, Jan 11, 2014 at 4:25 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

   Thanks, Stefano.



 Here again what I followed up or tried:



 1) Put the file biblatex.module in the layouts folder

 I guess the /.lyx/layouts/ is meant ?

 or is it documentsmoduleBiblatex-citation-styles

 I have selected this and added to 'chosen' in right box

 or both, which I tried ??

 2) toolsreconfigure

 restart lyx

 3) documentsSettingsBibliography

 citation style: standard

 Processor: biber

 3) preamble

 \usepackage[style=authoryear,natbib=true]{biblatex}

 \addbibresource{name of bib-file with .bib-extension}

 in my case \addbibresource{PBRef.bib}

 tried also

 \addbibresource{/home/we/Photobiology2013/PBRFigFinal/PBRef.bib}



 4) InsertList/TOCBibTeX Bibliography...

 in my case PBRef

 style: plain

 and put it in LyX note (turns yellow)

 5) \printbibliography in ERT

 inserted after the yellow BibTeX Bibliography note

 6) ToolsSettingsOutputLaTeX

 processor: biber



 I did all this including reconfigure, the terminal says

 Running: biber PB-Biber

 INFO - This is Biber 1.6

 INFO - Logfile is 'PB-Biber.blg'

 INFO - Reading 'PB-Biber.bcf'

 INFO - Found 748 citekeys in bib section 0

 INFO - Processing section 0

 INFO - Looking for bibtex format file
 '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib' for section 0

 ERROR - Cannot find '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib'!

 INFO - ERRORS: 1

 support/Systemcall.cpp (273): Systemcall: 'biber PB-Biber' finished with
 exit code 2



 However, the PBRef.bib is there:

  so you can make up your own command by typing the following

  at a prompt, to get the complete path of file myfilename.bib

 

  $ls $PWD/myfilename.bib

 Dolphin tells me:

 /home/we/Photobiology2013/PBRFigFinal

 and your proposal:

 we@wolfgang:~/Photobiology2013/PBRFigFinal$ $ls $PWD/PBRef.bib

 bash: /home/we/Photobiology2013/PBRFigFinal/PBRef.bib: Keine Berechtigung

 (no admission)

 I changed the permission to include group, but still no change in output



 

  Ok, this is confusing. Are you getting the references in your pdf files?

  If so, it means that biber has found your bib file and has processed it

  correctly. If you are not getting the References section at the end,

  however, you may have forgotten and/or mispelled the /printbibliography

  command. Or latex may have choked on it due to some error in the bbl

  file.

 

  Can you confirm that:

 

  1. You are getting the correct citations in the pdf file

 yes, I do

  2. You have entered \printbibliography in ERT at the end of your

  document

 yes, I did

  3. You do not see a corresponding References or Works

  cited section with your full references at the end of your pdf file

 No, I don't



 I should perhaps add, that I use Koma script (book)

 I tried with the normal book style,

 but get an error

 Der Absatzstil `Publishers' wurde nicht gefunden.

 (paragraph style `Publishers' was not found

 The same with other book styles except Koma



 I have taken out all entrances in the preamble except



 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

 %could also be

 % \usepackage[style=authoryear,natbib=true]{biblatex}

 \addbibresource{/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib}



 but still no Bibliography output in the pdf

 although the references are cited in the pdf output



 I tried furthermore ps output, same problem: citations alright, but no
 Bibliography output.



 I tried also a (almost) minimal example with no success either.

 May I include this example and the bib file going with it? It is quite
 short and might help you in finding out what I do wrong.



 Thanks for all the help for and patience with me





 Wolfgang




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

I wonder whether my and Kim's difficulties with biber has to do with the 
versions of biber and biblatex.
According to the biber handbook (Kime, UK) the latest are
Biber version 1.8
Biblatex version 2.8
If I check via synaptic (debian)
I have 0.9.9+release-1 for Biber
and 1.7-1 for biblatex.

Since I have installed texlive 2013
I searched for biber and found it to be in 
/usr/local/texlive/2013/bin/x86-64-linux/
/usr/local/texlive/2013/texmf-dist/doc/bibtex/
/usr/local/texlive/2013/texmf-dist/source/bibtex/

and biblatex in
/usr/local/texlive/2013/texmf-dist/doc/latex/
/usr/local/texlive/2013/texmf-dist/bibtex/csf/
/usr/local/texlive/2013/texmf-dist/bibtex/bst/
/usr/local/texlive/2013/texmf-dist/tex/latex/
/usr/local/texlive/2013/texmf-dist/bibtex/bib/biblatex/

Two questions:

How can I find out the version of these?
How can I find out, that they are used by lyx

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Sat, Jan 11, 2014 at 9:10 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:



 I wonder whether my and Kim's difficulties with biber has to do with the
 versions of biber and biblatex.

 According to the biber handbook (Kime, UK) the latest are

 Biber version 1.8

 Biblatex version 2.8

 If I check via synaptic (debian)

 I have 0.9.9+release-1 for Biber

 and 1.7-1 for biblatex.




Thos are very old version. I would not recommend using biblatex 2


 Since I have installed texlive 2013

 I searched for biber and found it to be in

 /usr/local/texlive/2013/bin/x86-64-linux/

 /usr/local/texlive/2013/texmf-dist/doc/bibtex/

 /usr/local/texlive/2013/texmf-dist/source/bibtex/





 and biblatex in

 /usr/local/texlive/2013/texmf-dist/doc/latex/

 /usr/local/texlive/2013/texmf-dist/bibtex/csf/

 /usr/local/texlive/2013/texmf-dist/bibtex/bst/

 /usr/local/texlive/2013/texmf-dist/tex/latex/

 /usr/local/texlive/2013/texmf-dist/bibtex/bib/biblatex/



 Two questions:



 How can I find out the version of these?


for biber type
biber --version
at a prompt

for biblatex, the easier way is to look at the latex log. Whn biblatex is
loaded (at the beginning of the log) it will tell you the version

How can I find out, that they are used by lyx


If you have multiple versions of biber, it may get complicated. It all
depends on your PATH variable, but there are additional complications if
you start lyx from  the GUI. If you start lyx from the command line
(recommended), then lyx will find the biber program whose version you saw
with biber --version and which is located in the output of which biber.
If you start it from the GUI (double-clicking on a lyx file, using the F2
shortcut in Kde, etcetera), it all depends on how you set up KDE. I never
got the hang of it, to be frank, so I always start it from the command line.

Cheers,

Stefano




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 15:54:44 stefano franchi wrote:
 Wolfgang, Kamarul,
 
 my guess is that you have the same problem. Namely, biber cannot find
 the bib file. Or perhaps biber is not launched at all.
 
 Try looking at the latex log (DocumentLaTeX log), and check out both
 the latex log proper and the bibtex log (the two choices in  the
 dropdown menu). You should get an idea of what is going wrong. If biber
 cannot find the file, you should see something like the following in
 the bibtex log:
 
 [181] Biber.pm:3190 INFO - Looking for bibtex format file '[YOUR BIB
 FILENAME HERE]' for section 0
 [252] Utils.pm:185 ERROR - Cannot find '[YOUR BIB FILENAME HERE]'!
 [253] Biber.pm:109 INFO - ERRORS: 1
 
 To sort out if there is something wrong with your installation, try out
 the enclosed files:
 1. first, copy the lisp.bb file to /tmp (that is the tmp directory
 directly under root, not in your home folder. It is generally writable
 on linux systems).
 2. then try typesetting the lyx file from within lyx
 3. If your result is identical to the pdf file I am enclosing we'll know
 your installation is all right and we can focus on what is wrong with
 your lyx files
 
Doing 1 and 2 gives me in the pdf file:

Testing biber and biblatex
Here is a reference to McCarthy’s history of lisp (808387 ), followed by
the same reference in traditional author-year-format (808387 ).

compared to your pdf file:

Testing biber and biblatex
Here is a reference to McCarthy’s history of lisp (1978), followed by the
same reference in traditional author-year-format (McCarthy, 1978).
References
McCarthy, John (1978). “History of LISP”. In: SIGPLAN Not. 13.8, pp. 217–
223. issn: 0362-1340. doi: http : / / doi . acm . org / 10 . 1145 / 960118 
.
808387.

That means, my installation is not working properly.
Perhaps what I mentioned in my EMail Today 16:10:42?
(old versions of biber and biblatex)

So I should first find out which versions are in Texlive2013 (see my EMail 
Today 16:10:42

How to?

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
   On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
  
  
  Two questions:
  
  
  
  How can I find out the version of these?
 
 for biber type
 biber --version

it is 1.6


 at a prompt
 
 for biblatex, the easier way is to look at the latex log. Whn biblatex
 is loaded (at the beginning of the log) it will tell you the version

 biblatex 2013/05/01 v2.6

 
 How can I find out, that they are used by lyx
 
 
 If you have multiple versions of biber, it may get complicated. It all
 depends on your PATH variable, but there are additional complications if
 you start lyx from  the GUI. If you start lyx from the command line
 (recommended), then lyx will find the biber program whose version you
 saw with biber --version and which is located in the output of which
 biber. If you start it from the GUI (double-clicking on a lyx file,
 using the F2 shortcut in Kde, etcetera), it all depends on how you set
 up KDE. I never got the hang of it, to be frank, so I always start it
 from the command line.
so do I


Thanks, Stefano, will try later.

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

  On Saturday 11 January 2014 16:23:41 stefano franchi wrote:

   On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
  for biber type

  biber --version



 it is 1.6


  for biblatex, the easier way is to look at the latex log. Whn biblatex

  is loaded (at the beginning of the log) it will tell you the version



 biblatex 2013/05/01 v2.6


You're all right then---biblatex 2.6 wants biber 1.6, so everything is fine
on that front.

I still think you may have path-related  issues in the preamble.

Do check the capitalization of your home directory (WE vs we) as per my
previous message.


Cheers,

S.
-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[KIM Musak]

Dear Stefano, unfortunately I still can't get lyx to
1) show Author-Year , instead the bibtexkey shown
2) no bibliography listed at the end of the text

I am pretty sure the problem happens during generation of the PDF file. The
reasons being, I could see all the reference in my Lyx document, I could
cite the selected reference. They are nicely shown in lyx file, and nicely
shown as Author-Year.  The only problem is when I click preview, the PDF
only shows the citation but only in bibtexkey and no bibliography printed.
Anything to do with the module? or Windows 8? or probably with Lyx 2.0.6?

--, what have I done wrong? still clueless ---

Regards,

Kamarul


On Sat, Jan 11, 2014 at 1:30 AM, Stefano Franchi  wrote:

>
>
>
> On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak  wrote:
>
>> Dear Stefano and all,
>>
>> Coming back to setting Lyx to work with biblatex, I am not so sure how to
>> make it works in my Lyx. I have tried the steps listed at
>> http://wiki.lyx.org/BibTeX/Biblatex , which includes
>> 1) Put the file biblatex.module in the layouts folder
>>
> 2) Reconfigure Lyx - then restart
>>
>
>
>> 3) Setting the Preamble with
>> a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
>>
>
> you should really use biber instead of bibtex with bibblatex. It is not
> mandatory but I strongly recommend it. Many biblatex features only wotk
> with biber. So replace your line with:
>
> \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
>
> (actually biber is the default, so you clould eliminate the backend clause
> completely, but just for clarity)
>
>> b) \usepackage[style=numeric,backend=bibtex]{biblatex}
>>
>
> This is wrong. You should only load biblatex once, with the style you
> want. So either load it with style=authoryear, or with style=numeric, but
> do not load it twice
>
> Stefano, yes, I used only
 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

c) \addbibresource{}
>>
>
> You should have the complete path from root here, otherwise biblatex won't
> find you bib file. This is actually  lyx's problem, not biblatex's. The
> problem is that when you instruct lix to typeset your file into a a pdf,
> lyx first copies your lyx-converted tex  file to a temp directory, then it
> runs (pdf)latex and biber/bibtex on it. At that point, the relative path
> you had inserted in the preamble becomes meaningless since you are no
> longer in the original location.
> IN SHORT: always use absolute paths in your \addbibresource commands in
> the preamble.
>

Stefano, i did use the complete the path and also the file name only

>
>
>
>> 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
>> LyX note or comment
>>
> good
>

I can confirmed that I did this

>
>
>> 5) enter \printbibliography in ERT
>>
> good
>

I can confirm that i did this

>
> 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
>> change the bibtex
>>
> good
>

I can confirm I did this

>
> 7) pass the option backend=biber
>>
> see comment to point 3a above
>

I did add this and without this

>
>
>> When I inserted the citation, Lyx managed to find it.
>> But when I previewed it, the citation is not in author-year and no
>> bibliography printed
>>
>> Did I miss any steps? I am using Lyx 2.0.6
>>
>>
>
>
> Let me know if it works.
>
> Cheers,
> Stefano
> --
> __
> Stefano Franchi
> Associate Research Professor
> Department of Hispanic StudiesPh:   +1 (979) 845-2125
> Texas A University  Fax:  +1 (979) 845-6421
> College Station, Texas, USA
>
> stef...@tamu.edu
> http://stefano.cleinias.org
>

Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

 Thanks, Stefano. 

Here again what I followed up or tried:

1) Put the file biblatex.module in the layouts folder
I guess the /.lyx/layouts/  is meant ?
 or is it documents>module>Biblatex-citation-styles  
 I have selected this and added to 'chosen' in right box
 or both, which I tried ??
 2) tools>reconfigure
  restart lyx
 3) documents>Settings>Bibliography
  citation style: standard
  Processor: biber
 3) preamble>
 \usepackage[style=authoryear,natbib=true]{biblatex}
 \addbibresource{}
  in my case \addbibresource{PBRef.bib}
  tried also  
   \addbibresource{/home/we/Photobiology2013/PBRFigFinal/PBRef.bib}

 4) Insert>List/TOC>BibTeX Bibliography...
  in my case PBRef
  style: plain
  and put it in LyX note (turns yellow)
 5)  \printbibliography in ERT 
inserted after the yellow BibTeX Bibliography note
 6) Tools>Settings>Output>LaTeX
 processor: biber

 I did all this including reconfigure, the terminal says
Running: biber "PB-Biber"
INFO - This is Biber 1.6
INFO - Logfile is 'PB-Biber.blg'
INFO - Reading 'PB-Biber.bcf'
INFO - Found 748 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 
'/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib' for section 0
ERROR - Cannot find '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib'!
INFO - ERRORS: 1
support/Systemcall.cpp (273): Systemcall: 'biber "PB-Biber"' finished with 
exit code 2

However, the PBRef.bib is there:
> so you can make up your own command by typing the following
> at a prompt, to get the complete path of file  "myfilename.bib"
> 
> $>ls $PWD/myfilename.bib
Dolphin tells me:
/home/we/Photobiology2013/PBRFigFinal
and your proposal:
we@wolfgang:~/Photobiology2013/PBRFigFinal$ $ls $PWD/PBRef.bib
bash: /home/we/Photobiology2013/PBRFigFinal/PBRef.bib: Keine Berechtigung 
(no admission)
I changed the permission to include group, but still no change in output

> 
> Ok, this is confusing. Are you getting the references in your pdf files?
> If so, it means that biber has found your bib file and has processed it
> correctly. If you are not getting the "References" section at the end,
> however, you may have forgotten and/or mispelled the /printbibliography
> command. Or latex may have choked on it due to some error in the bbl
> file.
> 
> Can you confirm that:
> 
> 1. You are getting the correct citations in the pdf file
yes, I do
> 2. You have entered \printbibliography in ERT at the end of your
> document 
yes, I did
> 3. You do not see a corresponding  "References" or "Works
> cited" section with your full references at the end of your pdf file
No, I don't

I should perhaps add, that I use Koma script (book)
I tried with the normal book style,
but get an error 
Der Absatzstil `Publishers' wurde nicht gefunden.
(paragraph style  `Publishers' was not found
The same with other book styles except Koma

I have taken out all entrances in the preamble except 

 \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
%could also be
% \usepackage[style=authoryear,natbib=true]{biblatex}
\addbibresource{/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib}

but still no Bibliography output in the pdf
although the references are cited in the pdf output

I tried furthermore ps output, same problem: citations alright, but no 
Bibliography output.

I tried also a (almost) minimal example with no success either. 
May I include this example and the bib file going with it? It is quite short 
and might help you in finding out what I do wrong.

Thanks for all the help for and patience with me 


Wolfgang
% This file was created with JabRef 2.7b.
% Encoding: ISO8859_1

@ARTICLE{Hennessey1991,
  author = {Hennessey, T. L. and Field, C. B.},
  title = {Circadian rhythms in photosynthesis},
  journal = {Plant Physiol},
  year = {1991},
  volume = {96},
  pages = {831--836},
  owner = {wolfgang},
  timestamp = {2012.02.25}
}

@comment{jabref-meta: selector_publisher:}

@comment{jabref-meta: selector_author:}

@comment{jabref-meta: selector_journal:}

@comment{jabref-meta: selector_keywords:}



PB-BiberXX.lyx
Description: application/lyx

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 09:34:17 KIM Musak wrote:

Just saw this; its the same issue I have posted just now under
Biblatex and LyX issue #was: Re: Author-year in Lyx

Wolfgang

> Dear Stefano, unfortunately I still can't get lyx to
> 1) show Author-Year , instead the bibtexkey shown
> 2) no bibliography listed at the end of the text
> 
> I am pretty sure the problem happens during generation of the PDF file.
> The reasons being, I could see all the reference in my Lyx document, I
> could cite the selected reference. They are nicely shown in lyx file,
> and nicely shown as Author-Year.  The only problem is when I click
> preview, the PDF only shows the citation but only in bibtexkey and no
> bibliography printed. Anything to do with the module? or Windows 8? or
> probably with Lyx 2.0.6?
> 
> --, what have I done wrong? still clueless ---
> 
> Regards,
> 
> Kamarul
> 
> On Sat, Jan 11, 2014 at 1:30 AM, Stefano Franchi <stef...@tamu.edu> 
wrote:
> > On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak <kim2u4...@gmail.com> 
wrote:
> >> Dear Stefano and all,
> >> 
> >> Coming back to setting Lyx to work with biblatex, I am not so sure
> >> how to make it works in my Lyx. I have tried the steps listed at
> >> http://wiki.lyx.org/BibTeX/Biblatex , which includes
> >> 1) Put the file biblatex.module in the layouts folder
> > 
> > 2) Reconfigure Lyx - then restart
> > 
> >> 3) Setting the Preamble with
> >> a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
> > 
> > you should really use biber instead of bibtex with bibblatex. It is
> > not mandatory but I strongly recommend it. Many biblatex features
> > only wotk with biber. So replace your line with:
> > 
> > \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
> > 
> > (actually biber is the default, so you clould eliminate the backend
> > clause completely, but just for clarity)
> > 
> >> b) \usepackage[style=numeric,backend=bibtex]{biblatex}
> > 
> > This is wrong. You should only load biblatex once, with the style you
> > want. So either load it with style=authoryear, or with style=numeric,
> > but do not load it twice
> > 
> > Stefano, yes, I used only
> 
>  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
> 
> c) \addbibresource{}
> 
> > You should have the complete path from root here, otherwise biblatex
> > won't find you bib file. This is actually  lyx's problem, not
> > biblatex's. The problem is that when you instruct lix to typeset your
> > file into a a pdf, lyx first copies your lyx-converted tex  file to a
> > temp directory, then it runs (pdf)latex and biber/bibtex on it. At
> > that point, the relative path you had inserted in the preamble
> > becomes meaningless since you are no longer in the original location.
> > IN SHORT: always use absolute paths in your \addbibresource commands
> > in the preamble.
> 
> Stefano, i did use the complete the path and also the file name only
> 
> >> 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
> >> in a LyX note or comment
> > 
> > good
> 
> I can confirmed that I did this
> 
> >> 5) enter \printbibliography in ERT
> > 
> > good
> 
> I can confirm that i did this
> 
> > 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
> > 
> >> change the bibtex
> > 
> > good
> 
> I can confirm I did this
> 
> > 7) pass the option backend=biber
> > 
> > see comment to point 3a above
> 
> I did add this and without this
> 
> >> When I inserted the citation, Lyx managed to find it.
> >> But when I previewed it, the citation is not in author-year and no
> >> bibliography printed
> >> 
> >> Did I miss any steps? I am using Lyx 2.0.6
> > 
> > Let me know if it works.
> > 
> > Cheers,
> > Stefano
> > --
> > __
> > Stefano Franchi
> > Associate Research Professor
> > Department of Hispanic StudiesPh:   +1 (979) 845-2125
> > Texas A University  Fax:  +1 (979) 845-6421
> > College Station, Texas, USA
> > 
> > stef...@tamu.edu
> > http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

Wolfgang,

your file had an error in the preamble. You had

\addbibresource{/home/stefano/Desktop/PBRef.bib}


but the file you enclosed is called PBReffXX.bib


Once I fixed the filename to PBRefXX.bib the file compiled fine, and the
references and bibliography appeared in the pdf output (I also had to
change the directory, of course).


Stefano


On Sat, Jan 11, 2014 at 4:25 AM, Wolfgang Engelmann <
engelm...@uni-tuebingen.de> wrote:

>   Thanks, Stefano.
>
>
>
> Here again what I followed up or tried:
>
>
>
> 1) Put the file biblatex.module in the layouts folder
>
> I guess the /.lyx/layouts/ is meant ?
>
> or is it documents>module>Biblatex-citation-styles
>
> I have selected this and added to 'chosen' in right box
>
> or both, which I tried ??
>
> 2) tools>reconfigure
>
> restart lyx
>
> 3) documents>Settings>Bibliography
>
> citation style: standard
>
> Processor: biber
>
> 3) preamble>
>
> \usepackage[style=authoryear,natbib=true]{biblatex}
>
> \addbibresource{}
>
> in my case \addbibresource{PBRef.bib}
>
> tried also
>
> \addbibresource{/home/we/Photobiology2013/PBRFigFinal/PBRef.bib}
>
>
>
> 4) Insert>List/TOC>BibTeX Bibliography...
>
> in my case PBRef
>
> style: plain
>
> and put it in LyX note (turns yellow)
>
> 5) \printbibliography in ERT
>
> inserted after the yellow BibTeX Bibliography note
>
> 6) Tools>Settings>Output>LaTeX
>
> processor: biber
>
>
>
> I did all this including reconfigure, the terminal says
>
> Running: biber "PB-Biber"
>
> INFO - This is Biber 1.6
>
> INFO - Logfile is 'PB-Biber.blg'
>
> INFO - Reading 'PB-Biber.bcf'
>
> INFO - Found 748 citekeys in bib section 0
>
> INFO - Processing section 0
>
> INFO - Looking for bibtex format file
> '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib' for section 0
>
> ERROR - Cannot find '/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib'!
>
> INFO - ERRORS: 1
>
> support/Systemcall.cpp (273): Systemcall: 'biber "PB-Biber"' finished with
> exit code 2
>
>
>
> However, the PBRef.bib is there:
>
> > so you can make up your own command by typing the following
>
> > at a prompt, to get the complete path of file "myfilename.bib"
>
> >
>
> > $>ls $PWD/myfilename.bib
>
> Dolphin tells me:
>
> /home/we/Photobiology2013/PBRFigFinal
>
> and your proposal:
>
> we@wolfgang:~/Photobiology2013/PBRFigFinal$ $ls $PWD/PBRef.bib
>
> bash: /home/we/Photobiology2013/PBRFigFinal/PBRef.bib: Keine Berechtigung
>
> (no admission)
>
> I changed the permission to include group, but still no change in output
>
>
>
> >
>
> > Ok, this is confusing. Are you getting the references in your pdf files?
>
> > If so, it means that biber has found your bib file and has processed it
>
> > correctly. If you are not getting the "References" section at the end,
>
> > however, you may have forgotten and/or mispelled the /printbibliography
>
> > command. Or latex may have choked on it due to some error in the bbl
>
> > file.
>
> >
>
> > Can you confirm that:
>
> >
>
> > 1. You are getting the correct citations in the pdf file
>
> yes, I do
>
> > 2. You have entered \printbibliography in ERT at the end of your
>
> > document
>
> yes, I did
>
> > 3. You do not see a corresponding "References" or "Works
>
> > cited" section with your full references at the end of your pdf file
>
> No, I don't
>
>
>
> I should perhaps add, that I use Koma script (book)
>
> I tried with the normal book style,
>
> but get an error
>
> Der Absatzstil `Publishers' wurde nicht gefunden.
>
> (paragraph style `Publishers' was not found
>
> The same with other book styles except Koma
>
>
>
> I have taken out all entrances in the preamble except
>
>
>
> \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
>
> %could also be
>
> % \usepackage[style=authoryear,natbib=true]{biblatex}
>
> \addbibresource{/home/WE/Photobiology2013/PBRFigFinal/PBRef.bib}
>
>
>
> but still no Bibliography output in the pdf
>
> although the references are cited in the pdf output
>
>
>
> I tried furthermore ps output, same problem: citations alright, but no
> Bibliography output.
>
>
>
> I tried also a (almost) minimal example with no success either.
>
> May I include this example and the bib file going with it? It is quite
> short and might help you in finding out what I do wrong.
>
>
>
> Thanks for all the help for and patience with me
>
>
>
>
>
> Wolfgang
>



-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:

I wonder whether my and Kim's difficulties with biber has to do with the 
versions of biber and biblatex.
According to the biber handbook (Kime, UK) the latest are
Biber version 1.8
Biblatex version 2.8
If I check via synaptic (debian)
I have 0.9.9+release-1 for Biber
and 1.7-1 for biblatex.

Since I have installed texlive 2013
I searched for biber and found it to be in 
/usr/local/texlive/2013/bin/x86-64-linux/
/usr/local/texlive/2013/texmf-dist/doc/bibtex/
/usr/local/texlive/2013/texmf-dist/source/bibtex/

and biblatex in
/usr/local/texlive/2013/texmf-dist/doc/latex/
/usr/local/texlive/2013/texmf-dist/bibtex/csf/
/usr/local/texlive/2013/texmf-dist/bibtex/bst/
/usr/local/texlive/2013/texmf-dist/tex/latex/
/usr/local/texlive/2013/texmf-dist/bibtex/bib/biblatex/

Two questions:

How can I find out the version of these?
How can I find out, that they are used by lyx

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Sat, Jan 11, 2014 at 9:10 AM, Wolfgang Engelmann <
engelm...@uni-tuebingen.de> wrote:

>  On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
>
>
>
> I wonder whether my and Kim's difficulties with biber has to do with the
> versions of biber and biblatex.
>
> According to the biber handbook (Kime, UK) the latest are
>
> Biber version 1.8
>
> Biblatex version 2.8
>
> If I check via synaptic (debian)
>
> I have 0.9.9+release-1 for Biber
>
> and 1.7-1 for biblatex.
>
>
>

Thos are very old version. I would not recommend using biblatex <2


> Since I have installed texlive 2013
>
> I searched for biber and found it to be in
>
> /usr/local/texlive/2013/bin/x86-64-linux/
>
> /usr/local/texlive/2013/texmf-dist/doc/bibtex/
>
> /usr/local/texlive/2013/texmf-dist/source/bibtex/
>
>
>

>
> and biblatex in
>
> /usr/local/texlive/2013/texmf-dist/doc/latex/
>
> /usr/local/texlive/2013/texmf-dist/bibtex/csf/
>
> /usr/local/texlive/2013/texmf-dist/bibtex/bst/
>
> /usr/local/texlive/2013/texmf-dist/tex/latex/
>
> /usr/local/texlive/2013/texmf-dist/bibtex/bib/biblatex/
>
>
>
> Two questions:
>
>
>
> How can I find out the version of these?
>

for biber type
biber --version
at a prompt

for biblatex, the easier way is to look at the latex log. Whn biblatex is
loaded (at the beginning of the log) it will tell you the version

How can I find out, that they are used by lyx
>

If you have multiple versions of biber, it may get complicated. It all
depends on your PATH variable, but there are additional complications if
you start lyx from  the GUI. If you start lyx from the command line
(recommended), then lyx will find the biber program whose version you saw
with "biber --version" and which is located in the output of "which biber".
If you start it from the GUI (double-clicking on a lyx file, using the F2
shortcut in Kde, etcetera), it all depends on how you set up KDE. I never
got the hang of it, to be frank, so I always start it from the command line.

Cheers,

Stefano




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 15:54:44 stefano franchi wrote:
> Wolfgang, Kamarul,
> 
> my guess is that you have the same problem. Namely, biber cannot find
> the bib file. Or perhaps biber is not launched at all.
> 
> Try looking at the latex log (Document>>LaTeX log), and check out both
> the latex log proper and the bibtex log (the two choices in  the
> dropdown menu). You should get an idea of what is going wrong. If biber
> cannot find the file, you should see something like the following in
> the "bibtex" log:
> 
> [181] Biber.pm:3190> INFO - Looking for bibtex format file '[YOUR BIB
> FILENAME HERE]' for section 0
> [252] Utils.pm:185> ERROR - Cannot find '[YOUR BIB FILENAME HERE]'!
> [253] Biber.pm:109> INFO - ERRORS: 1
> 
> To sort out if there is something wrong with your installation, try out
> the enclosed files:
> 1. first, copy the lisp.bb file to /tmp (that is the tmp directory
> directly under root, not in your home folder. It is generally writable
> on linux systems).
> 2. then try typesetting the lyx file from within lyx
> 3. If your result is identical to the pdf file I am enclosing we'll know
> your installation is all right and we can focus on what is wrong with
> your lyx files
> 
Doing 1 and 2 gives me in the pdf file:

Testing biber and biblatex
Here is a reference to McCarthy’s history of lisp (808387 ), followed by
the same reference in traditional author-year-format (808387 ).

compared to your pdf file:

Testing biber and biblatex
Here is a reference to McCarthy’s history of lisp (1978), followed by the
same reference in traditional author-year-format (McCarthy, 1978).
References
McCarthy, John (1978). “History of LISP”. In: SIGPLAN Not. 13.8, pp. 217–
223. issn: 0362-1340. doi: http : / / doi . acm . org / 10 . 1145 / 960118 
.
808387.

That means, my installation is not working properly.
Perhaps what I mentioned in my EMail Today 16:10:42?
(old versions of biber and biblatex)

So I should first find out which versions are in Texlive2013 (see my EMail 
Today 16:10:42

How to?

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[Wolfgang Engelmann]

On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
> >  On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
> > 
> > 
> > Two questions:
> > 
> > 
> > 
> > How can I find out the version of these?
> 
> for biber type
> biber --version

it is 1.6


> at a prompt
> 
> for biblatex, the easier way is to look at the latex log. Whn biblatex
> is loaded (at the beginning of the log) it will tell you the version

 biblatex 2013/05/01 v2.6

> 
> How can I find out, that they are used by lyx
> 
> 
> If you have multiple versions of biber, it may get complicated. It all
> depends on your PATH variable, but there are additional complications if
> you start lyx from  the GUI. If you start lyx from the command line
> (recommended), then lyx will find the biber program whose version you
> saw with "biber --version" and which is located in the output of "which
> biber". If you start it from the GUI (double-clicking on a lyx file,
> using the F2 shortcut in Kde, etcetera), it all depends on how you set
> up KDE. I never got the hang of it, to be frank, so I always start it
> from the command line.
so do I


Thanks, Stefano, will try later.

Wolfgang

Re: Biblatex and LyX issue #was: Re: Author-year in Lyx

[stefano franchi]

On Sat, Jan 11, 2014 at 10:47 AM, Wolfgang Engelmann <
engelm...@uni-tuebingen.de> wrote:

>  On Saturday 11 January 2014 16:23:41 stefano franchi wrote:
>
> > > On Saturday 11 January 2014 11:25:43 Wolfgang Engelmann wrote:
> > for biber type
>
> > biber --version
>
>
>
> it is 1.6
>
>
> > for biblatex, the easier way is to look at the latex log. Whn biblatex
>
> > is loaded (at the beginning of the log) it will tell you the version
>
>
>
> biblatex 2013/05/01 v2.6
>
>
You're all right then---biblatex 2.6 wants biber 1.6, so everything is fine
on that front.

I still think you may have path-related  issues in the preamble.

Do check the capitalization of your home directory (WE vs we) as per my
previous message.


Cheers,

S.
-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[KIM Musak]

Dear Stefano and all,

Coming back to setting Lyx to work with biblatex, I am not so sure how to
make it works in my Lyx. I have tried the steps listed at
http://wiki.lyx.org/BibTeX/Biblatex , which includes
1) Put the file biblatex.module in the layouts folder
2) Reconfigure Lyx - then restart
3) Setting the Preamble with
a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
b) \usepackage[style=numeric,backend=bibtex]{biblatex}
c) \addbibresource{name of bib-file with .bib-extension}
4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
LyX note or comment
5) enter \printbibliography in ERT
6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
change the bibtex
7) pass the option backend=biber

When I inserted the citation, Lyx managed to find it.
But when I previewed it, the citation is not in author-year and no
bibliography printed

Did I miss any steps? I am using Lyx 2.0.6

Regards,

Kamarul




On Thu, Jan 9, 2014 at 9:26 PM, Stefano Franchi stef...@tamu.edu wrote:

 Hi Kamarul,

 in order to use author-year you need to use natbib. If you use bibtex as
 your reference processor, all you need to do is to put
 \usepackage{natbib} in your preamble (DocumentSettingsPreamble) and
 choose Natbib in DocumentSettingsBibliography. When you insert your
 bibliography file (InsertList/TOCBibTeX Bibliography), you should
 choose plainnat as a style. This gives you the basic setting. Many more
 things are possible, including changing the style and so on. See the lyx
 wiki page on bibliography for a first description of the package  [1].
 There is also documentation for natbib in your latex installation (search
 for the file natbib.pdf on your computer or type texdoc natbib at a
 terminal). I enclosed a minimal  example as a working LyX file (with a
 minimal bib file).

 The above assumes you are using bibtex. If, instead, you are using
 biblatex (like me), you should proceed differently. Write again and I'll
 explain how (it is very easy).

 Also, please write to the whole lyx users list---your chances to get help
 will increase substantially

 Cheers,

 Stefano


 [1] http://wiki.lyx.org/BibTeX/Background#natbib


 On Thu, Jan 9, 2014 at 12:26 AM, Kamarul Imran kim4...@gmail.com wrote:

 Dear Prof Franchi,

 I stumbled a post by you on setting the author-year citation in Lyx. I
 have problems in writing the citation using author-year style in Lyx. I
 have tried a few links and the suggested workaround on Lyx website, but
 nothing works.

 I guess the problems lie in the 'Document setting' and 'Tools' in Lyx. I
 am using Lyx 2.0.6 on Windows 8. My citation does not show properly and no
 bibliography generated, even though the bib files were correctly
 set/linked.

 Would you mind, list the correct (your working) setting in Lyx so that I
 might be able to test it on my laptop.

 Thanks very much.

 Best wishes,

 Kamarul Imran Musa
 Malaysia




 --
 __
 Stefano Franchi
 Associate Research Professor
 Department of Hispanic StudiesPh:   +1 (979) 845-2125
 Texas AM University  Fax:  +1 (979) 845-6421
 College Station, Texas, USA

 stef...@tamu.edu
 http://stefano.cleinias.org

Re: Author-year in Lyx

[Stefano Franchi]

On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com wrote:

 Dear Stefano and all,

 Coming back to setting Lyx to work with biblatex, I am not so sure how to
 make it works in my Lyx. I have tried the steps listed at
 http://wiki.lyx.org/BibTeX/Biblatex , which includes
 1) Put the file biblatex.module in the layouts folder

2) Reconfigure Lyx - then restart



 3) Setting the Preamble with
 a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}


you should really use biber instead of bibtex with bibblatex. It is not
mandatory but I strongly recommend it. Many biblatex features only wotk
with biber. So replace your line with:

\usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

(actually biber is the default, so you clould eliminate the backend clause
completely, but just for clarity)

 b) \usepackage[style=numeric,backend=bibtex]{biblatex}


This is wrong. You should only load biblatex once, with the style you want.
So either load it with style=authoryear, or with style=numeric, but do not
load it twice

c) \addbibresource{name of bib-file with .bib-extension}


You should have the complete path from root here, otherwise biblatex won't
find you bib file. This is actually  lyx's problem, not biblatex's. The
problem is that when you instruct lix to typeset your file into a a pdf,
lyx first copies your lyx-converted tex  file to a temp directory, then it
runs (pdf)latex and biber/bibtex on it. At that point, the relative path
you had inserted in the preamble becomes meaningless since you are no
longer in the original location.
IN SHORT: always use absolute paths in your \addbibresource commands in the
preamble.



 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
 LyX note or comment

good


 5) enter \printbibliography in ERT

good

6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
 change the bibtex

good

7) pass the option backend=biber

see comment to point 3a above


 When I inserted the citation, Lyx managed to find it.
 But when I previewed it, the citation is not in author-year and no
 bibliography printed

 Did I miss any steps? I am using Lyx 2.0.6




Let me know if it works.

Cheers,
Stefano
-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Friday 10 January 2014 18:30:34 Stefano Franchi wrote:
Having asked recently for the van von della etc names 
I remembered that biblatex/biber takes apparently care of it. So I tried 
to use biber with the procedure given:

 On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak 
kim2u4...@gmail.com wrote:
  Dear Stefano and all,
  
  Coming back to setting Lyx to work with biblatex, I am not so sure 
how
  to make it works in my Lyx. I have tried the steps listed at
  http://wiki.lyx.org/BibTeX/Biblatex , which includes
  1) Put the file biblatex.module in the layouts folder
 
 2) Reconfigure Lyx - then restart
 
  3) Setting the Preamble with
 \usepackage[style=authoryear,natbib=true,backend=biber]
{biblatex}
 
 (actually biber is the default, so you clould eliminate the backend
 clause completely, but just for clarity)
  
 c) \addbibresource{name of bib-file with .bib-extension}
 
  
  4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
  in a LyX note or comment

Question: what about the style in the BibTeX Bibliography? plain?
  
  5) enter \printbibliography in ERT
 
 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX 
and
##
should this be 
 6) to change from bibtex to biber, go to Tools→Settings→Output→LaTeX 
and change processor to biber
??
###
 
  change the bibtex
 
 good
 
 7) pass the option backend=biber
 
 see comment to point 3a above
#
i.e. it is not necessary to enter backend=biber in options
i.e. just leave options empty ?

#
what about
--documentsettingsreferencescitation style
plain?
and
--documentsettingsreferencesprocessor
biber?

I did all this including reconfigure,
but on the terminal it says

Cannot find '~/Photobiology2013/PBRFigFinal/PB-ref-20140108'

although I included it in
\addbibresource{~/Photobiology2013/PBRFigFinal/PB-ref-
N20140108.bib}

Is there a linux command which, being at the site of the bib file, tells me 
the whole path I have to use?

I tried also
/home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}
and
./home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}

but the pdf output does not contain the Bibliography either. The 
citations are in the pdf-document.

I am using Debian and Lyx 2.0.6

Wolfgang

Re: Author-year in Lyx

[stefano franchi]

On Jan 10, 2014 2:08 PM, Wolfgang Engelmann engelm...@uni-tuebingen.de
wrote:

  On Friday 10 January 2014 18:30:34 Stefano Franchi wrote:

 Having asked recently for the van von della etc names

 I remembered that biblatex/biber takes apparently care of it. So I tried
 to use biber with the procedure given:



  On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com wrote:

   Dear Stefano and all,

  

   Coming back to setting Lyx to work with biblatex, I am not so sure how

   to make it works in my Lyx. I have tried the steps listed at

   http://wiki.lyx.org/BibTeX/Biblatex , which includes

   1) Put the file biblatex.module in the layouts folder

 

  2) Reconfigure Lyx - then restart

 

   3) Setting the Preamble with

  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

 

  (actually biber is the default, so you clould eliminate the backend

  clause completely, but just for clarity)

 


To be clear, the loading instruction could be just:
\usepackage[style=authoryear, natbib=true]{biblatex}


  c) \addbibresource{name of bib-file with .bib-extension}

 

 

   4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )

   in a LyX note or comment

 

 Question: what about the style in the BibTeX Bibliography? plain?


It does not matter. Lyx will ignore the bibtex bibliography when exporting
to latex (prior to typesetting). Just leave it to plain.


  

   5) enter \printbibliography in ERT

 

  6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and

 ##

 should this be

 6) to change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
 change processor to biber

 ??



Actually, I prefer to do it on a document-by-document basis with:
DocumentSettings?Bibliography
and then choosing biber from the drop-down menu in Bibliography
Generation/ processor


###

 

   change the bibtex

 

  good

 

  7) pass the option backend=biber

 

  see comment to point 3a above

 #

 i.e. it is not necessary to enter backend=biber in options

 i.e. just leave options empty ?


 See above. To repeat: you can just write \usepackage[style=authoryear,
natbib=true]{biblatex} in the preamble


 #

 what about

 --documentsettingsreferencescitation style

 plain?


See above. It is irrelevant, as Lyx ignores it. Just leave it plain

 and

 --documentsettingsreferencesprocessor

 biber?


see above. This is my favorite option,



 I did all this including reconfigure,

 but on the terminal it says



 Cannot find '~/Photobiology2013/PBRFigFinal/PB-ref-20140108'



 although I included it in

 \addbibresource{~/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}



 Is there a linux command which, being at the site of the bib file, tells
 me the whole path I have to use?


There is no linux command that I know of that would do the trick of
printing a file with its absolute path. However, if you are in the
directory where the file resides,
$pwd
gives you the present working directory, i.e. the absolute path of where
you are .You can then cut and paste the output in fornt of the file name.
The environmental variable $PWD contains the same present working
directory, so you can make up your own command by typing the following at a
prompt, to get the complete path of file  myfilename.bib

$ls $PWD/myfilename.bib

Alternatively, in a GUI: if you are using KDE, you can take advantage of
the Dolphin file manages copy command. Just navigate to your bib file,
select it and hit ctrl-C. You'll get an absolute path, prepended by
file:// in the clipboard. You can then paste it directly into Lyx's
preamble (and remove the file:// prefix afterwards). I think Gnome has a
similar functionality in its file manager, but I never used it.



 I tried also

 /home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}


this is the correct form. Avoid all relative references in path names (~,
., etc.).


 and

 ./home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}




Incorrect. Lyx will copy the file to something like /tmp/.  and at that
point your . directory will be completely different


 but the pdf output does not contain the Bibliography either. The citationsare 
 in the pdf-document.




Ok, this is confusing. Are you getting the references in your pdf files? If
so, it means that biber has found your bib file and has processed it
correctly. If you are not getting the References section at the end,
however, you may have forgotten and/or mispelled the /printbibliography
command. Or latex may have choked on it due to some error in the bbl file.

Can you confirm that:

1. You are getting the correct citations in the pdf file
2. You have entered \printbibliography in ERT at the end of your document
3. You do not see a corresponding  References or Works cited section
with your full references at the end of your pdf file


Let us know about your progress.


Cheers,

Stefano

Re: Author-year in Lyx

[KIM Musak]

Dear Stefano and all,

Coming back to setting Lyx to work with biblatex, I am not so sure how to
make it works in my Lyx. I have tried the steps listed at
http://wiki.lyx.org/BibTeX/Biblatex , which includes
1) Put the file biblatex.module in the layouts folder
2) Reconfigure Lyx - then restart
3) Setting the Preamble with
a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
b) \usepackage[style=numeric,backend=bibtex]{biblatex}
c) \addbibresource{name of bib-file with .bib-extension}
4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
LyX note or comment
5) enter \printbibliography in ERT
6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
change the bibtex
7) pass the option backend=biber

When I inserted the citation, Lyx managed to find it.
But when I previewed it, the citation is not in author-year and no
bibliography printed

Did I miss any steps? I am using Lyx 2.0.6

Regards,

Kamarul




On Thu, Jan 9, 2014 at 9:26 PM, Stefano Franchi stef...@tamu.edu wrote:

 Hi Kamarul,

 in order to use author-year you need to use natbib. If you use bibtex as
 your reference processor, all you need to do is to put
 \usepackage{natbib} in your preamble (DocumentSettingsPreamble) and
 choose Natbib in DocumentSettingsBibliography. When you insert your
 bibliography file (InsertList/TOCBibTeX Bibliography), you should
 choose plainnat as a style. This gives you the basic setting. Many more
 things are possible, including changing the style and so on. See the lyx
 wiki page on bibliography for a first description of the package  [1].
 There is also documentation for natbib in your latex installation (search
 for the file natbib.pdf on your computer or type texdoc natbib at a
 terminal). I enclosed a minimal  example as a working LyX file (with a
 minimal bib file).

 The above assumes you are using bibtex. If, instead, you are using
 biblatex (like me), you should proceed differently. Write again and I'll
 explain how (it is very easy).

 Also, please write to the whole lyx users list---your chances to get help
 will increase substantially

 Cheers,

 Stefano


 [1] http://wiki.lyx.org/BibTeX/Background#natbib


 On Thu, Jan 9, 2014 at 12:26 AM, Kamarul Imran kim4...@gmail.com wrote:

 Dear Prof Franchi,

 I stumbled a post by you on setting the author-year citation in Lyx. I
 have problems in writing the citation using author-year style in Lyx. I
 have tried a few links and the suggested workaround on Lyx website, but
 nothing works.

 I guess the problems lie in the 'Document setting' and 'Tools' in Lyx. I
 am using Lyx 2.0.6 on Windows 8. My citation does not show properly and no
 bibliography generated, even though the bib files were correctly
 set/linked.

 Would you mind, list the correct (your working) setting in Lyx so that I
 might be able to test it on my laptop.

 Thanks very much.

 Best wishes,

 Kamarul Imran Musa
 Malaysia




 --
 __
 Stefano Franchi
 Associate Research Professor
 Department of Hispanic StudiesPh:   +1 (979) 845-2125
 Texas AM University  Fax:  +1 (979) 845-6421
 College Station, Texas, USA

 stef...@tamu.edu
 http://stefano.cleinias.org

Re: Author-year in Lyx

[Stefano Franchi]

On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com wrote:

 Dear Stefano and all,

 Coming back to setting Lyx to work with biblatex, I am not so sure how to
 make it works in my Lyx. I have tried the steps listed at
 http://wiki.lyx.org/BibTeX/Biblatex , which includes
 1) Put the file biblatex.module in the layouts folder

2) Reconfigure Lyx - then restart



 3) Setting the Preamble with
 a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}


you should really use biber instead of bibtex with bibblatex. It is not
mandatory but I strongly recommend it. Many biblatex features only wotk
with biber. So replace your line with:

\usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

(actually biber is the default, so you clould eliminate the backend clause
completely, but just for clarity)

 b) \usepackage[style=numeric,backend=bibtex]{biblatex}


This is wrong. You should only load biblatex once, with the style you want.
So either load it with style=authoryear, or with style=numeric, but do not
load it twice

c) \addbibresource{name of bib-file with .bib-extension}


You should have the complete path from root here, otherwise biblatex won't
find you bib file. This is actually  lyx's problem, not biblatex's. The
problem is that when you instruct lix to typeset your file into a a pdf,
lyx first copies your lyx-converted tex  file to a temp directory, then it
runs (pdf)latex and biber/bibtex on it. At that point, the relative path
you had inserted in the preamble becomes meaningless since you are no
longer in the original location.
IN SHORT: always use absolute paths in your \addbibresource commands in the
preamble.



 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
 LyX note or comment

good


 5) enter \printbibliography in ERT

good

6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
 change the bibtex

good

7) pass the option backend=biber

see comment to point 3a above


 When I inserted the citation, Lyx managed to find it.
 But when I previewed it, the citation is not in author-year and no
 bibliography printed

 Did I miss any steps? I am using Lyx 2.0.6




Let me know if it works.

Cheers,
Stefano
-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Friday 10 January 2014 18:30:34 Stefano Franchi wrote:
Having asked recently for the van von della etc names 
I remembered that biblatex/biber takes apparently care of it. So I tried 
to use biber with the procedure given:

 On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak 
kim2u4...@gmail.com wrote:
  Dear Stefano and all,
  
  Coming back to setting Lyx to work with biblatex, I am not so sure 
how
  to make it works in my Lyx. I have tried the steps listed at
  http://wiki.lyx.org/BibTeX/Biblatex , which includes
  1) Put the file biblatex.module in the layouts folder
 
 2) Reconfigure Lyx - then restart
 
  3) Setting the Preamble with
 \usepackage[style=authoryear,natbib=true,backend=biber]
{biblatex}
 
 (actually biber is the default, so you clould eliminate the backend
 clause completely, but just for clarity)
  
 c) \addbibresource{name of bib-file with .bib-extension}
 
  
  4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
  in a LyX note or comment

Question: what about the style in the BibTeX Bibliography? plain?
  
  5) enter \printbibliography in ERT
 
 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX 
and
##
should this be 
 6) to change from bibtex to biber, go to Tools→Settings→Output→LaTeX 
and change processor to biber
??
###
 
  change the bibtex
 
 good
 
 7) pass the option backend=biber
 
 see comment to point 3a above
#
i.e. it is not necessary to enter backend=biber in options
i.e. just leave options empty ?

#
what about
--documentsettingsreferencescitation style
plain?
and
--documentsettingsreferencesprocessor
biber?

I did all this including reconfigure,
but on the terminal it says

Cannot find '~/Photobiology2013/PBRFigFinal/PB-ref-20140108'

although I included it in
\addbibresource{~/Photobiology2013/PBRFigFinal/PB-ref-
N20140108.bib}

Is there a linux command which, being at the site of the bib file, tells me 
the whole path I have to use?

I tried also
/home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}
and
./home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}

but the pdf output does not contain the Bibliography either. The 
citations are in the pdf-document.

I am using Debian and Lyx 2.0.6

Wolfgang

Re: Author-year in Lyx

[stefano franchi]

On Jan 10, 2014 2:08 PM, Wolfgang Engelmann engelm...@uni-tuebingen.de
wrote:

  On Friday 10 January 2014 18:30:34 Stefano Franchi wrote:

 Having asked recently for the van von della etc names

 I remembered that biblatex/biber takes apparently care of it. So I tried
 to use biber with the procedure given:



  On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak kim2u4...@gmail.com wrote:

   Dear Stefano and all,

  

   Coming back to setting Lyx to work with biblatex, I am not so sure how

   to make it works in my Lyx. I have tried the steps listed at

   http://wiki.lyx.org/BibTeX/Biblatex , which includes

   1) Put the file biblatex.module in the layouts folder

 

  2) Reconfigure Lyx - then restart

 

   3) Setting the Preamble with

  \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

 

  (actually biber is the default, so you clould eliminate the backend

  clause completely, but just for clarity)

 


To be clear, the loading instruction could be just:
\usepackage[style=authoryear, natbib=true]{biblatex}


  c) \addbibresource{name of bib-file with .bib-extension}

 

 

   4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )

   in a LyX note or comment

 

 Question: what about the style in the BibTeX Bibliography? plain?


It does not matter. Lyx will ignore the bibtex bibliography when exporting
to latex (prior to typesetting). Just leave it to plain.


  

   5) enter \printbibliography in ERT

 

  6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and

 ##

 should this be

 6) to change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
 change processor to biber

 ??



Actually, I prefer to do it on a document-by-document basis with:
DocumentSettings?Bibliography
and then choosing biber from the drop-down menu in Bibliography
Generation/ processor


###

 

   change the bibtex

 

  good

 

  7) pass the option backend=biber

 

  see comment to point 3a above

 #

 i.e. it is not necessary to enter backend=biber in options

 i.e. just leave options empty ?


 See above. To repeat: you can just write \usepackage[style=authoryear,
natbib=true]{biblatex} in the preamble


 #

 what about

 --documentsettingsreferencescitation style

 plain?


See above. It is irrelevant, as Lyx ignores it. Just leave it plain

 and

 --documentsettingsreferencesprocessor

 biber?


see above. This is my favorite option,



 I did all this including reconfigure,

 but on the terminal it says



 Cannot find '~/Photobiology2013/PBRFigFinal/PB-ref-20140108'



 although I included it in

 \addbibresource{~/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}



 Is there a linux command which, being at the site of the bib file, tells
 me the whole path I have to use?


There is no linux command that I know of that would do the trick of
printing a file with its absolute path. However, if you are in the
directory where the file resides,
$pwd
gives you the present working directory, i.e. the absolute path of where
you are .You can then cut and paste the output in fornt of the file name.
The environmental variable $PWD contains the same present working
directory, so you can make up your own command by typing the following at a
prompt, to get the complete path of file  myfilename.bib

$ls $PWD/myfilename.bib

Alternatively, in a GUI: if you are using KDE, you can take advantage of
the Dolphin file manages copy command. Just navigate to your bib file,
select it and hit ctrl-C. You'll get an absolute path, prepended by
file:// in the clipboard. You can then paste it directly into Lyx's
preamble (and remove the file:// prefix afterwards). I think Gnome has a
similar functionality in its file manager, but I never used it.



 I tried also

 /home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}


this is the correct form. Avoid all relative references in path names (~,
., etc.).


 and

 ./home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}




Incorrect. Lyx will copy the file to something like /tmp/.  and at that
point your . directory will be completely different


 but the pdf output does not contain the Bibliography either. The citationsare 
 in the pdf-document.




Ok, this is confusing. Are you getting the references in your pdf files? If
so, it means that biber has found your bib file and has processed it
correctly. If you are not getting the References section at the end,
however, you may have forgotten and/or mispelled the /printbibliography
command. Or latex may have choked on it due to some error in the bbl file.

Can you confirm that:

1. You are getting the correct citations in the pdf file
2. You have entered \printbibliography in ERT at the end of your document
3. You do not see a corresponding  References or Works cited section
with your full references at the end of your pdf file


Let us know about your progress.


Cheers,

Stefano

Re: Author-year in Lyx

[KIM Musak]

Dear Stefano and all,

Coming back to setting Lyx to work with biblatex, I am not so sure how to
make it works in my Lyx. I have tried the steps listed at
http://wiki.lyx.org/BibTeX/Biblatex , which includes
1) Put the file biblatex.module in the layouts folder
2) Reconfigure Lyx - then restart
3) Setting the Preamble with
a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
b) \usepackage[style=numeric,backend=bibtex]{biblatex}
c) \addbibresource{}
4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
LyX note or comment
5) enter \printbibliography in ERT
6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
change the bibtex
7) pass the option backend=biber

When I inserted the citation, Lyx managed to find it.
But when I previewed it, the citation is not in author-year and no
bibliography printed

Did I miss any steps? I am using Lyx 2.0.6

Regards,

Kamarul




On Thu, Jan 9, 2014 at 9:26 PM, Stefano Franchi  wrote:

> Hi Kamarul,
>
> in order to use author-year you need to use natbib. If you use bibtex as
> your reference processor, all you need to do is to put
> "\usepackage{natbib}" in your preamble (Document>>Settings>>Preamble) and
> choose Natbib in Document>>Settings>>Bibliography. When you insert your
> bibliography file (Insert>>List/TOC>>BibTeX Bibliography), you should
> choose "plainnat" as a style. This gives you the basic setting. Many more
> things are possible, including changing the style and so on. See the lyx
> wiki page on bibliography for a first description of the package  [1].
> There is also documentation for natbib in your latex installation (search
> for the file natbib.pdf on your computer or type "texdoc natbib" at a
> terminal). I enclosed a minimal  example as a working LyX file (with a
> minimal bib file).
>
> The above assumes you are using bibtex. If, instead, you are using
> biblatex (like me), you should proceed differently. Write again and I'll
> explain how (it is very easy).
>
> Also, please write to the whole lyx users list---your chances to get help
> will increase substantially
>
> Cheers,
>
> Stefano
>
>
> [1] http://wiki.lyx.org/BibTeX/Background#natbib
>
>
> On Thu, Jan 9, 2014 at 12:26 AM, Kamarul Imran  wrote:
>
>> Dear Prof Franchi,
>>
>> I stumbled a post by you on setting the author-year citation in Lyx. I
>> have problems in writing the citation using author-year style in Lyx. I
>> have tried a few links and the suggested workaround on Lyx website, but
>> nothing works.
>>
>> I guess the problems lie in the 'Document setting' and 'Tools' in Lyx. I
>> am using Lyx 2.0.6 on Windows 8. My citation does not show properly and no
>> bibliography generated, even though the bib files were correctly
>> set/linked.
>>
>> Would you mind, list the correct (your working) setting in Lyx so that I
>> might be able to test it on my laptop.
>>
>> Thanks very much.
>>
>> Best wishes,
>>
>> Kamarul Imran Musa
>> Malaysia
>>
>
>
>
> --
> __
> Stefano Franchi
> Associate Research Professor
> Department of Hispanic StudiesPh:   +1 (979) 845-2125
> Texas A University  Fax:  +1 (979) 845-6421
> College Station, Texas, USA
>
> stef...@tamu.edu
> http://stefano.cleinias.org
>

Re: Author-year in Lyx

[Stefano Franchi]

On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak  wrote:

> Dear Stefano and all,
>
> Coming back to setting Lyx to work with biblatex, I am not so sure how to
> make it works in my Lyx. I have tried the steps listed at
> http://wiki.lyx.org/BibTeX/Biblatex , which includes
> 1) Put the file biblatex.module in the layouts folder
>
2) Reconfigure Lyx - then restart
>


> 3) Setting the Preamble with
> a) \usepackage[style=authoryear,natbib=true,backend=bibtex]{biblatex}
>

you should really use biber instead of bibtex with bibblatex. It is not
mandatory but I strongly recommend it. Many biblatex features only wotk
with biber. So replace your line with:

\usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}

(actually biber is the default, so you clould eliminate the backend clause
completely, but just for clarity)

> b) \usepackage[style=numeric,backend=bibtex]{biblatex}
>

This is wrong. You should only load biblatex once, with the style you want.
So either load it with style=authoryear, or with style=numeric, but do not
load it twice

c) \addbibresource{}
>

You should have the complete path from root here, otherwise biblatex won't
find you bib file. This is actually  lyx's problem, not biblatex's. The
problem is that when you instruct lix to typeset your file into a a pdf,
lyx first copies your lyx-converted tex  file to a temp directory, then it
runs (pdf)latex and biber/bibtex on it. At that point, the relative path
you had inserted in the preamble becomes meaningless since you are no
longer in the original location.
IN SHORT: always use absolute paths in your \addbibresource commands in the
preamble.



> 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... ) in a
> LyX note or comment
>
good


> 5) enter \printbibliography in ERT
>
good

6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
> change the bibtex
>
good

7) pass the option backend=biber
>
see comment to point 3a above


> When I inserted the citation, Lyx managed to find it.
> But when I previewed it, the citation is not in author-year and no
> bibliography printed
>
> Did I miss any steps? I am using Lyx 2.0.6
>
>


Let me know if it works.

Cheers,
Stefano
-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org

Re: Author-year in Lyx

[Wolfgang Engelmann]

On Friday 10 January 2014 18:30:34 Stefano Franchi wrote:
Having asked recently for the van von della etc names 
I remembered that biblatex/biber takes apparently care of it. So I tried 
to use biber with the procedure given:

> On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak 
 wrote:
> > Dear Stefano and all,
> > 
> > Coming back to setting Lyx to work with biblatex, I am not so sure 
how
> > to make it works in my Lyx. I have tried the steps listed at
> > http://wiki.lyx.org/BibTeX/Biblatex , which includes
> > 1) Put the file biblatex.module in the layouts folder
> 
> 2) Reconfigure Lyx - then restart
> 
> > 3) Setting the Preamble with
> \usepackage[style=authoryear,natbib=true,backend=biber]
{biblatex}
> 
> (actually biber is the default, so you clould eliminate the backend
> clause completely, but just for clarity)
>  
> c) \addbibresource{}
> 
>  
> > 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
> > in a LyX note or comment

Question: what about the style in the BibTeX Bibliography? plain?
> > 
> > 5) enter \printbibliography in ERT
> 
> 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX 
and
##
should this be 
 6) to change from bibtex to biber, go to Tools→Settings→Output→LaTeX 
and change processor to biber
??
###
> 
> > change the bibtex
> 
> good
> 
> 7) pass the option backend=biber
> 
> see comment to point 3a above
#
i.e. it is not necessary to enter backend=biber in options
i.e. just leave options empty ?

#
what about
-->document>settings>references>citation style
plain?
and
-->document>settings>references>processor
biber?

I did all this including reconfigure,
but on the terminal it says

Cannot find '~/Photobiology2013/PBRFigFinal/PB-ref-20140108'

although I included it in
\addbibresource{~/Photobiology2013/PBRFigFinal/PB-ref-
N20140108.bib}

Is there a linux command which, being at the site of the bib file, tells me 
the whole path I have to use?

I tried also
/home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}
and
./home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}

but the pdf output does not contain the Bibliography either. The 
citations are in the pdf-document.

I am using Debian and Lyx 2.0.6

Wolfgang

Re: Author-year in Lyx

[stefano franchi]

On Jan 10, 2014 2:08 PM, "Wolfgang Engelmann" 
wrote:

>  On Friday 10 January 2014 18:30:34 Stefano Franchi wrote:
>
> Having asked recently for the van von della etc names
>
> I remembered that biblatex/biber takes apparently care of it. So I tried
> to use biber with the procedure given:
>
>
>
> > On Fri, Jan 10, 2014 at 10:49 AM, KIM Musak  wrote:
>
> > > Dear Stefano and all,
>
> > >
>
> > > Coming back to setting Lyx to work with biblatex, I am not so sure how
>
> > > to make it works in my Lyx. I have tried the steps listed at
>
> > > http://wiki.lyx.org/BibTeX/Biblatex , which includes
>
> > > 1) Put the file biblatex.module in the layouts folder
>
> >
>
> > 2) Reconfigure Lyx - then restart
>
> >
>
> > > 3) Setting the Preamble with
>
> > \usepackage[style=authoryear,natbib=true,backend=biber]{biblatex}
>
> >
>
> > (actually biber is the default, so you clould eliminate the backend
>
> > clause completely, but just for clarity)
>
> >
>

To be clear, the loading instruction could be just:
\usepackage[style=authoryear, natbib=true]{biblatex}


> > c) \addbibresource{}
>
> >
>
> >
>
> > > 4) insert the BibTeX inset (Insert→List/TOC→BibTeX Bibliography... )
>
> > > in a LyX note or comment
>
> 
>
> Question: what about the style in the BibTeX Bibliography? plain?
>

It does not matter. Lyx will ignore the bibtex bibliography when exporting
to latex (prior to typesetting). Just leave it to plain.


> > >
>
> > > 5) enter \printbibliography in ERT
>
> >
>
> > 6) change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
>
> ##
>
> should this be
>
> 6) to change from bibtex to biber, go to Tools→Settings→Output→LaTeX and
> change processor to biber
>
> ??
>


Actually, I prefer to do it on a document-by-document basis with:
Document>>Settings?>>Bibliography
and then choosing biber from the drop-down menu in "Bibliography
Generation/ processor"


###
>
> >
>
> > > change the bibtex
>
> >
>
> > good
>
> >
>
> > 7) pass the option backend=biber
>
> >
>
> > see comment to point 3a above
>
> #
>
> i.e. it is not necessary to enter backend=biber in options
>
> i.e. just leave options empty ?
>
>
> See above. To repeat: you can just write \usepackage[style=authoryear,
natbib=true]{biblatex} in the preamble


> #
>
> what about
>
> -->document>settings>references>citation style
>
> plain?
>

See above. It is irrelevant, as Lyx ignores it. Just leave it "plain"

> and
>
> -->document>settings>references>processor
>
> biber?
>
>
see above. This is my favorite option,

>
>
> I did all this including reconfigure,
>
> but on the terminal it says
>
>
>
> Cannot find '~/Photobiology2013/PBRFigFinal/PB-ref-20140108'
>
>
>
> although I included it in
>
> \addbibresource{~/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}
>
>
>
> Is there a linux command which, being at the site of the bib file, tells
> me the whole path I have to use?
>
>
There is no linux command that I know of that would do the trick of
printing a file with its absolute path. However, if you are in the
directory where the file resides,
$>pwd
gives you the present working directory, i.e. the absolute path of where
you are .You can then cut and paste the output in fornt of the file name.
The environmental variable $PWD contains the same present working
directory, so you can make up your own command by typing the following at a
prompt, to get the complete path of file  "myfilename.bib"

$>ls $PWD/myfilename.bib

Alternatively, in a GUI: if you are using KDE, you can take advantage of
the Dolphin file manages "copy" command. Just navigate to your bib file,
select it and hit ctrl-C. You'll get an absolute path, prepended by
"file://" in the clipboard. You can then paste it directly into Lyx's
preamble (and remove the file:// prefix afterwards). I think Gnome has a
similar functionality in its file manager, but I never used it.


>
> I tried also
>
> /home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}
>
>
this is the correct form. Avoid all relative references in path names (~,
., etc.).


> and
>
> ./home/WE/Photobiology2013/PBRFigFinal/PB-ref-N20140108.bib}
>
>
>

Incorrect. Lyx will copy the file to something like /tmp/.  and at that
point your . directory will be completely different


> but the pdf output does not contain the Bibliography either. The citationsare 
> in the pdf-document.
>
>
>

Ok, this is confusing. Are you getting the references in your pdf files? If
so, it means that biber has found your bib file and has processed it
correctly. If you are not getting the "References" section at the end,
however, you may have forgotten and/or mispelled the /printbibliography
command. Or latex may have choked on it due to some error in the bbl file.

Can you confirm that:

1. You are getting the correct citations in the pdf file
2. You have entered \printbibliography in ERT at the end of your document
3. You do not see a corresponding  "References" or "Works 

Re: Author-year in Lyx

[Stefano Franchi]

Hi Kamarul,

in order to use author-year you need to use natbib. If you use bibtex as
your reference processor, all you need to do is to put
\usepackage{natbib} in your preamble (DocumentSettingsPreamble) and
choose Natbib in DocumentSettingsBibliography. When you insert your
bibliography file (InsertList/TOCBibTeX Bibliography), you should
choose plainnat as a style. This gives you the basic setting. Many more
things are possible, including changing the style and so on. See the lyx
wiki page on bibliography for a first description of the package  [1].
There is also documentation for natbib in your latex installation (search
for the file natbib.pdf on your computer or type texdoc natbib at a
terminal). I enclosed a minimal  example as a working LyX file (with a
minimal bib file).

The above assumes you are using bibtex. If, instead, you are using biblatex
(like me), you should proceed differently. Write again and I'll explain how
(it is very easy).

Also, please write to the whole lyx users list---your chances to get help
will increase substantially

Cheers,

Stefano


[1] http://wiki.lyx.org/BibTeX/Background#natbib


On Thu, Jan 9, 2014 at 12:26 AM, Kamarul Imran kim4...@gmail.com wrote:

 Dear Prof Franchi,

 I stumbled a post by you on setting the author-year citation in Lyx. I
 have problems in writing the citation using author-year style in Lyx. I
 have tried a few links and the suggested workaround on Lyx website, but
 nothing works.

 I guess the problems lie in the 'Document setting' and 'Tools' in Lyx. I
 am using Lyx 2.0.6 on Windows 8. My citation does not show properly and no
 bibliography generated, even though the bib files were correctly
 set/linked.

 Would you mind, list the correct (your working) setting in Lyx so that I
 might be able to test it on my laptop.

 Thanks very much.

 Best wishes,

 Kamarul Imran Musa
 Malaysia




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org


testing-natbib.lyx
Description: application/lyx
@article{808387,
 author = {John McCarthy},
 title = {History of LISP},
 journal = {SIGPLAN Not.},
 volume = {13},
 number = {8},
 year = {1978},
 issn = {0362-1340},
 pages = {217--223},
 doi = {http://doi.acm.org/10.1145/960118.808387},
 publisher = {ACM Press},
 address = {New York, NY, USA},
 }

Re: Author-year in Lyx

[Stefano Franchi]

Hi Kamarul,

in order to use author-year you need to use natbib. If you use bibtex as
your reference processor, all you need to do is to put
\usepackage{natbib} in your preamble (DocumentSettingsPreamble) and
choose Natbib in DocumentSettingsBibliography. When you insert your
bibliography file (InsertList/TOCBibTeX Bibliography), you should
choose plainnat as a style. This gives you the basic setting. Many more
things are possible, including changing the style and so on. See the lyx
wiki page on bibliography for a first description of the package  [1].
There is also documentation for natbib in your latex installation (search
for the file natbib.pdf on your computer or type texdoc natbib at a
terminal). I enclosed a minimal  example as a working LyX file (with a
minimal bib file).

The above assumes you are using bibtex. If, instead, you are using biblatex
(like me), you should proceed differently. Write again and I'll explain how
(it is very easy).

Also, please write to the whole lyx users list---your chances to get help
will increase substantially

Cheers,

Stefano


[1] http://wiki.lyx.org/BibTeX/Background#natbib


On Thu, Jan 9, 2014 at 12:26 AM, Kamarul Imran kim4...@gmail.com wrote:

 Dear Prof Franchi,

 I stumbled a post by you on setting the author-year citation in Lyx. I
 have problems in writing the citation using author-year style in Lyx. I
 have tried a few links and the suggested workaround on Lyx website, but
 nothing works.

 I guess the problems lie in the 'Document setting' and 'Tools' in Lyx. I
 am using Lyx 2.0.6 on Windows 8. My citation does not show properly and no
 bibliography generated, even though the bib files were correctly
 set/linked.

 Would you mind, list the correct (your working) setting in Lyx so that I
 might be able to test it on my laptop.

 Thanks very much.

 Best wishes,

 Kamarul Imran Musa
 Malaysia




-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas AM University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org


testing-natbib.lyx
Description: application/lyx
@article{808387,
 author = {John McCarthy},
 title = {History of LISP},
 journal = {SIGPLAN Not.},
 volume = {13},
 number = {8},
 year = {1978},
 issn = {0362-1340},
 pages = {217--223},
 doi = {http://doi.acm.org/10.1145/960118.808387},
 publisher = {ACM Press},
 address = {New York, NY, USA},
 }

Re: Author-year in Lyx

[Stefano Franchi]

Hi Kamarul,

in order to use author-year you need to use natbib. If you use bibtex as
your reference processor, all you need to do is to put
"\usepackage{natbib}" in your preamble (Document>>Settings>>Preamble) and
choose Natbib in Document>>Settings>>Bibliography. When you insert your
bibliography file (Insert>>List/TOC>>BibTeX Bibliography), you should
choose "plainnat" as a style. This gives you the basic setting. Many more
things are possible, including changing the style and so on. See the lyx
wiki page on bibliography for a first description of the package  [1].
There is also documentation for natbib in your latex installation (search
for the file natbib.pdf on your computer or type "texdoc natbib" at a
terminal). I enclosed a minimal  example as a working LyX file (with a
minimal bib file).

The above assumes you are using bibtex. If, instead, you are using biblatex
(like me), you should proceed differently. Write again and I'll explain how
(it is very easy).

Also, please write to the whole lyx users list---your chances to get help
will increase substantially

Cheers,

Stefano


[1] http://wiki.lyx.org/BibTeX/Background#natbib


On Thu, Jan 9, 2014 at 12:26 AM, Kamarul Imran  wrote:

> Dear Prof Franchi,
>
> I stumbled a post by you on setting the author-year citation in Lyx. I
> have problems in writing the citation using author-year style in Lyx. I
> have tried a few links and the suggested workaround on Lyx website, but
> nothing works.
>
> I guess the problems lie in the 'Document setting' and 'Tools' in Lyx. I
> am using Lyx 2.0.6 on Windows 8. My citation does not show properly and no
> bibliography generated, even though the bib files were correctly
> set/linked.
>
> Would you mind, list the correct (your working) setting in Lyx so that I
> might be able to test it on my laptop.
>
> Thanks very much.
>
> Best wishes,
>
> Kamarul Imran Musa
> Malaysia
>



-- 
__
Stefano Franchi
Associate Research Professor
Department of Hispanic StudiesPh:   +1 (979) 845-2125
Texas A University  Fax:  +1 (979) 845-6421
College Station, Texas, USA

stef...@tamu.edu
http://stefano.cleinias.org


testing-natbib.lyx
Description: application/lyx
@article{808387,
 author = {John McCarthy},
 title = {History of LISP},
 journal = {SIGPLAN Not.},
 volume = {13},
 number = {8},
 year = {1978},
 issn = {0362-1340},
 pages = {217--223},
 doi = {http://doi.acm.org/10.1145/960118.808387},
 publisher = {ACM Press},
 address = {New York, NY, USA},
 }

Re: author-year citation lyx with bibtex

[Paul A. Rubin]

[posted and mailed]

Tobias Kraus [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]: 

 Hi!
 I want a certain citation style like this:
 
 In the text there must be: textextext (Author, Year)
 In the reference at the end there should be: [Number] Author, Year,
 Chapter ..
 
 
 I am using bibtex and lyx 1.2.1 and in Layout/Document I can only
 chose between Author/Year or numeric citation concerning both, text
 and reference. 
 
 
 Thanks
 
 Tobi
 
 

Check out natbib.

-- Paul

*
Paul A. Rubin  Phone:(517) 432-3509
Department of Management   Fax:  (517) 432-
The Eli Broad Graduate School of ManagementE-mail:   [EMAIL PROTECTED]
Michigan State University  http://www.msu.edu/~rubin/
East Lansing, MI  48824-1122  (USA)
*
Mathematicians are like Frenchmen:  whenever you say something to them,
they translate it into their own language, and at once it is something
entirely different.J. W. v. GOETHE

Re: author-year citation lyx with bibtex

[Paul A. Rubin]

[posted and mailed]

Tobias Kraus [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]: 

 Hi!
 I want a certain citation style like this:
 
 In the text there must be: textextext (Author, Year)
 In the reference at the end there should be: [Number] Author, Year,
 Chapter ..
 
 
 I am using bibtex and lyx 1.2.1 and in Layout/Document I can only
 chose between Author/Year or numeric citation concerning both, text
 and reference. 
 
 
 Thanks
 
 Tobi
 
 

Check out natbib.

-- Paul

*
Paul A. Rubin  Phone:(517) 432-3509
Department of Management   Fax:  (517) 432-
The Eli Broad Graduate School of ManagementE-mail:   [EMAIL PROTECTED]
Michigan State University  http://www.msu.edu/~rubin/
East Lansing, MI  48824-1122  (USA)
*
Mathematicians are like Frenchmen:  whenever you say something to them,
they translate it into their own language, and at once it is something
entirely different.J. W. v. GOETHE

Re: author-year citation lyx with bibtex

[Paul A. Rubin]

[posted and mailed]

Tobias Kraus <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]: 

> Hi!
> I want a certain citation style like this:
> 
> In the text there must be: textextext (Author, Year)
> In the reference at the end there should be: [Number] Author, Year,
> Chapter ..
> 
> 
> I am using bibtex and lyx 1.2.1 and in Layout/Document I can only
> chose between Author/Year or numeric citation concerning both, text
> and reference. 
> 
> 
> Thanks
> 
> Tobi
> 
> 

Check out natbib.

-- Paul

*
Paul A. Rubin  Phone:(517) 432-3509
Department of Management   Fax:  (517) 432-
The Eli Broad Graduate School of ManagementE-mail:   [EMAIL PROTECTED]
Michigan State University  http://www.msu.edu/~rubin/
East Lansing, MI  48824-1122  (USA)
*
Mathematicians are like Frenchmen:  whenever you say something to them,
they translate it into their own language, and at once it is something
entirely different.J. W. v. GOETHE