Re: Biber Biblatex Lyx Jabref > solved

2019-04-05 Thread Wolfgang Engelmann 



On 04.04.19 15:10, Wolfgang Engelmann wrote:


On 04.04.19 15:03, Axel Dessecker wrote:

Am Donnerstag, 4. April 2019, 14:41:08 CEST schrieb Wolfgang Engelmann:

On 04.04.19 12:44, Jürgen Spitzmüller wrote:

Am Do., 4. Apr. 2019 um 10:27 Uhr schrieb Wolfgang Engelmann

mailto:engelm...@uni-tuebingen.de>>:
 On 03.04.19 16:30, Jürgen Spitzmüller wrote:
 > As with BibTeX, the encoding should ideally match the encoding
  of he
  > document. If it differs, you can add bibencoding=utf8 
to Document >

 > Settings > Bibliography > Citation Style > Options
  Thanks, Jürgen. Could you or somebody else kindly try 
this one, to

 see
 whether the Umlaute are ok?
   @Article{Buenning1935,
    author  = {Bünning, E.},
    title   = {Zur {K}enntnis der erblichen {T}agesperiodizität 
bei

 den
 {P}rimärblättern von \emph{{P}haseolus multiflorus}},
    journal = {Jb. wiss. Bot.},
    year    = {1935},
    volume  = {81},
    pages   = {411--418},
 }

We need a real minimal example file (lyx file and bib) in order to
help you.

Jürgen

In preparing a minimal example I created a new minimal lyx file and a
new bib file with just one entrance (the one above) and, voila, the
problem with the Umlaute was gone. If I use the old bib file (with many
literature references) this one item does not show the Umlaute, 
although

only this item is required.

Conclusion: The problem is with the (jabref) bib file and is not a lyx
question.

But I am not sure how to proceed. If I copy my references from the old
bib file in the new one, the umlaute problem comes back, even with the
one which were correct before (I had copy/pasted them separately in the
new bib file). Perhaps someone of the Jabref users might have an idea?

Thanks for all the help

Wolfgang


Are you sure about the correct formatting of your older entries 
containing

umlauts? Have you recoded the .bib file to UTF-8?

Axel


Yes, I did.

Just found out, that apparently the new Jabref 4.3.1 needs 
Java-8-openjdk, not Java-9-openjdk, or alternatively openjfx.


Will try, and thanks

Wolfgang

installing openjdk-8-jdk and reinstalling jabref 2.10 solved my problem. 
I appreciated the help I received.


Wolfgang

Re: Biber Biblatex Lyx Jabref

2019-04-04 Thread Wolfgang Engelmann 



On 04.04.19 15:03, Axel Dessecker wrote:

Am Donnerstag, 4. April 2019, 14:41:08 CEST schrieb Wolfgang Engelmann:

On 04.04.19 12:44, Jürgen Spitzmüller wrote:

Am Do., 4. Apr. 2019 um 10:27 Uhr schrieb Wolfgang Engelmann

mailto:engelm...@uni-tuebingen.de>>:
 On 03.04.19 16:30, Jürgen Spitzmüller wrote:
 > As with BibTeX, the encoding should ideally match the encoding
 
 of he
 
 > document. If it differs, you can add bibencoding=utf8 to Document >

 > Settings > Bibliography > Citation Style > Options
 
 Thanks, Jürgen. Could you or somebody else kindly try this one, to

 see
 whether the Umlaute are ok?
 
 
 @Article{Buenning1935,

author  = {Bünning, E.},
title   = {Zur {K}enntnis der erblichen {T}agesperiodizität bei
 den
 {P}rimärblättern von \emph{{P}haseolus multiflorus}},
journal = {Jb. wiss. Bot.},
year= {1935},
volume  = {81},
pages   = {411--418},
 }

We need a real minimal example file (lyx file and bib) in order to
help you.

Jürgen

In preparing a minimal example I created a new minimal lyx file and a
new bib file with just one entrance (the one above) and, voila, the
problem with the Umlaute was gone. If I use the old bib file (with many
literature references) this one item does not show the Umlaute, although
only this item is required.

Conclusion: The problem is with the (jabref) bib file and is not a lyx
question.

But I am not sure how to proceed. If I copy my references from the old
bib file in the new one, the umlaute problem comes back, even with the
one which were correct before (I had copy/pasted them separately in the
new bib file). Perhaps someone of the Jabref users might have an idea?

Thanks for all the help

Wolfgang


Are you sure about the correct formatting of your older entries containing
umlauts? Have you recoded the .bib file to UTF-8?

Axel


Yes, I did.

Just found out, that apparently the new Jabref 4.3.1 needs 
Java-8-openjdk, not Java-9-openjdk, or alternatively openjfx.


Will try, and thanks

Wolfgang

Re: Biber Biblatex Lyx Jabref

2019-04-04 Thread Axel Dessecker 
Am Donnerstag, 4. April 2019, 14:41:08 CEST schrieb Wolfgang Engelmann:
> On 04.04.19 12:44, Jürgen Spitzmüller wrote:
> > Am Do., 4. Apr. 2019 um 10:27 Uhr schrieb Wolfgang Engelmann
> > 
> > mailto:engelm...@uni-tuebingen.de>>:
> > On 03.04.19 16:30, Jürgen Spitzmüller wrote:
> > > As with BibTeX, the encoding should ideally match the encoding
> > 
> > of he
> > 
> > > document. If it differs, you can add bibencoding=utf8 to Document >
> > > Settings > Bibliography > Citation Style > Options
> > 
> > Thanks, Jürgen. Could you or somebody else kindly try this one, to
> > see
> > whether the Umlaute are ok?
> > 
> > 
> > @Article{Buenning1935,
> >author  = {Bünning, E.},
> >title   = {Zur {K}enntnis der erblichen {T}agesperiodizität bei
> > den
> > {P}rimärblättern von \emph{{P}haseolus multiflorus}},
> >journal = {Jb. wiss. Bot.},
> >year= {1935},
> >volume  = {81},
> >pages   = {411--418},
> > }
> > 
> > We need a real minimal example file (lyx file and bib) in order to
> > help you.
> > 
> > Jürgen
> 
> In preparing a minimal example I created a new minimal lyx file and a
> new bib file with just one entrance (the one above) and, voila, the
> problem with the Umlaute was gone. If I use the old bib file (with many
> literature references) this one item does not show the Umlaute, although
> only this item is required.
> 
> Conclusion: The problem is with the (jabref) bib file and is not a lyx
> question.
> 
> But I am not sure how to proceed. If I copy my references from the old
> bib file in the new one, the umlaute problem comes back, even with the
> one which were correct before (I had copy/pasted them separately in the
> new bib file). Perhaps someone of the Jabref users might have an idea?
> 
> Thanks for all the help
> 
> Wolfgang


Are you sure about the correct formatting of your older entries containing 
umlauts? Have you recoded the .bib file to UTF-8?

Axel



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Description: This is a digitally signed message part.

Re: Biber Biblatex Lyx Jabref

2019-04-04 Thread Wolfgang Engelmann 


On 04.04.19 12:44, Jürgen Spitzmüller wrote:
Am Do., 4. Apr. 2019 um 10:27 Uhr schrieb Wolfgang Engelmann 
mailto:engelm...@uni-tuebingen.de>>:



On 03.04.19 16:30, Jürgen Spitzmüller wrote:
> As with BibTeX, the encoding should ideally match the encoding
of he
> document. If it differs, you can add bibencoding=utf8 to Document >
> Settings > Bibliography > Citation Style > Options

Thanks, Jürgen. Could you or somebody else kindly try this one, to
see
whether the Umlaute are ok?


@Article{Buenning1935,
   author  = {Bünning, E.},
   title   = {Zur {K}enntnis der erblichen {T}agesperiodizität bei
den
{P}rimärblättern von \emph{{P}haseolus multiflorus}},
   journal = {Jb. wiss. Bot.},
   year    = {1935},
   volume  = {81},
   pages   = {411--418},
}


We need a real minimal example file (lyx file and bib) in order to 
help you.


Jürgen


In preparing a minimal example I created a new minimal lyx file and a 
new bib file with just one entrance (the one above) and, voila, the 
problem with the Umlaute was gone. If I use the old bib file (with many 
literature references) this one item does not show the Umlaute, although 
only this item is required.


Conclusion: The problem is with the (jabref) bib file and is not a lyx 
question.


But I am not sure how to proceed. If I copy my references from the old 
bib file in the new one, the umlaute problem comes back, even with the 
one which were correct before (I had copy/pasted them separately in the 
new bib file). Perhaps someone of the Jabref users might have an idea?


Thanks for all the help

Wolfgang

Re: Biber Biblatex Lyx Jabref

2019-04-04 Thread Jürgen Spitzmüller 
Am Do., 4. Apr. 2019 um 10:27 Uhr schrieb Wolfgang Engelmann <
engelm...@uni-tuebingen.de>:

>
> On 03.04.19 16:30, Jürgen Spitzmüller wrote:
> > As with BibTeX, the encoding should ideally match the encoding of he
> > document. If it differs, you can add bibencoding=utf8 to Document >
> > Settings > Bibliography > Citation Style > Options
>
> Thanks, Jürgen. Could you or somebody else kindly try this one, to see
> whether the Umlaute are ok?
>
>
> @Article{Buenning1935,
>author  = {Bünning, E.},
>title   = {Zur {K}enntnis der erblichen {T}agesperiodizität bei den
> {P}rimärblättern von \emph{{P}haseolus multiflorus}},
>journal = {Jb. wiss. Bot.},
>year= {1935},
>volume  = {81},
>pages   = {411--418},
> }
>

We need a real minimal example file (lyx file and bib) in order to help you.

Jürgen

Re: Biber Biblatex Lyx Jabref

2019-04-04 Thread Wolfgang Engelmann 


On 04.04.19 10:27, Wolfgang Engelmann wrote:


On 03.04.19 16:30, Jürgen Spitzmüller wrote:
As with BibTeX, the encoding should ideally match the encoding of he 
document. If it differs, you can add bibencoding=utf8 to Document > 
Settings > Bibliography > Citation Style > Options


Thanks, Jürgen. Could you or somebody else kindly try this one, to see 
whether the Umlaute are ok?



@Article{Buenning1935,
  author  = {Bünning, E.},
  title   = {Zur {K}enntnis der erblichen {T}agesperiodizität bei den 
{P}rimärblättern von \emph{{P}haseolus multiflorus}},

  journal = {Jb. wiss. Bot.},
  year    = {1935},
  volume  = {81},
  pages   = {411--418},
}

I do not get them even after using your proposal (Bookstyle Komascript 
English)


Wolfgang



ps: I also did this before in the bib file

https://tex.stackexchange.com/questions/81716/umlauts-in-a-jabref-managed-bibtex-file-and-file-encoding

#
That's right. If your bib-File is rather old, check in Jabref 
(Preferences->General->Encoding) that you use UTF8 and convert the file 
via |iconv -f ISO-8859-1 -t UTF-8 jabref_old.bib > jabref_new.bib|. It 
seems (tex.stackexchange.com/questions/97252/… 
) 
that |\usepackage[utf8]{inputenc}| is still needed, too. – mpy 
 Mar 2 '13 at 15:05 
 


#
Thanks for the answer. I'll try this next week and let you know whether 
it works fine. @mpy Thank you too for your comment. I never came across 
|iconv| so far. – halirutan 
 Mar 2 '13 at 19:59 
 


#
3
But bibtex does not handle some utf8 characters (umlauts) from bib 
files. It will look fine in JabRef but will give errors when compiling. 
Switching to biblatex/biber solves the issue. – remus 
 Apr 24 '13 at 19:41 



however, I tried this one in the preamplewhich was refused by Lyx since 
utf8 was already defined:


|\usepackage[utf8]{inputenc}
|

|do I need to include inputenc and where would I do that?|

|Wolfgang
|

Re: Biber Biblatex Lyx Jabref

2019-04-04 Thread Wolfgang Engelmann 



On 03.04.19 16:30, Jürgen Spitzmüller wrote:
As with BibTeX, the encoding should ideally match the encoding of he 
document. If it differs, you can add bibencoding=utf8 to Document > 
Settings > Bibliography > Citation Style > Options


Thanks, Jürgen. Could you or somebody else kindly try this one, to see 
whether the Umlaute are ok?



@Article{Buenning1935,
  author  = {Bünning, E.},
  title   = {Zur {K}enntnis der erblichen {T}agesperiodizität bei den 
{P}rimärblättern von \emph{{P}haseolus multiflorus}},

  journal = {Jb. wiss. Bot.},
  year    = {1935},
  volume  = {81},
  pages   = {411--418},
}

I do not get them even after using your proposal (Bookstyle Komascript 
English)


Wolfgang

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Jürgen Spitzmüller 
Am Mi., 3. Apr. 2019 um 16:20 Uhr schrieb Wolfgang Engelmann <
engelm...@uni-tuebingen.de>:

> Is standard coding UTF8 ok?
>

As with BibTeX, the encoding should ideally match the encoding of he
document. If it differs, you can add bibencoding=utf8 to Document >
Settings > Bibliography > Citation Style > Options

Jürgen

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Wolfgang Engelmann 



On 03.04.19 15:53, Axel Dessecker wrote:

Wolfgang,

Am Mittwoch, 3. April 2019, 15:47:58 CEST schrieb Jürgen Spitzmüller:

Am Mi., 3. Apr. 2019 um 15:36 Uhr schrieb Wolfgang Engelmann <

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

I read this and made the settings, but can't find under
tools>preferences>output>latex the setting for biber.

It should be listed in Bibliography Generation > Processor (given biber is
correctly installed).
But you shouldn't need to set it explicitly. Biber is used if "Automatic"
is set.


What about jabref? special settings for biblatex?

I don't use jabref.

Jürgen

You can select a biblatex mode in JabRef.

Axel


Thanks, Axel, yes. I had selected it already under 
>options>preferences>standard bibliography mode


Is standard coding UTF8 ok?

Wolfgang

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Wolfgang Engelmann 


On 03.04.19 15:47, Jürgen Spitzmüller wrote:
Am Mi., 3. Apr. 2019 um 15:36 Uhr schrieb Wolfgang Engelmann 
mailto:engelm...@uni-tuebingen.de>>:


I read this and made the settings, but can't find under
tools>preferences>output>latex the setting for biber.


It should be listed in Bibliography Generation > Processor (given 
biber is correctly installed).
But you shouldn't need to set it explicitly. Biber is used if 
"Automatic" is set.


I did not have biber installed. Will try now.

Thanks a lot, Jürgen

Wolfgang


What about jabref? special settings for biblatex?

I don't use jabref.

Jürgen

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Axel Dessecker 
Wolfgang,

Am Mittwoch, 3. April 2019, 15:47:58 CEST schrieb Jürgen Spitzmüller:
> Am Mi., 3. Apr. 2019 um 15:36 Uhr schrieb Wolfgang Engelmann <
> 
> engelm...@uni-tuebingen.de>:
> > I read this and made the settings, but can't find under
> > tools>preferences>output>latex the setting for biber.
> 
> It should be listed in Bibliography Generation > Processor (given biber is
> correctly installed).
> But you shouldn't need to set it explicitly. Biber is used if "Automatic"
> is set.
> 
> > What about jabref? special settings for biblatex?
> 
> I don't use jabref.
> 
> Jürgen

You can select a biblatex mode in JabRef.

Axel

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Jürgen Spitzmüller 
Am Mi., 3. Apr. 2019 um 15:36 Uhr schrieb Wolfgang Engelmann <
engelm...@uni-tuebingen.de>:

> I read this and made the settings, but can't find under
> tools>preferences>output>latex the setting for biber.
>

It should be listed in Bibliography Generation > Processor (given biber is
correctly installed).
But you shouldn't need to set it explicitly. Biber is used if "Automatic"
is set.

> What about jabref? special settings for biblatex?
>
I don't use jabref.

Jürgen

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Wolfgang Engelmann 


On 03.04.19 15:15, Jürgen Spitzmüller wrote:
Am Mi., 3. Apr. 2019 um 15:07 Uhr schrieb Wolfgang Engelmann 
mailto:engelm...@uni-tuebingen.de>>:


Where can I get infos re Biber Biblatex Jabref Lyx?


UserGuide, 6.5.2.2.


I read this and made the settings, but can't find under 
tools>preferences>output>latex the setting for biber.


What about jabref? special settings for biblatex?

Wolfgang



and

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

Jürgen

Re: Biber Biblatex Lyx Jabref

2019-04-03 Thread Jürgen Spitzmüller 
Am Mi., 3. Apr. 2019 um 15:07 Uhr schrieb Wolfgang Engelmann <
engelm...@uni-tuebingen.de>:

> Where can I get infos re Biber Biblatex Jabref Lyx?
>

UserGuide, 6.5.2.2.

and

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

Jürgen

Re: Biber and biblatex issue on lyx

2016-10-17 Thread Riccardo 
Perfect. Thanks.
Riccardo

2016-10-17 12:06 GMT+02:00 Charles de Miramon :

> Riccardo wrote:
>
> > Hello,
> > I have the following configuration:
> >
> >
> >- texlive-full (including texlive-bibtex-extra) from unofficial
> >ppa:jonathonf/texlive-2016
> >- biber 2.5
> >- Lyx 2.2.1 from ppa:lyx-devel/release
> >
> >
> > After the last update, LyX show me a compatibility error message.
> >
> > [761] Utils.pm:165> ERROR - Error: Found biblatex control file version
> > [3.2,
> > expected version 3.1.
> >
> > But:
> >
> >- biber version is 2.5 (system-wide, and no other versions present
> >anywhere)
> >- documentations suggest biblatex 3.4. The .bcf file in the folder has
> >the following header:
> >
> > 
> > https://sourceforge.net/projects/biblatex;>
> >
> > Can you help me fix this? The bibliography of my document results now in
> > an empty page. I'm asking here since my system appears to have the
> correct
> > packages. For completeness, I "Reconfigured" lyx just after the package
> > update.
> > Riccardo
>
> You need to install biber 2.6 which is not yet packaged as far as I know
> for
> ubuntu.
>
> 1) uninstall biber 2.5
> 2) download https://sourceforge.net/projects/biblatex-biber/files/
> biblatex-biber/current/binaries/Linux/
> 3) extract it and install it as root in /usr/local/bin
>
>

Re: Biber and biblatex issue on lyx

2016-10-17 Thread Charles de Miramon 
Riccardo wrote:

> Hello,
> I have the following configuration:
> 
> 
>- texlive-full (including texlive-bibtex-extra) from unofficial
>ppa:jonathonf/texlive-2016
>- biber 2.5
>- Lyx 2.2.1 from ppa:lyx-devel/release
> 
> 
> After the last update, LyX show me a compatibility error message.
> 
> [761] Utils.pm:165> ERROR - Error: Found biblatex control file version
> [3.2,
> expected version 3.1.
> 
> But:
> 
>- biber version is 2.5 (system-wide, and no other versions present
>anywhere)
>- documentations suggest biblatex 3.4. The .bcf file in the folder has
>the following header:
> 
> 
> https://sourceforge.net/projects/biblatex;>
> 
> Can you help me fix this? The bibliography of my document results now in
> an empty page. I'm asking here since my system appears to have the correct
> packages. For completeness, I "Reconfigured" lyx just after the package
> update.
> Riccardo

You need to install biber 2.6 which is not yet packaged as far as I know for 
ubuntu.

1) uninstall biber 2.5
2) download 
https://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/current/binaries/Linux/
3) extract it and install it as root in /usr/local/bin

Re: biber

2016-05-12 Thread Wolfgang Engelmann 

Thanks for your advice, Påvel
Wolfgang

On 11.05.2016 21:56, Påvel Nicklasson wrote:

I think it would be better to put it in /usr/local/bin.
Restart and it will work.

2016-05-11 10:50 GMT+02:00 Wolfgang Engelmann 
>:




On 11.05.2016 10:46, Wolfgang Engelmann wrote:

I downloaded the latest biber-linux_x86_64.tar.gz from
SourceForge and extracted it in my /home/Downloads/
Can it remain there or where should it better be? Is a texhash
sufficient to make it available to lyx?
Wolfgang

The old biber is at
which biber
/usr/bin/biber
Could I just replace it with the ne one?
Wolfgang

Re: biber

2016-05-11 Thread Påvel Nicklasson 
I think it would be better to put it in /usr/local/bin.
Restart and it will work.

2016-05-11 10:50 GMT+02:00 Wolfgang Engelmann :

>
>
> On 11.05.2016 10:46, Wolfgang Engelmann wrote:
>
>> I downloaded the latest biber-linux_x86_64.tar.gz from SourceForge and
>> extracted it in my /home/Downloads/
>> Can it remain there or where should it better be? Is a texhash sufficient
>> to make it available to lyx?
>> Wolfgang
>>
> The old biber is at
> which biber
> /usr/bin/biber
> Could I just replace it with the ne one?
> Wolfgang
>

Re: biber

2016-05-11 Thread Påvel Nicklasson 
Of course you must also make biber executable.

2016-05-11 21:56 GMT+02:00 Påvel Nicklasson :

> I think it would be better to put it in /usr/local/bin.
> Restart and it will work.
>
> 2016-05-11 10:50 GMT+02:00 Wolfgang Engelmann 
> :
>
>>
>>
>> On 11.05.2016 10:46, Wolfgang Engelmann wrote:
>>
>>> I downloaded the latest biber-linux_x86_64.tar.gz from SourceForge and
>>> extracted it in my /home/Downloads/
>>> Can it remain there or where should it better be? Is a texhash
>>> sufficient to make it available to lyx?
>>> Wolfgang
>>>
>> The old biber is at
>> which biber
>> /usr/bin/biber
>> Could I just replace it with the ne one?
>> Wolfgang
>>
>
>

Re: biber

2016-05-11 Thread Wolfgang Engelmann 



On 11.05.2016 10:46, Wolfgang Engelmann wrote:
I downloaded the latest biber-linux_x86_64.tar.gz from SourceForge and 
extracted it in my /home/Downloads/
Can it remain there or where should it better be? Is a texhash 
sufficient to make it available to lyx?

Wolfgang

The old biber is at
which biber
/usr/bin/biber
Could I just replace it with the ne one?
Wolfgang

Re: Biber produces errors where bibtex8 does not

2014-06-22 Thread Jürgen Spitzmüller 
2014-06-21 16:29 GMT+02:00 Benedict Holland:

 Which begs the question why are they not automatically escaped? I have a
 bibliography of over 70 references. Getting an item error because there is
 a problem in my references which has an easy workaround but hours of work
 tracing it to the source is bad.

Well, this is a task of the bibliography manager, not LyX.


 Can lyx or biber do preprocessing to fix these bugs?


biber probably can.

Jürgen


 Thanks,
 ~Ben

Re: Biber produces errors where bibtex8 does not

2014-06-22 Thread Jürgen Spitzmüller 
2014-06-21 16:29 GMT+02:00 Benedict Holland:

 Which begs the question why are they not automatically escaped? I have a
 bibliography of over 70 references. Getting an item error because there is
 a problem in my references which has an easy workaround but hours of work
 tracing it to the source is bad.

Well, this is a task of the bibliography manager, not LyX.


 Can lyx or biber do preprocessing to fix these bugs?


biber probably can.

Jürgen


 Thanks,
 ~Ben

Re: Biber produces errors where bibtex8 does not

2014-06-22 Thread Jürgen Spitzmüller 
2014-06-21 16:29 GMT+02:00 Benedict Holland:

> Which begs the question why are they not automatically escaped? I have a
> bibliography of over 70 references. Getting an item error because there is
> a problem in my references which has an easy workaround but hours of work
> tracing it to the source is bad.
>
Well, this is a task of the bibliography manager, not LyX.


> Can lyx or biber do preprocessing to fix these bugs?
>

biber probably can.

Jürgen


> Thanks,
> ~Ben
>

Re: Biber produces errors where bibtex8 does not

2014-06-21 Thread Jürgen Spitzmüller 
2014-06-20 23:47 GMT+02:00 Benedict Holland:

 So it appears that the reason is that biber does not escape the abstract
 of a reference, even if it doesn't at all display that abstract.
 Specifically this is occurring if a percentage sign is within the abstract.
 Apparently all percentage signs must be escaped? Is this a bug with lyx or
 with biber?



Actually, I wonder why bibtex8 does not choke on this. These kind of
characters need to be escaped in general.

Jürgen

Re: Biber produces errors where bibtex8 does not

2014-06-21 Thread Benedict Holland 
Which begs the question why are they not automatically escaped? I have a
bibliography of over 70 references. Getting an item error because there is
a problem in my references which has an easy workaround but hours of work
tracing it to the source is bad. Can lyx or biber do preprocessing to fix
these bugs?

Thanks,
~Ben
On Jun 21, 2014 3:53 AM, Jürgen Spitzmüller sp...@lyx.org wrote:

 2014-06-20 23:47 GMT+02:00 Benedict Holland:

 So it appears that the reason is that biber does not escape the abstract
 of a reference, even if it doesn't at all display that abstract.
 Specifically this is occurring if a percentage sign is within the abstract.
 Apparently all percentage signs must be escaped? Is this a bug with lyx or
 with biber?



 Actually, I wonder why bibtex8 does not choke on this. These kind of
 characters need to be escaped in general.

 Jürgen

Re: Biber produces errors where bibtex8 does not

2014-06-21 Thread Jürgen Spitzmüller 
2014-06-20 23:47 GMT+02:00 Benedict Holland:

 So it appears that the reason is that biber does not escape the abstract
 of a reference, even if it doesn't at all display that abstract.
 Specifically this is occurring if a percentage sign is within the abstract.
 Apparently all percentage signs must be escaped? Is this a bug with lyx or
 with biber?



Actually, I wonder why bibtex8 does not choke on this. These kind of
characters need to be escaped in general.

Jürgen

Re: Biber produces errors where bibtex8 does not

2014-06-21 Thread Benedict Holland 
Which begs the question why are they not automatically escaped? I have a
bibliography of over 70 references. Getting an item error because there is
a problem in my references which has an easy workaround but hours of work
tracing it to the source is bad. Can lyx or biber do preprocessing to fix
these bugs?

Thanks,
~Ben
On Jun 21, 2014 3:53 AM, Jürgen Spitzmüller sp...@lyx.org wrote:

 2014-06-20 23:47 GMT+02:00 Benedict Holland:

 So it appears that the reason is that biber does not escape the abstract
 of a reference, even if it doesn't at all display that abstract.
 Specifically this is occurring if a percentage sign is within the abstract.
 Apparently all percentage signs must be escaped? Is this a bug with lyx or
 with biber?



 Actually, I wonder why bibtex8 does not choke on this. These kind of
 characters need to be escaped in general.

 Jürgen

Re: Biber produces errors where bibtex8 does not

2014-06-21 Thread Jürgen Spitzmüller 
2014-06-20 23:47 GMT+02:00 Benedict Holland:

> So it appears that the reason is that biber does not escape the abstract
> of a reference, even if it doesn't at all display that abstract.
> Specifically this is occurring if a percentage sign is within the abstract.
> Apparently all percentage signs must be escaped? Is this a bug with lyx or
> with biber?
>


Actually, I wonder why bibtex8 does not choke on this. These kind of
characters need to be escaped in general.

Jürgen

Re: Biber produces errors where bibtex8 does not

2014-06-21 Thread Benedict Holland 
Which begs the question why are they not automatically escaped? I have a
bibliography of over 70 references. Getting an item error because there is
a problem in my references which has an easy workaround but hours of work
tracing it to the source is bad. Can lyx or biber do preprocessing to fix
these bugs?

Thanks,
~Ben
On Jun 21, 2014 3:53 AM, "Jürgen Spitzmüller"  wrote:

> 2014-06-20 23:47 GMT+02:00 Benedict Holland:
>
>> So it appears that the reason is that biber does not escape the abstract
>> of a reference, even if it doesn't at all display that abstract.
>> Specifically this is occurring if a percentage sign is within the abstract.
>> Apparently all percentage signs must be escaped? Is this a bug with lyx or
>> with biber?
>>
>
>
> Actually, I wonder why bibtex8 does not choke on this. These kind of
> characters need to be escaped in general.
>
> Jürgen
>
>

Re: Biber produces errors where bibtex8 does not

2014-06-20 Thread Benedict Holland 
So it appears that the reason is that biber does not escape the abstract of
a reference, even if it doesn't at all display that abstract. Specifically
this is occurring if a percentage sign is within the abstract. Apparently
all percentage signs must be escaped? Is this a bug with lyx or with biber?

~Ben


On Fri, Jun 20, 2014 at 5:21 PM, Benedict Holland 
benedict.m.holl...@gmail.com wrote:

 Hello,

 I tried using biber and biblatex following the instructions here:

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

 I received some very strange errors like Lonely \item - perhaps a missing
 list environment when some of my references were included. It was actually
 2/35 which were throwing the error except the error wasn't anywhere near
 those references. Even so, there was nothing wrong with the references and
 they worked perfectly well when generated using bibtex8. I examined the two
 references which caused problems and they were exactly the same as any
 other reference. Again, they work in bibtex8 but not biber.

 Does anyone know what could cause this error? When these two references
 are removed the document compiles but I need these references.

 ~Ben

Re: Biber produces errors where bibtex8 does not

2014-06-20 Thread Benedict Holland 
So it appears that the reason is that biber does not escape the abstract of
a reference, even if it doesn't at all display that abstract. Specifically
this is occurring if a percentage sign is within the abstract. Apparently
all percentage signs must be escaped? Is this a bug with lyx or with biber?

~Ben


On Fri, Jun 20, 2014 at 5:21 PM, Benedict Holland 
benedict.m.holl...@gmail.com wrote:

 Hello,

 I tried using biber and biblatex following the instructions here:

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

 I received some very strange errors like Lonely \item - perhaps a missing
 list environment when some of my references were included. It was actually
 2/35 which were throwing the error except the error wasn't anywhere near
 those references. Even so, there was nothing wrong with the references and
 they worked perfectly well when generated using bibtex8. I examined the two
 references which caused problems and they were exactly the same as any
 other reference. Again, they work in bibtex8 but not biber.

 Does anyone know what could cause this error? When these two references
 are removed the document compiles but I need these references.

 ~Ben

Re: Biber produces errors where bibtex8 does not

2014-06-20 Thread Benedict Holland 
So it appears that the reason is that biber does not escape the abstract of
a reference, even if it doesn't at all display that abstract. Specifically
this is occurring if a percentage sign is within the abstract. Apparently
all percentage signs must be escaped? Is this a bug with lyx or with biber?

~Ben


On Fri, Jun 20, 2014 at 5:21 PM, Benedict Holland <
benedict.m.holl...@gmail.com> wrote:

> Hello,
>
> I tried using biber and biblatex following the instructions here:
>
> http://wiki.lyx.org/BibTeX/Biblatex
>
> I received some very strange errors like "Lonely \item - perhaps a missing
> list environment" when some of my references were included. It was actually
> 2/35 which were throwing the error except the error wasn't anywhere near
> those references. Even so, there was nothing wrong with the references and
> they worked perfectly well when generated using bibtex8. I examined the two
> references which caused problems and they were exactly the same as any
> other reference. Again, they work in bibtex8 but not biber.
>
> Does anyone know what could cause this error? When these two references
> are removed the document compiles but I need these references.
>
> ~Ben
>

Re: Biber documentation

2012-11-29 Thread Wolfgang Engelmann 
Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:

Thanks, Stefano, for your help and advices and references. Will work on it. 
By the way, Springer publisher wants the Vancouver style. 
In the net it is mentioned:

by TeXnical Designs on Tue Aug 30th, 2011 
LaTeX has a Vancouver citation style which you can use and can be found 
here. As far as doing it in LyX, it is possible. This PDF should explain 
things.
But the PDF mentioned does not mention LyX at all. 

Is there a Vancouver.layout file available?

Wolfgang
http://latex-community.org/forum/styles/terran_tribune/imageset/icon_post_target.gif

Re: Biber documentation

2012-11-29 Thread Alex Vergara Gil 

Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:
Thanks, Stefano, for your help and advices and references. Will work on it. 
By the way, Springer publisher wants the Vancouver style.

In the net it is mentioned:
by TeXnical Designs on Tue Aug 30th, 2011
LaTeX has a Vancouver citation style which you can use and can be found 
here. As far as doing it in LyX, it is possible. This PDF should explain 
things.

But the PDF mentioned does not mention LyX at all.
Is there a Vancouver.layout file available?
Wolfgang


You don't need the layout because it is present in latex, if you use bibtex 
just double click in the gray box and choose the vancouver style


Regards

Alex

Re: Biber documentation

2012-11-29 Thread stefano franchi 
Hi Wolfgang,

the Vancouver style you linked to is a .bst file. In other words, it is a
style file for use with bibtex. It cannot be used with biblatex. As far as
I know, there is no Vancouver style available for biblatex. You'll have to
start with a standard style, e.g. authoryear, and then modified it by hand.
That is a painful task when your knoledge of biblatex is still limited.
One alternative is to switch to bibtex.

Cheers,

Stefano


On Thu, Nov 29, 2012 at 10:22 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

 **

 Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:

 Thanks, Stefano, for your help and advices and references. Will work on
 it. By the way, Springer publisher wants the Vancouver style.

 In the net it is mentioned:

 http://latex-community.org/forum/viewtopic.php?p=55203sid=4e75f7381f759f06ba38ad74e4819fdf#p55203by
 TeXnical 
 Designshttp://latex-community.org/forum/memberlist.php?mode=viewprofileu=18308sid=4e75f7381f759f06ba38ad74e4819fdfon
  Tue Aug 30th, 2011
 LaTeX has a Vancouver citation style which you can use and can be found
 here http://www.ctan.org/tex-archive/biblio/bibtex/contrib/vancouver.
 As far as doing it in LyX, it is possible. This 
 PDFhttp://wiki.lyx.org/uploads/BibTeX/biblioexample.pdfshould explain 
 things.

 But the PDF mentioned does not mention LyX at all.

 Is there a Vancouver.layout file available?

 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: Biber documentation

2012-11-29 Thread Wolfgang Engelmann 
Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:

Thanks, Stefano, for your help and advices and references. Will work on it. 
By the way, Springer publisher wants the Vancouver style. 
In the net it is mentioned:

by TeXnical Designs on Tue Aug 30th, 2011 
LaTeX has a Vancouver citation style which you can use and can be found 
here. As far as doing it in LyX, it is possible. This PDF should explain 
things.
But the PDF mentioned does not mention LyX at all. 

Is there a Vancouver.layout file available?

Wolfgang
http://latex-community.org/forum/styles/terran_tribune/imageset/icon_post_target.gif

Re: Biber documentation

2012-11-29 Thread Alex Vergara Gil 

Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:
Thanks, Stefano, for your help and advices and references. Will work on it. 
By the way, Springer publisher wants the Vancouver style.

In the net it is mentioned:
by TeXnical Designs on Tue Aug 30th, 2011
LaTeX has a Vancouver citation style which you can use and can be found 
here. As far as doing it in LyX, it is possible. This PDF should explain 
things.

But the PDF mentioned does not mention LyX at all.
Is there a Vancouver.layout file available?
Wolfgang


You don't need the layout because it is present in latex, if you use bibtex 
just double click in the gray box and choose the vancouver style


Regards

Alex

Re: Biber documentation

2012-11-29 Thread stefano franchi 
Hi Wolfgang,

the Vancouver style you linked to is a .bst file. In other words, it is a
style file for use with bibtex. It cannot be used with biblatex. As far as
I know, there is no Vancouver style available for biblatex. You'll have to
start with a standard style, e.g. authoryear, and then modified it by hand.
That is a painful task when your knoledge of biblatex is still limited.
One alternative is to switch to bibtex.

Cheers,

Stefano


On Thu, Nov 29, 2012 at 10:22 AM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

 **

 Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:

 Thanks, Stefano, for your help and advices and references. Will work on
 it. By the way, Springer publisher wants the Vancouver style.

 In the net it is mentioned:

 http://latex-community.org/forum/viewtopic.php?p=55203sid=4e75f7381f759f06ba38ad74e4819fdf#p55203by
 TeXnical 
 Designshttp://latex-community.org/forum/memberlist.php?mode=viewprofileu=18308sid=4e75f7381f759f06ba38ad74e4819fdfon
  Tue Aug 30th, 2011
 LaTeX has a Vancouver citation style which you can use and can be found
 here http://www.ctan.org/tex-archive/biblio/bibtex/contrib/vancouver.
 As far as doing it in LyX, it is possible. This 
 PDFhttp://wiki.lyx.org/uploads/BibTeX/biblioexample.pdfshould explain 
 things.

 But the PDF mentioned does not mention LyX at all.

 Is there a Vancouver.layout file available?

 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: Biber documentation

2012-11-29 Thread Wolfgang Engelmann 
Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:

Thanks, Stefano, for your help and advices and references. Will work on it. 
By the way, Springer publisher wants the Vancouver style. 
In the net it is mentioned:

by TeXnical Designs on Tue Aug 30th, 2011 
LaTeX has a Vancouver citation style which you can use and can be found 
here. As far as doing it in LyX, it is possible. This PDF should explain 
things.
But the PDF mentioned does not mention LyX at all. 

Is there a Vancouver.layout file available?

Wolfgang
<>

Re: Biber documentation

2012-11-29 Thread Alex Vergara Gil 

Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:
Thanks, Stefano, for your help and advices and references. Will work on it. 
By the way, Springer publisher wants the Vancouver style.

In the net it is mentioned:
by TeXnical Designs on Tue Aug 30th, 2011
LaTeX has a Vancouver citation style which you can use and can be found 
here. As far as doing it in LyX, it is possible. This PDF should explain 
things.

But the PDF mentioned does not mention LyX at all.
Is there a Vancouver.layout file available?
Wolfgang


You don't need the layout because it is present in latex, if you use bibtex 
just double click in the gray box and choose the vancouver style


Regards

Alex

Re: Biber documentation

2012-11-29 Thread stefano franchi 
Hi Wolfgang,

the Vancouver style you linked to is a .bst file. In other words, it is a
style file for use with bibtex. It cannot be used with biblatex. As far as
I know, there is no Vancouver style available for biblatex. You'll have to
start with a standard style, e.g. authoryear, and then modified it by hand.
That is a painful task when your knoledge of biblatex is still limited.
One alternative is to switch to bibtex.

Cheers,

Stefano


On Thu, Nov 29, 2012 at 10:22 AM, Wolfgang Engelmann <
engelm...@uni-tuebingen.de> wrote:

> **
>
> Am Mittwoch, 28. November 2012, 20:02:55 schrieb stefano franchi:
>
> Thanks, Stefano, for your help and advices and references. Will work on
> it. By the way, Springer publisher wants the Vancouver style.
>
> In the net it is mentioned:
>
> by
> TeXnical 
> Designson
>  Tue Aug 30th, 2011
> LaTeX has a Vancouver citation style which you can use and can be found
> here .
> As far as doing it in LyX, it is possible. This 
> PDFshould explain 
> things.
>
> But the PDF mentioned does not mention LyX at all.
>
> Is there a Vancouver.layout file available?
>
> 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: Biber documentation

2012-11-28 Thread stefano franchi 
The biblatex manual should be installed on your system by your Tex
distribution. The command
texdoc biblatex
should bring it up. TexLive installs it in

/usr/local/texlive/2012/texmf-dist/doc/latex/biblatex/biblatex.pdf

If you use Debian's TEx, however, it may be in a different place---Debian's
Tex used to have a different directory structure than TexLive.

Similarly, the biber manual is called biber.pdf and texlive puts it in

/usr/local/texlive/2012/texmf-dist/doc/bibtex/biber/biber.pdf

A search for either file on your system (with, e.g.  locate
biber|biblatex.pdf) should tell you where they are.

You can also google either file and you'll get to them quickly. Here is
biber.pdf on sourceforge:

http://iweb.dl.sourceforge.net/project/biblatex-biber/biblatex-biber/1.4/documentation/biber.pdf

and here is biblatex.pdf on Ctan:

ftp://www.ctan.org/ctan/macros/latex/exptl/biblatex/doc/biblatex.pdf


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: Biber documentation

2012-11-28 Thread Wolfgang Engelmann 
Am Mittwoch, 28. November 2012, 14:20:00 schrieb stefano franchi:
 The biblatex manual should be installed on your system by your Tex
 distribution. The command
 
 texdoc biblatex
 
 should bring it up. 

Thanks, Stefano

Its a long documentation and not easy for the novice to find what one 
needs/wants. Is there somewhere a document with various examples for the 
citation styles and the various reference styles.

E.g. with my 
\usepackage[backend=biber, style=authoryear,natbib=true]{biblatex}
I get e.g.
Jang, Sung-Wuk et al. (2010). “N-acetylserotonin activates TrkB receptor in 
a circadian rhythm.” eng. In: P Natl Acad Sci USA 107, pp. 3876–3881.
while I would like to have 
Jang, S.-W. et al. (2010). N-acetylserotonin activates TrkB receptor in a 
circadian rhythm. In: P Natl Acad Sci USA 107, pp. 3876–3881.

and
Jewett, M. E., D. W. Rimmer, et al. (1997). “Human circadian pacemaker is 
sensitive to light throughout subjective day without evidence of 
transients”. In: Am J Physiol 273, R1800–R1809.
while I want 
Jewett, M. E. et al. (1997). Human circadian pacemaker is sensitive to
light throughout subjective day without evidence of transients. In: Am J 
Physiol 273, R1800–R1809.

Where would I find the option in the handbook to get rid of eng. (first 
citation) and the number of authors cited. Searching for eng. was not 
successfull

Wolfgang

Re: Biber documentation

2012-11-28 Thread stefano franchi 
On Wed, Nov 28, 2012 at 12:38 PM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

 Am Mittwoch, 28. November 2012, 14:20:00 schrieb stefano franchi:
 E.g. with my
 \usepackage[backend=biber, style=authoryear,natbib=true]{biblatex}
 I get e.g.
 Jang, Sung-Wuk et al. (2010). “N-acetylserotonin activates TrkB receptor in
 a circadian rhythm.” eng. In: P Natl Acad Sci USA 107, pp. 3876–3881.
 while I would like to have
 Jang, S.-W. et al. (2010). N-acetylserotonin activates TrkB receptor in a
 circadian rhythm. In: P Natl Acad Sci USA 107, pp. 3876–3881.

 and
 Jewett, M. E., D. W. Rimmer, et al. (1997). “Human circadian pacemaker is
 sensitive to light throughout subjective day without evidence of
 transients”. In: Am J Physiol 273, R1800–R1809.
 while I want
 Jewett, M. E. et al. (1997). Human circadian pacemaker is sensitive to
 light throughout subjective day without evidence of transients. In: Am J
 Physiol 273, R1800–R1809.


The eng. is probably coming from your citation--an abbreviation for
english in the Note field perhaps? Check your bib file, and see where it
comes from.
Once you have found the filed, you can simply erase its content. In case of
multiple citations having the same issue, you can exclude the filed from
the output with the command

\DeclareFieldFormat{note}{}

in your preamble (for the note filed, of course, change note to the name
of the field that contains spurious data if otherwise)



For the second problem, you control how many authors are cited with a
biblatex option. Manual, p.52:

maxnames=integer default: 3
A threshold affecting all lists of names (author, editor, etc.). If a list
exceeds this threshold,
i. e., if it holds more than integer names, it is automatically truncated
according to the
setting of the minnames option. maxnames is the master option which sets
both maxbibnames
and maxcitenames.

minnames=integer default: 1
A limit affecting all lists of names (author, editor, etc.). If a list
holds more than
hmaxnamesi names, it is automatically truncated to minnames names. The
minnames
value must be smaller than or equal to maxnames. minnames is the master
option which
sets both minbibnames and mincitenames.


In brief,, setting maxbibnames=1 (in the call to biblatex or, even better,
within a \ExecuteBibliographyOptions command in the preamble, see manual,
p.71), should solve your problem with citation 2.


Let me say, however, that there is no easy way into biblatex. The package
is so flexible and so powerful that, inevitably, the learning curve is a
bit steep. You should definitely read chapter 3 of the manual (User guide)
and check out the numerous examples that come with the package. In Tex Live
they are installed in
usr/local/texlive/2012/texmf-dist/doc/latex/biblatex/examples/
searching for a file such as 50-style-authoryear.pdf (one of the examples)
should lead you to the right directory if otherwise.
More generally, you can ask more complex questions (how to customize
styles, etcetera) on Comp,text.tex, where a lot of biblatex users hang out.

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: Biber documentation

2012-11-28 Thread stefano franchi 
The biblatex manual should be installed on your system by your Tex
distribution. The command
texdoc biblatex
should bring it up. TexLive installs it in

/usr/local/texlive/2012/texmf-dist/doc/latex/biblatex/biblatex.pdf

If you use Debian's TEx, however, it may be in a different place---Debian's
Tex used to have a different directory structure than TexLive.

Similarly, the biber manual is called biber.pdf and texlive puts it in

/usr/local/texlive/2012/texmf-dist/doc/bibtex/biber/biber.pdf

A search for either file on your system (with, e.g.  locate
biber|biblatex.pdf) should tell you where they are.

You can also google either file and you'll get to them quickly. Here is
biber.pdf on sourceforge:

http://iweb.dl.sourceforge.net/project/biblatex-biber/biblatex-biber/1.4/documentation/biber.pdf

and here is biblatex.pdf on Ctan:

ftp://www.ctan.org/ctan/macros/latex/exptl/biblatex/doc/biblatex.pdf


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: Biber documentation

2012-11-28 Thread Wolfgang Engelmann 
Am Mittwoch, 28. November 2012, 14:20:00 schrieb stefano franchi:
 The biblatex manual should be installed on your system by your Tex
 distribution. The command
 
 texdoc biblatex
 
 should bring it up. 

Thanks, Stefano

Its a long documentation and not easy for the novice to find what one 
needs/wants. Is there somewhere a document with various examples for the 
citation styles and the various reference styles.

E.g. with my 
\usepackage[backend=biber, style=authoryear,natbib=true]{biblatex}
I get e.g.
Jang, Sung-Wuk et al. (2010). “N-acetylserotonin activates TrkB receptor in 
a circadian rhythm.” eng. In: P Natl Acad Sci USA 107, pp. 3876–3881.
while I would like to have 
Jang, S.-W. et al. (2010). N-acetylserotonin activates TrkB receptor in a 
circadian rhythm. In: P Natl Acad Sci USA 107, pp. 3876–3881.

and
Jewett, M. E., D. W. Rimmer, et al. (1997). “Human circadian pacemaker is 
sensitive to light throughout subjective day without evidence of 
transients”. In: Am J Physiol 273, R1800–R1809.
while I want 
Jewett, M. E. et al. (1997). Human circadian pacemaker is sensitive to
light throughout subjective day without evidence of transients. In: Am J 
Physiol 273, R1800–R1809.

Where would I find the option in the handbook to get rid of eng. (first 
citation) and the number of authors cited. Searching for eng. was not 
successfull

Wolfgang

Re: Biber documentation

2012-11-28 Thread stefano franchi 
On Wed, Nov 28, 2012 at 12:38 PM, Wolfgang Engelmann 
engelm...@uni-tuebingen.de wrote:

 Am Mittwoch, 28. November 2012, 14:20:00 schrieb stefano franchi:
 E.g. with my
 \usepackage[backend=biber, style=authoryear,natbib=true]{biblatex}
 I get e.g.
 Jang, Sung-Wuk et al. (2010). “N-acetylserotonin activates TrkB receptor in
 a circadian rhythm.” eng. In: P Natl Acad Sci USA 107, pp. 3876–3881.
 while I would like to have
 Jang, S.-W. et al. (2010). N-acetylserotonin activates TrkB receptor in a
 circadian rhythm. In: P Natl Acad Sci USA 107, pp. 3876–3881.

 and
 Jewett, M. E., D. W. Rimmer, et al. (1997). “Human circadian pacemaker is
 sensitive to light throughout subjective day without evidence of
 transients”. In: Am J Physiol 273, R1800–R1809.
 while I want
 Jewett, M. E. et al. (1997). Human circadian pacemaker is sensitive to
 light throughout subjective day without evidence of transients. In: Am J
 Physiol 273, R1800–R1809.


The eng. is probably coming from your citation--an abbreviation for
english in the Note field perhaps? Check your bib file, and see where it
comes from.
Once you have found the filed, you can simply erase its content. In case of
multiple citations having the same issue, you can exclude the filed from
the output with the command

\DeclareFieldFormat{note}{}

in your preamble (for the note filed, of course, change note to the name
of the field that contains spurious data if otherwise)



For the second problem, you control how many authors are cited with a
biblatex option. Manual, p.52:

maxnames=integer default: 3
A threshold affecting all lists of names (author, editor, etc.). If a list
exceeds this threshold,
i. e., if it holds more than integer names, it is automatically truncated
according to the
setting of the minnames option. maxnames is the master option which sets
both maxbibnames
and maxcitenames.

minnames=integer default: 1
A limit affecting all lists of names (author, editor, etc.). If a list
holds more than
hmaxnamesi names, it is automatically truncated to minnames names. The
minnames
value must be smaller than or equal to maxnames. minnames is the master
option which
sets both minbibnames and mincitenames.


In brief,, setting maxbibnames=1 (in the call to biblatex or, even better,
within a \ExecuteBibliographyOptions command in the preamble, see manual,
p.71), should solve your problem with citation 2.


Let me say, however, that there is no easy way into biblatex. The package
is so flexible and so powerful that, inevitably, the learning curve is a
bit steep. You should definitely read chapter 3 of the manual (User guide)
and check out the numerous examples that come with the package. In Tex Live
they are installed in
usr/local/texlive/2012/texmf-dist/doc/latex/biblatex/examples/
searching for a file such as 50-style-authoryear.pdf (one of the examples)
should lead you to the right directory if otherwise.
More generally, you can ask more complex questions (how to customize
styles, etcetera) on Comp,text.tex, where a lot of biblatex users hang out.

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: Biber documentation

2012-11-28 Thread stefano franchi 
The biblatex manual should be installed on your system by your Tex
distribution. The command
>texdoc biblatex
should bring it up. TexLive installs it in

/usr/local/texlive/2012/texmf-dist/doc/latex/biblatex/biblatex.pdf

If you use Debian's TEx, however, it may be in a different place---Debian's
Tex used to have a different directory structure than TexLive.

Similarly, the biber manual is called biber.pdf and texlive puts it in

/usr/local/texlive/2012/texmf-dist/doc/bibtex/biber/biber.pdf

A search for either file on your system (with, e.g.  >locate
biber|biblatex.pdf) should tell you where they are.

You can also google either file and you'll get to them quickly. Here is
biber.pdf on sourceforge:

http://iweb.dl.sourceforge.net/project/biblatex-biber/biblatex-biber/1.4/documentation/biber.pdf

and here is biblatex.pdf on Ctan:

ftp://www.ctan.org/ctan/macros/latex/exptl/biblatex/doc/biblatex.pdf


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: Biber documentation

2012-11-28 Thread Wolfgang Engelmann 
Am Mittwoch, 28. November 2012, 14:20:00 schrieb stefano franchi:
> The biblatex manual should be installed on your system by your Tex
> distribution. The command
> 
> >texdoc biblatex
> 
> should bring it up. 

Thanks, Stefano

Its a long documentation and not easy for the novice to find what one 
needs/wants. Is there somewhere a document with various examples for the 
citation styles and the various reference styles.

E.g. with my 
\usepackage[backend=biber, style=authoryear,natbib=true]{biblatex}
I get e.g.
Jang, Sung-Wuk et al. (2010). “N-acetylserotonin activates TrkB receptor in 
a circadian rhythm.” eng. In: P Natl Acad Sci USA 107, pp. 3876–3881.
while I would like to have 
Jang, S.-W. et al. (2010). N-acetylserotonin activates TrkB receptor in a 
circadian rhythm. In: P Natl Acad Sci USA 107, pp. 3876–3881.

and
Jewett, M. E., D. W. Rimmer, et al. (1997). “Human circadian pacemaker is 
sensitive to light throughout subjective day without evidence of 
transients”. In: Am J Physiol 273, R1800–R1809.
while I want 
Jewett, M. E. et al. (1997). Human circadian pacemaker is sensitive to
light throughout subjective day without evidence of transients. In: Am J 
Physiol 273, R1800–R1809.

Where would I find the option in the handbook to get rid of eng. (first 
citation) and the number of authors cited. Searching for eng. was not 
successfull

Wolfgang

Re: Biber documentation

2012-11-28 Thread stefano franchi 
On Wed, Nov 28, 2012 at 12:38 PM, Wolfgang Engelmann <
engelm...@uni-tuebingen.de> wrote:

> Am Mittwoch, 28. November 2012, 14:20:00 schrieb stefano franchi:
> E.g. with my
> \usepackage[backend=biber, style=authoryear,natbib=true]{biblatex}
> I get e.g.
> Jang, Sung-Wuk et al. (2010). “N-acetylserotonin activates TrkB receptor in
> a circadian rhythm.” eng. In: P Natl Acad Sci USA 107, pp. 3876–3881.
> while I would like to have
> Jang, S.-W. et al. (2010). N-acetylserotonin activates TrkB receptor in a
> circadian rhythm. In: P Natl Acad Sci USA 107, pp. 3876–3881.
>
> and
> Jewett, M. E., D. W. Rimmer, et al. (1997). “Human circadian pacemaker is
> sensitive to light throughout subjective day without evidence of
> transients”. In: Am J Physiol 273, R1800–R1809.
> while I want
> Jewett, M. E. et al. (1997). Human circadian pacemaker is sensitive to
> light throughout subjective day without evidence of transients. In: Am J
> Physiol 273, R1800–R1809.
>
>
The "eng." is probably coming from your citation--an abbreviation for
"english" in the Note field perhaps? Check your bib file, and see where it
comes from.
Once you have found the filed, you can simply erase its content. In case of
multiple citations having the same issue, you can exclude the filed from
the output with the command

\DeclareFieldFormat{note}{}

in your preamble (for the note filed, of course, change "note" to the name
of the field that contains spurious data if otherwise)



For the second problem, you control how many authors are cited with a
biblatex option. Manual, p.52:

maxnames= default: 3
A threshold affecting all lists of names (author, editor, etc.). If a list
exceeds this threshold,
i. e., if it holds more than  names, it is automatically truncated
according to the
setting of the minnames option. maxnames is the master option which sets
both maxbibnames
and maxcitenames.

minnames= default: 1
A limit affecting all lists of names (author, editor, etc.). If a list
holds more than
hmaxnamesi names, it is automatically truncated to  names. The

value must be smaller than or equal to . minnames is the master
option which
sets both minbibnames and mincitenames.


In brief,, setting maxbibnames=1 (in the call to biblatex or, even better,
within a \ExecuteBibliographyOptions command in the preamble, see manual,
p.71), should solve your problem with citation 2.


Let me say, however, that there is no easy way into biblatex. The package
is so flexible and so powerful that, inevitably, the learning curve is a
bit steep. You should definitely read chapter 3 of the manual (User guide)
and check out the numerous examples that come with the package. In Tex Live
they are installed in
usr/local/texlive/2012/texmf-dist/doc/latex/biblatex/examples/
searching for a file such as 50-style-authoryear.pdf (one of the examples)
should lead you to the right directory if otherwise.
More generally, you can ask more complex questions (how to customize
styles, etcetera) on Comp,text.tex, where a lot of biblatex users hang out.

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: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 Dear all. I want to try biber on Ubuntu Natty. I installed it both as
 an standalone package with TexLive 2009 and included in Texlive 2011.
 In both cases I get the following error while compiling a document:
 
 [0] Config.pm:254 INFO - This is biber 0.9.5
 [0] Config.pm:257 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:108 INFO - === Thu Aug 25, 2011, 18:48:31
 [35] Biber.pm:198 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?
 
 I have already included \typeout{File: \jobname.bcf} in the preamble
 as suggested by the wiki. I have also defined biber as the
 bibliographic engine in both, the document and lyx.  Any ideas?

biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with 
that rsion as well? (It might be that the newer biber version is incompatible 
with your biblatex version, or it might be a bug in this version).

HTH,
Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
I removed the version of biber I had previously installed.

jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
biber version: 0.9.4

But Lyx is still looking for textlive 2009 (which is also installed).
Do you know how can I make it to look at texlive 2011 (yes, I
reconfigured several times after installation)?

Regards.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 11:50 AM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 Dear all. I want to try biber on Ubuntu Natty. I installed it both as
 an standalone package with TexLive 2009 and included in Texlive 2011.
 In both cases I get the following error while compiling a document:

 [0] Config.pm:254 INFO - This is biber 0.9.5
 [0] Config.pm:257 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:108 INFO - === Thu Aug 25, 2011, 18:48:31
 [35] Biber.pm:198 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?

 I have already included \typeout{File: \jobname.bcf} in the preamble
 as suggested by the wiki. I have also defined biber as the
 bibliographic engine in both, the document and lyx.  Any ideas?

 biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with
 that rsion as well? (It might be that the newer biber version is incompatible
 with your biblatex version, or it might be a bug in this version).

 HTH,
 Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
I made Lyx find texlive 2011 binaries, by runnning it from the command
prompt. Nonetheless, the problem is still there:

[0] Config.pm:253 INFO - This is biber 0.9.4
[0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
[1] biber:112 INFO - === Fri Aug 26, 2011, 14:51:50
[56] Biber.pm:197 FATAL - Cannot find control file
'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
BibLaTeX?

Ideas? Thanks in advance.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 2:48 PM, Julio Rojas jcredbe...@gmail.com wrote:
 I removed the version of biber I had previously installed.

 jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
 biber version: 0.9.4

 But Lyx is still looking for textlive 2009 (which is also installed).
 Do you know how can I make it to look at texlive 2011 (yes, I
 reconfigured several times after installation)?

 Regards.
 -
 Julio Rojas
 jcredbe...@gmail.com



 On Fri, Aug 26, 2011 at 11:50 AM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 Dear all. I want to try biber on Ubuntu Natty. I installed it both as
 an standalone package with TexLive 2009 and included in Texlive 2011.
 In both cases I get the following error while compiling a document:

 [0] Config.pm:254 INFO - This is biber 0.9.5
 [0] Config.pm:257 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:108 INFO - === Thu Aug 25, 2011, 18:48:31
 [35] Biber.pm:198 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?

 I have already included \typeout{File: \jobname.bcf} in the preamble
 as suggested by the wiki. I have also defined biber as the
 bibliographic engine in both, the document and lyx.  Any ideas?

 biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with
 that rsion as well? (It might be that the newer biber version is incompatible
 with your biblatex version, or it might be a bug in this version).

 HTH,
 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 I removed the version of biber I had previously installed.
 
 jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
 biber version: 0.9.4
 
 But Lyx is still looking for textlive 2009 (which is also installed).
 Do you know how can I make it to look at texlive 2011 (yes, I
 reconfigured several times after installation)?

I suppose you have to adjust your path settings. In your local profile file 
(~/.profile most probably), add the following (if the file does not exist yet, 
create it):

#
# Set some environment variables for TeX/LaTeX
#
export TEXMFCNF=/usr/local/texlive/2011/texmf/web2c:$TEXMFCNF
export PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH

After relogin, LyX should find the right binaries. See also sec. 3.4.1 of the 
texlive manual:
http://www.tug.org/texlive/doc/texlive-en/texlive-en.html

I have created a symlink here from /usr/local/texlive/current to 
/usr/local/texlive/2011 and set all pathes to current instead of 2011. This 
way, I need only change the symlink after a distribution upgrade.

HTH,
Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 I made Lyx find texlive 2011 binaries, by runnning it from the command
 prompt. Nonetheless, the problem is still there:
 
 [0] Config.pm:253 INFO - This is biber 0.9.4
 [0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:112 INFO - === Fri Aug 26, 2011, 14:51:50
 [56] Biber.pm:197 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?
 
 Ideas? Thanks in advance.

What is your biblatex version? (Look in the log file, it is well possible that 
an older version from texlive 2009 is used, unless you have adjusted the path 
settings).

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Paths updated. Compiling with bibtex everything is fine. Version shown:

This is 8-bit Big BibTeX version 0.99d

Biber, same error. Maybe some permission problem as to where this .bcf
file is created?

Thx Jürgen.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 3:08 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 I made Lyx find texlive 2011 binaries, by runnning it from the command
 prompt. Nonetheless, the problem is still there:

 [0] Config.pm:253 INFO - This is biber 0.9.4
 [0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:112 INFO - === Fri Aug 26, 2011, 14:51:50
 [56] Biber.pm:197 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?

 Ideas? Thanks in advance.

 What is your biblatex version? (Look in the log file, it is well possible that
 an older version from texlive 2009 is used, unless you have adjusted the path
 settings).

 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 Paths updated. Compiling with bibtex everything is fine. Version shown:
 
 This is 8-bit Big BibTeX version 0.99d
 
 Biber, same error. Maybe some permission problem as to where this .bcf
 file is created?

Again: what biblatex version does your LaTeX log file report? 
Also, what does
kpsewhich biblatex.sty
return?

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Sorry Jürgen, I misread your question.

/usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
Package: biblatex 2011/07/29 v1.6 programmable bibliographies

It seems ok.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 3:44 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 Paths updated. Compiling with bibtex everything is fine. Version shown:

 This is 8-bit Big BibTeX version 0.99d

 Biber, same error. Maybe some permission problem as to where this .bcf
 file is created?

 Again: what biblatex version does your LaTeX log file report?
 Also, what does
 kpsewhich biblatex.sty
 return?

 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
 Package: biblatex 2011/07/29 v1.6 programmable bibliographies
 
 It seems ok.

Yes, it seems OK.

Now let's clarify if the basic settings are correct:

First, did you really pass the option backend=biber to biblatex?

Then, please tell us how you set up biber. Did you specify any options or just 
select biber from the dropdown list?

Also, posting the whole LaTeX log file might shed some light on things.

Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
 Julio Rojas wrote:
  I removed the version of biber I had previously installed.
  
  jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
  biber version: 0.9.4
  
  But Lyx is still looking for textlive 2009 (which is also installed).
  Do you know how can I make it to look at texlive 2011 (yes, I
  reconfigured several times after installation)?
 
 I suppose you have to adjust your path settings. In your local profile file
 (~/.profile most probably), add the following (if the file does not exist
 yet, create it):

This is not  sufficient. With this, the path is set only for programs called 
from the command line.
To make it available to the desktop you should consider to edit 
~/.pam_environment (Create it, if not already there)

The syntax is simple a list of shell-variables you want to set. Like this:
PATH 
OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin:/usr/sbin:/sbin:/bin:/usr/bin/X11:.

 #
 # Set some environment variables for TeX/LaTeX
 #
 export TEXMFCNF=/usr/local/texlive/2011/texmf/web2c:$TEXMFCNF
 export PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH
 
 After relogin, LyX should find the right binaries. See also sec. 3.4.1 of
 the texlive manual:
 http://www.tug.org/texlive/doc/texlive-en/texlive-en.html
 
 I have created a symlink here from /usr/local/texlive/current to
 /usr/local/texlive/2011 and set all pathes to current instead of 2011. This
 way, I need only change the symlink after a distribution upgrade.

Good idea

 HTH,
 Jürgen

Kornel


signature.asc
Description: This is a digitally signed message part.

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Kornel Benko wrote:
  I suppose you have to adjust your path settings. In your local profile
  file (~/.profile most probably), add the following (if the file does
  not exist
  yet, create it):
 This is not  sufficient. With this, the path is set only for programs called
 from the command line. To make it available to the desktop you should
 consider to edit ~/.pam_environment (Create it, if not already there)
 
 The syntax is simple a list of shell-variables you want to set. Like this:
 PATH
 OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin:/
 usr/sbin:/sbin:/bin:/usr/bin/X11:.

Sure? It works as I expect it here, also when calling LyX not from the cl.

Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 First, I just selected biber from the pulldown.

OK.

 Second, I have tried both, including and not including backend=biber in
 Document  Settings  Document Class  Custom
 and as well as in
 Document  Settings  Bibliography  Options

Both is wrong. You have to pass the option to biblatex directly with your 
package call, i.e.

\usepackage[...,backend=biber]{biblatex}

Please read the biblatex manual for details on how to load the package.

HTH,
Jürgen

 -
 Julio Rojas
 jcredbe...@gmail.com
 
 On Fri, Aug 26, 2011 at 4:01 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
  Julio Rojas wrote:
  /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
  Package: biblatex 2011/07/29 v1.6 programmable bibliographies
  
  It seems ok.
  
  Yes, it seems OK.
  
  Now let's clarify if the basic settings are correct:
  
  First, did you really pass the option backend=biber to biblatex?
  
  Then, please tell us how you set up biber. Did you specify any options
  or just select biber from the dropdown list?
  
  Also, posting the whole LaTeX log file might shed some light on things.
  
  Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
 Kornel Benko wrote:
   I suppose you have to adjust your path settings. In your local profile
   file (~/.profile most probably), add the following (if the file does
   not exist
  
   yet, create it):
  This is not  sufficient. With this, the path is set only for programs
  called from the command line. To make it available to the desktop you
  should consider to edit ~/.pam_environment (Create it, if not already
  there)
  
  The syntax is simple a list of shell-variables you want to set. Like this:
  PATH
  
  OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin
  :/ usr/sbin:/sbin:/bin:/usr/bin/X11:.
 
 Sure? It works as I expect it here, also when calling LyX not from the cl.
 
 Jürgen

At least some desktopts are starting, without reading ~/.profile first. (If 
you start lyx through a shell-script, then of course
you read .profile)

Kornel


signature.asc
Description: This is a digitally signed message part.

Re: Biber

2011-08-26 Thread Julio Rojas 
RTFM! Well, I added the option, and biber is running:

[0] Config.pm:253 INFO - This is biber 0.9.4
[0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
[1] biber:112 INFO - === Fri Aug 26, 2011, 16:55:40
[1] Biber.pm:304 INFO - Reading 'Tesis_Maestro.bcf'
[66] Biber.pm:606 INFO - Found 140 citekeys in bib section 0
[157] Biber.pm:2466 INFO - Processing bib section 0
[172] Biber.pm:2555 INFO - Looking for bibtex format file
'/home/jcredberry/Dropbox/Sulan/BD_tesis.bib' for section 0
[172] bibtex.pm:104 INFO - Found bibtex data file
'/home/jcredberry/Dropbox/Sulan/BD_tesis.bib'

Still, no references are produced:

Package biblatex Warning: No reference sections found on input line 189.
LaTeX Warning: Empty bibliography on input line 189.
LaTeX Warning: Empty bibliography on input line 190.

Thx for all your effort!
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 4:38 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 First, I just selected biber from the pulldown.

 OK.

 Second, I have tried both, including and not including backend=biber in
 Document  Settings  Document Class  Custom
 and as well as in
 Document  Settings  Bibliography  Options

 Both is wrong. You have to pass the option to biblatex directly with your
 package call, i.e.

 \usepackage[...,backend=biber]{biblatex}

 Please read the biblatex manual for details on how to load the package.

 HTH,
 Jürgen

 -
 Julio Rojas
 jcredbe...@gmail.com

 On Fri, Aug 26, 2011 at 4:01 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
  Julio Rojas wrote:
  /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
  Package: biblatex 2011/07/29 v1.6 programmable bibliographies
 
  It seems ok.
 
  Yes, it seems OK.
 
  Now let's clarify if the basic settings are correct:
 
  First, did you really pass the option backend=biber to biblatex?
 
  Then, please tell us how you set up biber. Did you specify any options
  or just select biber from the dropdown list?
 
  Also, posting the whole LaTeX log file might shed some light on things.
 
  Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 RTFM! Well, I added the option, and biber is running:
 
 [0] Config.pm:253 INFO - This is biber 0.9.4
 [0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:112 INFO - === Fri Aug 26, 2011, 16:55:40
 [1] Biber.pm:304 INFO - Reading 'Tesis_Maestro.bcf'
 [66] Biber.pm:606 INFO - Found 140 citekeys in bib section 0
 [157] Biber.pm:2466 INFO - Processing bib section 0
 [172] Biber.pm:2555 INFO - Looking for bibtex format file
 '/home/jcredberry/Dropbox/Sulan/BD_tesis.bib' for section 0
 [172] bibtex.pm:104 INFO - Found bibtex data file
 '/home/jcredberry/Dropbox/Sulan/BD_tesis.bib'
 
 Still, no references are produced:
 
 Package biblatex Warning: No reference sections found on input line 189.
 LaTeX Warning: Empty bibliography on input line 189.
 LaTeX Warning: Empty bibliography on input line 190.
 
 Thx for all your effort!

Can you set up a minimal example file (including the bib file)? Something else 
in your setup must be wrong.

Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Kornel Benko wrote:
 At least some desktopts are starting, without reading ~/.profile first.
 (If you start lyx through a shell-script, then of course you read .profile)

I see. Then it just happens to work here (KDE 4.7, openSuse 11.4).

Frankly, I never heard of the .pam_environment file before, but you are the 
expert.

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Small example working perfectly with biber. Even with the same
preamble and configuration (a parent file and a lorem ipsum child
file). The only change is a reduced bib file with some selected
entries. Maybe some problem processing the bib file itself?

Regards.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 5:49 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Kornel Benko wrote:
 At least some desktopts are starting, without reading ~/.profile first.
 (If you start lyx through a shell-script, then of course you read .profile)

 I see. Then it just happens to work here (KDE 4.7, openSuse 11.4).

 Frankly, I never heard of the .pam_environment file before, but you are the
 expert.

 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 Small example working perfectly with biber. Even with the same
 preamble and configuration (a parent file and a lorem ipsum child
 file). The only change is a reduced bib file with some selected
 entries. Maybe some problem processing the bib file itself?

Maybe. Try to sort that out by checking which entries are the culprit. A thing 
that comes to mind is encoding. Which encoding does the bib file have? If it 
differs from the encoding of the document (as set via inputenc), you have to 
declare that via the bibencoding option, e.g.

\usepackage{...,bibencoding=latin9,backend=biber]{biblatex}

Again, please refer to the biblatex manual for details.

Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
 Kornel Benko wrote:
  At least some desktopts are starting, without reading ~/.profile first.
  (If you start lyx through a shell-script, then of course you read
  .profile)
 
 I see. Then it just happens to work here (KDE 4.7, openSuse 11.4).
 
 Frankly, I never heard of the .pam_environment file before, but you are the
 expert.
 
 Jürgen

Kde starts as sh /usr/bin/startkde or such, that may work. Since I am working 
with csh, I never created
.profile. My .login and .cshrc were ignored if started from desktop. It 
took a while to discover .pam_environment file.

See 6.6.6 FILES, User specific environment file in

http://www.kernel.org/pub/linux/libs/pam/Linux-PAM-html/Linux-PAM_SAG.html

Kornel


signature.asc
Description: This is a digitally signed message part.

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 Dear all. I want to try biber on Ubuntu Natty. I installed it both as
 an standalone package with TexLive 2009 and included in Texlive 2011.
 In both cases I get the following error while compiling a document:
 
 [0] Config.pm:254 INFO - This is biber 0.9.5
 [0] Config.pm:257 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:108 INFO - === Thu Aug 25, 2011, 18:48:31
 [35] Biber.pm:198 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?
 
 I have already included \typeout{File: \jobname.bcf} in the preamble
 as suggested by the wiki. I have also defined biber as the
 bibliographic engine in both, the document and lyx.  Any ideas?

biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with 
that rsion as well? (It might be that the newer biber version is incompatible 
with your biblatex version, or it might be a bug in this version).

HTH,
Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
I removed the version of biber I had previously installed.

jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
biber version: 0.9.4

But Lyx is still looking for textlive 2009 (which is also installed).
Do you know how can I make it to look at texlive 2011 (yes, I
reconfigured several times after installation)?

Regards.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 11:50 AM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 Dear all. I want to try biber on Ubuntu Natty. I installed it both as
 an standalone package with TexLive 2009 and included in Texlive 2011.
 In both cases I get the following error while compiling a document:

 [0] Config.pm:254 INFO - This is biber 0.9.5
 [0] Config.pm:257 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:108 INFO - === Thu Aug 25, 2011, 18:48:31
 [35] Biber.pm:198 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?

 I have already included \typeout{File: \jobname.bcf} in the preamble
 as suggested by the wiki. I have also defined biber as the
 bibliographic engine in both, the document and lyx.  Any ideas?

 biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with
 that rsion as well? (It might be that the newer biber version is incompatible
 with your biblatex version, or it might be a bug in this version).

 HTH,
 Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
I made Lyx find texlive 2011 binaries, by runnning it from the command
prompt. Nonetheless, the problem is still there:

[0] Config.pm:253 INFO - This is biber 0.9.4
[0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
[1] biber:112 INFO - === Fri Aug 26, 2011, 14:51:50
[56] Biber.pm:197 FATAL - Cannot find control file
'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
BibLaTeX?

Ideas? Thanks in advance.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 2:48 PM, Julio Rojas jcredbe...@gmail.com wrote:
 I removed the version of biber I had previously installed.

 jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
 biber version: 0.9.4

 But Lyx is still looking for textlive 2009 (which is also installed).
 Do you know how can I make it to look at texlive 2011 (yes, I
 reconfigured several times after installation)?

 Regards.
 -
 Julio Rojas
 jcredbe...@gmail.com



 On Fri, Aug 26, 2011 at 11:50 AM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 Dear all. I want to try biber on Ubuntu Natty. I installed it both as
 an standalone package with TexLive 2009 and included in Texlive 2011.
 In both cases I get the following error while compiling a document:

 [0] Config.pm:254 INFO - This is biber 0.9.5
 [0] Config.pm:257 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:108 INFO - === Thu Aug 25, 2011, 18:48:31
 [35] Biber.pm:198 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?

 I have already included \typeout{File: \jobname.bcf} in the preamble
 as suggested by the wiki. I have also defined biber as the
 bibliographic engine in both, the document and lyx.  Any ideas?

 biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with
 that rsion as well? (It might be that the newer biber version is incompatible
 with your biblatex version, or it might be a bug in this version).

 HTH,
 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 I removed the version of biber I had previously installed.
 
 jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
 biber version: 0.9.4
 
 But Lyx is still looking for textlive 2009 (which is also installed).
 Do you know how can I make it to look at texlive 2011 (yes, I
 reconfigured several times after installation)?

I suppose you have to adjust your path settings. In your local profile file 
(~/.profile most probably), add the following (if the file does not exist yet, 
create it):

#
# Set some environment variables for TeX/LaTeX
#
export TEXMFCNF=/usr/local/texlive/2011/texmf/web2c:$TEXMFCNF
export PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH

After relogin, LyX should find the right binaries. See also sec. 3.4.1 of the 
texlive manual:
http://www.tug.org/texlive/doc/texlive-en/texlive-en.html

I have created a symlink here from /usr/local/texlive/current to 
/usr/local/texlive/2011 and set all pathes to current instead of 2011. This 
way, I need only change the symlink after a distribution upgrade.

HTH,
Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 I made Lyx find texlive 2011 binaries, by runnning it from the command
 prompt. Nonetheless, the problem is still there:
 
 [0] Config.pm:253 INFO - This is biber 0.9.4
 [0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:112 INFO - === Fri Aug 26, 2011, 14:51:50
 [56] Biber.pm:197 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?
 
 Ideas? Thanks in advance.

What is your biblatex version? (Look in the log file, it is well possible that 
an older version from texlive 2009 is used, unless you have adjusted the path 
settings).

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Paths updated. Compiling with bibtex everything is fine. Version shown:

This is 8-bit Big BibTeX version 0.99d

Biber, same error. Maybe some permission problem as to where this .bcf
file is created?

Thx Jürgen.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 3:08 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 I made Lyx find texlive 2011 binaries, by runnning it from the command
 prompt. Nonetheless, the problem is still there:

 [0] Config.pm:253 INFO - This is biber 0.9.4
 [0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:112 INFO - === Fri Aug 26, 2011, 14:51:50
 [56] Biber.pm:197 FATAL - Cannot find control file
 'Tesis_Maestro.bcf'! - did you pass the backend=biber option to
 BibLaTeX?

 Ideas? Thanks in advance.

 What is your biblatex version? (Look in the log file, it is well possible that
 an older version from texlive 2009 is used, unless you have adjusted the path
 settings).

 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 Paths updated. Compiling with bibtex everything is fine. Version shown:
 
 This is 8-bit Big BibTeX version 0.99d
 
 Biber, same error. Maybe some permission problem as to where this .bcf
 file is created?

Again: what biblatex version does your LaTeX log file report? 
Also, what does
kpsewhich biblatex.sty
return?

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Sorry Jürgen, I misread your question.

/usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
Package: biblatex 2011/07/29 v1.6 programmable bibliographies

It seems ok.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 3:44 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 Paths updated. Compiling with bibtex everything is fine. Version shown:

 This is 8-bit Big BibTeX version 0.99d

 Biber, same error. Maybe some permission problem as to where this .bcf
 file is created?

 Again: what biblatex version does your LaTeX log file report?
 Also, what does
 kpsewhich biblatex.sty
 return?

 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
 Package: biblatex 2011/07/29 v1.6 programmable bibliographies
 
 It seems ok.

Yes, it seems OK.

Now let's clarify if the basic settings are correct:

First, did you really pass the option backend=biber to biblatex?

Then, please tell us how you set up biber. Did you specify any options or just 
select biber from the dropdown list?

Also, posting the whole LaTeX log file might shed some light on things.

Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
 Julio Rojas wrote:
  I removed the version of biber I had previously installed.
  
  jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
  biber version: 0.9.4
  
  But Lyx is still looking for textlive 2009 (which is also installed).
  Do you know how can I make it to look at texlive 2011 (yes, I
  reconfigured several times after installation)?
 
 I suppose you have to adjust your path settings. In your local profile file
 (~/.profile most probably), add the following (if the file does not exist
 yet, create it):

This is not  sufficient. With this, the path is set only for programs called 
from the command line.
To make it available to the desktop you should consider to edit 
~/.pam_environment (Create it, if not already there)

The syntax is simple a list of shell-variables you want to set. Like this:
PATH 
OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin:/usr/sbin:/sbin:/bin:/usr/bin/X11:.

 #
 # Set some environment variables for TeX/LaTeX
 #
 export TEXMFCNF=/usr/local/texlive/2011/texmf/web2c:$TEXMFCNF
 export PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH
 
 After relogin, LyX should find the right binaries. See also sec. 3.4.1 of
 the texlive manual:
 http://www.tug.org/texlive/doc/texlive-en/texlive-en.html
 
 I have created a symlink here from /usr/local/texlive/current to
 /usr/local/texlive/2011 and set all pathes to current instead of 2011. This
 way, I need only change the symlink after a distribution upgrade.

Good idea

 HTH,
 Jürgen

Kornel


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Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Kornel Benko wrote:
  I suppose you have to adjust your path settings. In your local profile
  file (~/.profile most probably), add the following (if the file does
  not exist
  yet, create it):
 This is not  sufficient. With this, the path is set only for programs called
 from the command line. To make it available to the desktop you should
 consider to edit ~/.pam_environment (Create it, if not already there)
 
 The syntax is simple a list of shell-variables you want to set. Like this:
 PATH
 OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin:/
 usr/sbin:/sbin:/bin:/usr/bin/X11:.

Sure? It works as I expect it here, also when calling LyX not from the cl.

Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 First, I just selected biber from the pulldown.

OK.

 Second, I have tried both, including and not including backend=biber in
 Document  Settings  Document Class  Custom
 and as well as in
 Document  Settings  Bibliography  Options

Both is wrong. You have to pass the option to biblatex directly with your 
package call, i.e.

\usepackage[...,backend=biber]{biblatex}

Please read the biblatex manual for details on how to load the package.

HTH,
Jürgen

 -
 Julio Rojas
 jcredbe...@gmail.com
 
 On Fri, Aug 26, 2011 at 4:01 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
  Julio Rojas wrote:
  /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
  Package: biblatex 2011/07/29 v1.6 programmable bibliographies
  
  It seems ok.
  
  Yes, it seems OK.
  
  Now let's clarify if the basic settings are correct:
  
  First, did you really pass the option backend=biber to biblatex?
  
  Then, please tell us how you set up biber. Did you specify any options
  or just select biber from the dropdown list?
  
  Also, posting the whole LaTeX log file might shed some light on things.
  
  Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
 Kornel Benko wrote:
   I suppose you have to adjust your path settings. In your local profile
   file (~/.profile most probably), add the following (if the file does
   not exist
  
   yet, create it):
  This is not  sufficient. With this, the path is set only for programs
  called from the command line. To make it available to the desktop you
  should consider to edit ~/.pam_environment (Create it, if not already
  there)
  
  The syntax is simple a list of shell-variables you want to set. Like this:
  PATH
  
  OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin
  :/ usr/sbin:/sbin:/bin:/usr/bin/X11:.
 
 Sure? It works as I expect it here, also when calling LyX not from the cl.
 
 Jürgen

At least some desktopts are starting, without reading ~/.profile first. (If 
you start lyx through a shell-script, then of course
you read .profile)

Kornel


signature.asc
Description: This is a digitally signed message part.

Re: Biber

2011-08-26 Thread Julio Rojas 
RTFM! Well, I added the option, and biber is running:

[0] Config.pm:253 INFO - This is biber 0.9.4
[0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
[1] biber:112 INFO - === Fri Aug 26, 2011, 16:55:40
[1] Biber.pm:304 INFO - Reading 'Tesis_Maestro.bcf'
[66] Biber.pm:606 INFO - Found 140 citekeys in bib section 0
[157] Biber.pm:2466 INFO - Processing bib section 0
[172] Biber.pm:2555 INFO - Looking for bibtex format file
'/home/jcredberry/Dropbox/Sulan/BD_tesis.bib' for section 0
[172] bibtex.pm:104 INFO - Found bibtex data file
'/home/jcredberry/Dropbox/Sulan/BD_tesis.bib'

Still, no references are produced:

Package biblatex Warning: No reference sections found on input line 189.
LaTeX Warning: Empty bibliography on input line 189.
LaTeX Warning: Empty bibliography on input line 190.

Thx for all your effort!
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 4:38 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Julio Rojas wrote:
 First, I just selected biber from the pulldown.

 OK.

 Second, I have tried both, including and not including backend=biber in
 Document  Settings  Document Class  Custom
 and as well as in
 Document  Settings  Bibliography  Options

 Both is wrong. You have to pass the option to biblatex directly with your
 package call, i.e.

 \usepackage[...,backend=biber]{biblatex}

 Please read the biblatex manual for details on how to load the package.

 HTH,
 Jürgen

 -
 Julio Rojas
 jcredbe...@gmail.com

 On Fri, Aug 26, 2011 at 4:01 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
  Julio Rojas wrote:
  /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
  Package: biblatex 2011/07/29 v1.6 programmable bibliographies
 
  It seems ok.
 
  Yes, it seems OK.
 
  Now let's clarify if the basic settings are correct:
 
  First, did you really pass the option backend=biber to biblatex?
 
  Then, please tell us how you set up biber. Did you specify any options
  or just select biber from the dropdown list?
 
  Also, posting the whole LaTeX log file might shed some light on things.
 
  Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 RTFM! Well, I added the option, and biber is running:
 
 [0] Config.pm:253 INFO - This is biber 0.9.4
 [0] Config.pm:256 INFO - Logfile is 'Tesis_Maestro.blg'
 [1] biber:112 INFO - === Fri Aug 26, 2011, 16:55:40
 [1] Biber.pm:304 INFO - Reading 'Tesis_Maestro.bcf'
 [66] Biber.pm:606 INFO - Found 140 citekeys in bib section 0
 [157] Biber.pm:2466 INFO - Processing bib section 0
 [172] Biber.pm:2555 INFO - Looking for bibtex format file
 '/home/jcredberry/Dropbox/Sulan/BD_tesis.bib' for section 0
 [172] bibtex.pm:104 INFO - Found bibtex data file
 '/home/jcredberry/Dropbox/Sulan/BD_tesis.bib'
 
 Still, no references are produced:
 
 Package biblatex Warning: No reference sections found on input line 189.
 LaTeX Warning: Empty bibliography on input line 189.
 LaTeX Warning: Empty bibliography on input line 190.
 
 Thx for all your effort!

Can you set up a minimal example file (including the bib file)? Something else 
in your setup must be wrong.

Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Kornel Benko wrote:
 At least some desktopts are starting, without reading ~/.profile first.
 (If you start lyx through a shell-script, then of course you read .profile)

I see. Then it just happens to work here (KDE 4.7, openSuse 11.4).

Frankly, I never heard of the .pam_environment file before, but you are the 
expert.

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Small example working perfectly with biber. Even with the same
preamble and configuration (a parent file and a lorem ipsum child
file). The only change is a reduced bib file with some selected
entries. Maybe some problem processing the bib file itself?

Regards.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 5:49 PM, Jürgen Spitzmüller sp...@lyx.org wrote:
 Kornel Benko wrote:
 At least some desktopts are starting, without reading ~/.profile first.
 (If you start lyx through a shell-script, then of course you read .profile)

 I see. Then it just happens to work here (KDE 4.7, openSuse 11.4).

 Frankly, I never heard of the .pam_environment file before, but you are the
 expert.

 Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
 Small example working perfectly with biber. Even with the same
 preamble and configuration (a parent file and a lorem ipsum child
 file). The only change is a reduced bib file with some selected
 entries. Maybe some problem processing the bib file itself?

Maybe. Try to sort that out by checking which entries are the culprit. A thing 
that comes to mind is encoding. Which encoding does the bib file have? If it 
differs from the encoding of the document (as set via inputenc), you have to 
declare that via the bibencoding option, e.g.

\usepackage{...,bibencoding=latin9,backend=biber]{biblatex}

Again, please refer to the biblatex manual for details.

Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
 Kornel Benko wrote:
  At least some desktopts are starting, without reading ~/.profile first.
  (If you start lyx through a shell-script, then of course you read
  .profile)
 
 I see. Then it just happens to work here (KDE 4.7, openSuse 11.4).
 
 Frankly, I never heard of the .pam_environment file before, but you are the
 expert.
 
 Jürgen

Kde starts as sh /usr/bin/startkde or such, that may work. Since I am working 
with csh, I never created
.profile. My .login and .cshrc were ignored if started from desktop. It 
took a while to discover .pam_environment file.

See 6.6.6 FILES, User specific environment file in

http://www.kernel.org/pub/linux/libs/pam/Linux-PAM-html/Linux-PAM_SAG.html

Kornel


signature.asc
Description: This is a digitally signed message part.

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
> Dear all. I want to try biber on Ubuntu Natty. I installed it both as
> an standalone package with TexLive 2009 and included in Texlive 2011.
> In both cases I get the following error while compiling a document:
> 
> [0] Config.pm:254> INFO - This is biber 0.9.5
> [0] Config.pm:257> INFO - Logfile is 'Tesis_Maestro.blg'
> [1] biber:108> INFO - === Thu Aug 25, 2011, 18:48:31
> [35] Biber.pm:198> FATAL - Cannot find control file
> 'Tesis_Maestro.bcf'! - did you pass the "backend=biber" option to
> BibLaTeX?
> 
> I have already included "\typeout{File: \jobname.bcf}" in the preamble
> as suggested by the wiki. I have also defined biber as the
> bibliographic engine in both, the document and lyx.  Any ideas?

biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with 
that rsion as well? (It might be that the newer biber version is incompatible 
with your biblatex version, or it might be a bug in this version).

HTH,
Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
I removed the version of biber I had previously installed.

jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
biber version: 0.9.4

But Lyx is still looking for textlive 2009 (which is also installed).
Do you know how can I make it to look at texlive 2011 (yes, I
reconfigured several times after installation)?

Regards.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 11:50 AM, Jürgen Spitzmüller  wrote:
> Julio Rojas wrote:
>> Dear all. I want to try biber on Ubuntu Natty. I installed it both as
>> an standalone package with TexLive 2009 and included in Texlive 2011.
>> In both cases I get the following error while compiling a document:
>>
>> [0] Config.pm:254> INFO - This is biber 0.9.5
>> [0] Config.pm:257> INFO - Logfile is 'Tesis_Maestro.blg'
>> [1] biber:108> INFO - === Thu Aug 25, 2011, 18:48:31
>> [35] Biber.pm:198> FATAL - Cannot find control file
>> 'Tesis_Maestro.bcf'! - did you pass the "backend=biber" option to
>> BibLaTeX?
>>
>> I have already included "\typeout{File: \jobname.bcf}" in the preamble
>> as suggested by the wiki. I have also defined biber as the
>> bibliographic engine in both, the document and lyx.  Any ideas?
>
> biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with
> that rsion as well? (It might be that the newer biber version is incompatible
> with your biblatex version, or it might be a bug in this version).
>
> HTH,
> Jürgen
>

Re: Biber

2011-08-26 Thread Julio Rojas 
I made Lyx find texlive 2011 binaries, by runnning it from the command
prompt. Nonetheless, the problem is still there:

[0] Config.pm:253> INFO - This is biber 0.9.4
[0] Config.pm:256> INFO - Logfile is 'Tesis_Maestro.blg'
[1] biber:112> INFO - === Fri Aug 26, 2011, 14:51:50
[56] Biber.pm:197> FATAL - Cannot find control file
'Tesis_Maestro.bcf'! - did you pass the "backend=biber" option to
BibLaTeX?

Ideas? Thanks in advance.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 2:48 PM, Julio Rojas  wrote:
> I removed the version of biber I had previously installed.
>
> jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
> biber version: 0.9.4
>
> But Lyx is still looking for textlive 2009 (which is also installed).
> Do you know how can I make it to look at texlive 2011 (yes, I
> reconfigured several times after installation)?
>
> Regards.
> -
> Julio Rojas
> jcredbe...@gmail.com
>
>
>
> On Fri, Aug 26, 2011 at 11:50 AM, Jürgen Spitzmüller  wrote:
>> Julio Rojas wrote:
>>> Dear all. I want to try biber on Ubuntu Natty. I installed it both as
>>> an standalone package with TexLive 2009 and included in Texlive 2011.
>>> In both cases I get the following error while compiling a document:
>>>
>>> [0] Config.pm:254> INFO - This is biber 0.9.5
>>> [0] Config.pm:257> INFO - Logfile is 'Tesis_Maestro.blg'
>>> [1] biber:108> INFO - === Thu Aug 25, 2011, 18:48:31
>>> [35] Biber.pm:198> FATAL - Cannot find control file
>>> 'Tesis_Maestro.bcf'! - did you pass the "backend=biber" option to
>>> BibLaTeX?
>>>
>>> I have already included "\typeout{File: \jobname.bcf}" in the preamble
>>> as suggested by the wiki. I have also defined biber as the
>>> bibliographic engine in both, the document and lyx.  Any ideas?
>>
>> biber 0.9.5 is very recent. TeXLive 2011 still has 0.9.4. Did you try with
>> that rsion as well? (It might be that the newer biber version is incompatible
>> with your biblatex version, or it might be a bug in this version).
>>
>> HTH,
>> Jürgen
>>
>

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
> I removed the version of biber I had previously installed.
> 
> jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
> biber version: 0.9.4
> 
> But Lyx is still looking for textlive 2009 (which is also installed).
> Do you know how can I make it to look at texlive 2011 (yes, I
> reconfigured several times after installation)?

I suppose you have to adjust your path settings. In your local profile file 
(~/.profile most probably), add the following (if the file does not exist yet, 
create it):

#
# Set some environment variables for TeX/LaTeX
#
export TEXMFCNF=/usr/local/texlive/2011/texmf/web2c:$TEXMFCNF
export PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH

After relogin, LyX should find the right binaries. See also sec. 3.4.1 of the 
texlive manual:
http://www.tug.org/texlive/doc/texlive-en/texlive-en.html

I have created a symlink here from /usr/local/texlive/current to 
/usr/local/texlive/2011 and set all pathes to current instead of 2011. This 
way, I need only change the symlink after a distribution upgrade.

HTH,
Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
> I made Lyx find texlive 2011 binaries, by runnning it from the command
> prompt. Nonetheless, the problem is still there:
> 
> [0] Config.pm:253> INFO - This is biber 0.9.4
> [0] Config.pm:256> INFO - Logfile is 'Tesis_Maestro.blg'
> [1] biber:112> INFO - === Fri Aug 26, 2011, 14:51:50
> [56] Biber.pm:197> FATAL - Cannot find control file
> 'Tesis_Maestro.bcf'! - did you pass the "backend=biber" option to
> BibLaTeX?
> 
> Ideas? Thanks in advance.

What is your biblatex version? (Look in the log file, it is well possible that 
an older version from texlive 2009 is used, unless you have adjusted the path 
settings).

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Paths updated. Compiling with bibtex everything is fine. Version shown:

This is 8-bit Big BibTeX version 0.99d

Biber, same error. Maybe some permission problem as to where this .bcf
file is created?

Thx Jürgen.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 3:08 PM, Jürgen Spitzmüller  wrote:
> Julio Rojas wrote:
>> I made Lyx find texlive 2011 binaries, by runnning it from the command
>> prompt. Nonetheless, the problem is still there:
>>
>> [0] Config.pm:253> INFO - This is biber 0.9.4
>> [0] Config.pm:256> INFO - Logfile is 'Tesis_Maestro.blg'
>> [1] biber:112> INFO - === Fri Aug 26, 2011, 14:51:50
>> [56] Biber.pm:197> FATAL - Cannot find control file
>> 'Tesis_Maestro.bcf'! - did you pass the "backend=biber" option to
>> BibLaTeX?
>>
>> Ideas? Thanks in advance.
>
> What is your biblatex version? (Look in the log file, it is well possible that
> an older version from texlive 2009 is used, unless you have adjusted the path
> settings).
>
> Jürgen
>

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
> Paths updated. Compiling with bibtex everything is fine. Version shown:
> 
> This is 8-bit Big BibTeX version 0.99d
> 
> Biber, same error. Maybe some permission problem as to where this .bcf
> file is created?

Again: what biblatex version does your LaTeX log file report? 
Also, what does
kpsewhich biblatex.sty
return?

Jürgen

Re: Biber

2011-08-26 Thread Julio Rojas 
Sorry Jürgen, I misread your question.

/usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
Package: biblatex 2011/07/29 v1.6 programmable bibliographies

It seems ok.
-
Julio Rojas
jcredbe...@gmail.com



On Fri, Aug 26, 2011 at 3:44 PM, Jürgen Spitzmüller  wrote:
> Julio Rojas wrote:
>> Paths updated. Compiling with bibtex everything is fine. Version shown:
>>
>> This is 8-bit Big BibTeX version 0.99d
>>
>> Biber, same error. Maybe some permission problem as to where this .bcf
>> file is created?
>
> Again: what biblatex version does your LaTeX log file report?
> Also, what does
> kpsewhich biblatex.sty
> return?
>
> Jürgen
>

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
> /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
> Package: biblatex 2011/07/29 v1.6 programmable bibliographies
> 
> It seems ok.

Yes, it seems OK.

Now let's clarify if the basic settings are correct:

First, did you really pass the option backend=biber to biblatex?

Then, please tell us how you set up biber. Did you specify any options or just 
select biber from the dropdown list?

Also, posting the whole LaTeX log file might shed some light on things.

Jürgen

Re: Biber

2011-08-26 Thread Kornel Benko 
Am Freitag, 26. August 2011 schrieb Jürgen Spitzmüller:
> Julio Rojas wrote:
> > I removed the version of biber I had previously installed.
> > 
> > jcredberry@2e14-200305:/usr/local/texlive/2011/texmf/tex/latex$ biber -v
> > biber version: 0.9.4
> > 
> > But Lyx is still looking for textlive 2009 (which is also installed).
> > Do you know how can I make it to look at texlive 2011 (yes, I
> > reconfigured several times after installation)?
> 
> I suppose you have to adjust your path settings. In your local profile file
> (~/.profile most probably), add the following (if the file does not exist
> yet, create it):

This is not  sufficient. With this, the path is set only for programs called 
from the command line.
To make it available to the desktop you should consider to edit 
"~/.pam_environment" (Create it, if not already there)

The syntax is simple a list of shell-variables you want to set. Like this:
PATH 
OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin:/usr/sbin:/sbin:/bin:/usr/bin/X11:.

> #
> # Set some environment variables for TeX/LaTeX
> #
> export TEXMFCNF=/usr/local/texlive/2011/texmf/web2c:$TEXMFCNF
> export PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH
> 
> After relogin, LyX should find the right binaries. See also sec. 3.4.1 of
> the texlive manual:
> http://www.tug.org/texlive/doc/texlive-en/texlive-en.html
> 
> I have created a symlink here from /usr/local/texlive/current to
> /usr/local/texlive/2011 and set all pathes to current instead of 2011. This
> way, I need only change the symlink after a distribution upgrade.

Good idea

> HTH,
> Jürgen

Kornel


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Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Kornel Benko wrote:
> > I suppose you have to adjust your path settings. In your local profile
> > file (~/.profile most probably), add the following (if the file does
> > not exist
> > yet, create it):
> This is not  sufficient. With this, the path is set only for programs called
> from the command line. To make it available to the desktop you should
> consider to edit "~/.pam_environment" (Create it, if not already there)
> 
> The syntax is simple a list of shell-variables you want to set. Like this:
> PATH
> OVERRIDE=/usr/local/bin:/usr/local/texlive/2011/bin/x86_64-linux:/usr/bin:/
> usr/sbin:/sbin:/bin:/usr/bin/X11:.

Sure? It works as I expect it here, also when calling LyX not from the cl.

Jürgen

Re: Biber

2011-08-26 Thread Jürgen Spitzmüller 
Julio Rojas wrote:
> First, I just selected biber from the pulldown.

OK.

> Second, I have tried both, including and not including "backend=biber" in
> Document > Settings > Document Class > Custom
> and as well as in
> Document > Settings > Bibliography > Options

Both is wrong. You have to pass the option to biblatex directly with your 
package call, i.e.

\usepackage[...,backend=biber]{biblatex}

Please read the biblatex manual for details on how to load the package.

HTH,
Jürgen

> -
> Julio Rojas
> jcredbe...@gmail.com
> 
> On Fri, Aug 26, 2011 at 4:01 PM, Jürgen Spitzmüller  wrote:
> > Julio Rojas wrote:
> >> /usr/local/texlive/2011/texmf-dist/tex/latex/biblatex/biblatex.sty
> >> Package: biblatex 2011/07/29 v1.6 programmable bibliographies
> >> 
> >> It seems ok.
> > 
> > Yes, it seems OK.
> > 
> > Now let's clarify if the basic settings are correct:
> > 
> > First, did you really pass the option backend=biber to biblatex?
> > 
> > Then, please tell us how you set up biber. Did you specify any options
> > or just select biber from the dropdown list?
> > 
> > Also, posting the whole LaTeX log file might shed some light on things.
> > 
> > Jürgen

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