Re: missing glyphs error

[Scott Kostyshak]

On Fri, Feb 09, 2018 at 02:52:52AM +, Richard Opheim wrote:
> Hello users.
> I can't use certain Chinese characters such as 嗩吶 or 唢呐 in a lyx document.
> I wonder why that is.
> Please see attached example.
> Running Windows 10 LyX 2.2.3 Memoir

Hi Richard,

You need to use a font that has those characters. After changing the
font to "WenQuanYi Micro Hei" in Document > Settings > Fonts, your
document yields the attached PDF.

Scott


WenQuanYi.pdf
Description: Adobe PDF document


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missing glyphs error

[Richard Opheim]

Hello users.
I can't use certain Chinese characters such as 嗩吶 or 唢呐 in a lyx document.
I wonder why that is.
Please see attached example.
Running Windows 10 LyX 2.2.3 Memoir


Richard Opheim
PO box 2261
Arizona City, AZ 85123

Skype name: richard.opheim
Tel: 206-965-0564

Books published 
Editing 
J-E Translation

Self-publishing 

Now available on Amazon: *The Taste of Kyoto: A Guide to Dining and
Sightseeing in the Old Capital

*by
Richard Opheim


missing glyphs.lyx
Description: Binary data

Re: BibTeX issue: journal name not seen by LyX

[Paul A Rubin]

On 02/08/2018 11:34 AM, Rich Shepard wrote:


  Same here. Exporting to LaTeX(pdflatex) has this line:
\citep{Helsel2005b,Helsel2006,Helsel2009}.

  There's no .bib file exported with the .tex file.
There wouldn't be. The JabRef database is the .bib file, and you linked 
to it in the bibliography definition. LyX doesn't need to export it; 
like image files, it's considered to be already there.



 I still have to set up the BibTeX bibliography in the LyX document as
usual. The problem isn't with the citation, it's with the bibliography
entry. Assuming you are indeed using bibtex and not biblatex, it 
sounds as
if thek .bib file somehow got generated using biblatex syntax (or a 
mix?).


  Documents -> Settings -> Bibliography: Citation style is natbib,
Biblography style is plain, Biblography generation is set to bibtex 
with no

options.
It would be JabRef, not LyX, that would be set to use biblatex (which, 
you say below,it ain't).


  At the end of the document the bibliography settings show the 
correct (and

only) database with authordate4 as the style and the content set to all
cited references.

The only one saying "journaltitle", or the only one that won't 
publish (meaning there are others with "journaltitle" that are working)?


  Despite JabRef being set to 'bibtex' _all_ journal entries show
'journaltitle' in the Required Fields tab. At one point they all showed
'journal.'
Okay, I might have a partial handle on this. I just did a little 
experiment, using JabRef 2.10. The starting point was a .bib file in 
BibTeX format, meaning all journal titles were labeled "Journal = ...". 
I switched JabRef to biblatex (in advanced options), forcing a restart. 
The .bib file was untouched (all entries still used "Journal"). I added 
a new entry and saved the file. That entry used "Journaltitle"; the 
others were unchanged. Switch JabRef back to BibTeX, restarted and 
reloaded the database. No change (the new entry was still 
"Journaltitle", the others still "Journal"), but in the JabRef edit 
window the new entry had an empty Journal field. The "Journaltitle" 
field shows up in the BibTeX Source tab, but not in any of the other 
tabs ("Required fields", "Optional fields", "General", "Abstract" or 
"Review"). I think this is because biblatex translates "journal" to 
"journaltitle" but bibtex does not recognize"journaltitle".


So my guess is your problem child article (and maybe some others) were 
entered when JabRef was in biblatex mode. Once they're in the database, 
mode switches do not change them. I have not seen any indication of a 
tool (either in JabRef or external) for unscrewing this, so my guess is 
you'll need to open the .bib database in a text editor and do it the old 
fashioned way.


Paul

Re: BibTeX issue: journal name not seen by LyX [RESOLVED]

[Rich Shepard]

On Thu, 8 Feb 2018, Cris Fuhrman wrote:


  2. Copy all the entries from the existing "biblatex" library and paste
  them in the library created above.


Cris,

  This was not necessary but you pointed me to the problem ... now fixed.
Thanks very much!

  The one place I did not check was the jabrefdb.bib file. Opening that in
emacs I saw that the problem Helsel references had an entry for
'journaltitle' (the biblatex syntax), but other @Article entries displayed
the bibtex syntax of 'journal'. So, a quick global search-and-replace set
all @Article entries to 'journal,' 65 out of 620 entries of that type.

  Closed JabRef, re-opened it, processed the three Helsel citations from
JabRef to LyX et voila! All's well once again.

  How these 65 records were changed shall probably always remain a mystery.
But, it's a good lesson learned so I can fix the problem should it ever
arise again.

  My thanks to all of you: Scott, Juergen, Paul, and Cris.

Best regards,

Rich

Re: BibTeX issue: journal name not seen by LyX

[Jürgen Spitzmüller]

Am Donnerstag, den 08.02.2018, 08:35 -0800 schrieb Rich Shepard:
>   2.2.3 as of May 17, 2017.

Then it should work. Please check if you have an old stdciteformats.inc
file in your ~./lyx/layouts directory, and if so, remove that.

Jürgen

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Re: BibTeX issue: journal name not seen by LyX

[Cris Fuhrman]

>  I use bibtex and that's the way both JabRef and LyX are configured.
> Yes, so does version 3.8.2 that I use and none of the 'quality' checks do
anything.

The Check Integrity function I use is in JabRef 4.1 (the latest).

I'd suggest making sure your bibtex file is 100% bibtex as follows:

   1. In JabRef, create a new "bibtex" library.
   2. Copy all the entries from the existing "biblatex" library and paste
   them in the library created above.
   3. Run "Quality > Check Integrity" and resolve any "biblatex field only"
   issues.
   4. Save the library as the converted "bibtex" library.

Cheers,

C. Fuhrman

On Thu, Feb 8, 2018 at 10:52 AM, Rich Shepard 
wrote:

> On Thu, 8 Feb 2018, Cris Fuhrman wrote:
>
> If your JabRef format is biblatex, are you using LyX appropriately?
>> https://wiki.lyx.org/BibTeX/Biblatex
>>
>
> Chris,
>
>   No. I use bibtex and that's the way both JabRef and LyX are configured.
>
>  Otherwise, make sure you've updated to the latest Jabref.
>>
>
>   I cannot do this because it requires openjfx and that's available for
> only 64-bit processors. My desktop has a 32-bit CPU and this issue has come
> up only in this document and with references (now 2) from only a single
> author.
>
> It has some tools to validate the bib(la)tex files (Menu Quality > Check
>> Integrity, and Menu Quality > Cleanup entries > Convert to biblatex), etc.
>>
>
>   Yes, so does version 3.8.2 that I use and none of the 'quality' checks do
> anything.
>
> But beware of the many warnings about small things like non-standard
>> author formatting which doesn't matter (the integrity check can produce a
>> lot of noise). I had a problem once with a badly encoded accented
>> character in the .bib file that caused LyX to just not finish; it took me
>> hours to find it (before I knew that Jabref had those tools).
>>
>
>   I've checked each journal title field for unprintable characters and
> re-written them but nothing makes a difference.
>
> Rich
>

Re: BibTeX issue: journal name not seen by LyX

[Rich Shepard]

On Thu, 8 Feb 2018, Jürgen Spitzmüller wrote:


Which version of LyX is this? The journaltitle field is parsed by LyX as
of LyX 2.2.3. Earlier versions of LyX do not handle genuine biblatex
fields for the preview.


Jürgen,

  2.2.3 as of May 17, 2017.

Rich

Re: BibTeX issue: journal name not seen by LyX

[Rich Shepard]

On Thu, 8 Feb 2018, Paul A. Rubin wrote:


On my system, at least, the JabRef toolbar button just pushes the \cite{}
command into the LyX document at the current cursor location.


Paul,

  Same here. Exporting to LaTeX(pdflatex) has this line:
\citep{Helsel2005b,Helsel2006,Helsel2009}.

  There's no .bib file exported with the .tex file.


 I still have to set up the BibTeX bibliography in the LyX document as
usual. The problem isn't with the citation, it's with the bibliography
entry. Assuming you are indeed using bibtex and not biblatex, it sounds as
if thek .bib file somehow got generated using biblatex syntax (or a mix?).


  Documents -> Settings -> Bibliography: Citation style is natbib,
Biblography style is plain, Biblography generation is set to bibtex with no
options.

  At the end of the document the bibliography settings show the correct (and
only) database with authordate4 as the style and the content set to all
cited references.

The only one saying "journaltitle", or the only one that won't publish 
(meaning there are others with "journaltitle" that are working)?


  Despite JabRef being set to 'bibtex' _all_ journal entries show
'journaltitle' in the Required Fields tab. At one point they all showed
'journal.'

  Regardless, it was only the Helsel2006 entry that barfed, now it's both
2005b and 2006. The 2009 entry, and those of all others have the journal
title in the bibliography listing. This is why none of this makes any sense
to me.

Ah, but you'd be robbing some poor author of a citation (which we academics 
cherish). ;-)


  Yeah, but he's retired from the USGS now.

  Want more information? Ask.

Thanks,

Rich

Re: BibTeX issue: journal name not seen by LyX

[Jürgen Spitzmüller]

Am Donnerstag, den 08.02.2018, 07:59 -0800 schrieb Rich Shepard:
> What I'm trying to understand is why it's not shown in the
> lyx document. 

Which version of LyX is this? The journaltitle field is parsed by LyX
as of LyX 2.2.3. Earlier versions of LyX do not handle genuine biblatex
fields for the preview.

Jürgen

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Re: BibTeX issue: journal name not seen by LyX

[Rich Shepard]

On Thu, 8 Feb 2018, Rich Shepard wrote:


 I've checked each journal title field for unprintable characters and
re-written them but nothing makes a difference.


  Allow me to re-interate the problem. JabRef's bibtex entry for one of the
(now 2) problem references is:

@Article{Helsel2006,
  author   = {Helsel, D.R.},
  title= {Fabricating data: How substituting values for nondetects can 
ruin results, and what can be done about it},
  journaltitle = {Chemosphere},
  year = {2006},
  volume   = {65},
  pages= {2434--2439},

Regardless of the term 'journaltitle' or 'journal' the name is there within
brackets. What I'm trying to understand is why it's not shown in the lyx
document. Is this lyx or jabref? Again, this is the first time I've
encountered this issue and I've used these citations before with no
problems.

  JabRef is set to use ~/.lyx/lyxpipe and these exist as:

$ ll lyxpipe*
-rw-r--r-- 1 rshepard users 0 Sep 25  2013 lyxpipe
prw--- 1 rshepard users 0 Feb  8 07:47 lyxpipe.in|
prw--- 1 rshepard users 0 Feb  8 07:47 lyxpipe.out|

  All the other citations produce references with journal titles and I've
re-written these two multiple times. I'm frustrated that nothing seems amiss
yet I cannot fix this problem.

Rich

Re: BibTeX issue: journal name not seen by LyX

[Paul A. Rubin]

Rich,

On 02/08/2018 10:18 AM, Rich Shepard wrote:


Paul,

  If I remember correctly, 'journaltitle' is used with biblatex and
'journal' _should_ be used with bibtex.

Sounds correct to me.



Assuming you've exported your bibliography to a .bib file, try doing a
global search and replace to change all instances of "journaltitle" to
"journal", then see if the document compiles correctly.


  JabRef has a function (enabled by clicking on an icon) that inserts the
selected reference in the LyX document where the cursor is positioned. No
human action required.
On my system, at least, the JabRef toolbar button just pushes the 
\cite{} command into the LyX document at the current cursor location. I 
still have to set up the BibTeX bibliography in the LyX document as 
usual. The problem isn't with the citation, it's with the bibliography 
entry. Assuming you are indeed using bibtex and not biblatex, it sounds 
as if the .bib file somehow got generated using biblatex syntax (or a mix?).


  The frustrating point is that this is the only reference with this 
issue.
There are a dozen or so other references in this document, a couple of 
books
and the rest journal articles, and it is only this one that has the 
problem.
The only one saying "journaltitle", or the only one that won't publish 
(meaning there are others with "journaltitle" that are working)?


  If I can't fix it I'll just drop this one reference; the other two
certainly support the point I'm making.
Ah, but you'd be robbing some poor author of a citation (which we 
academics cherish). ;-)


Paul

Re: BibTeX issue: journal name not seen by LyX

[Rich Shepard]

On Thu, 8 Feb 2018, Cris Fuhrman wrote:


If your JabRef format is biblatex, are you using LyX appropriately?
https://wiki.lyx.org/BibTeX/Biblatex


Chris,

  No. I use bibtex and that's the way both JabRef and LyX are configured.


 Otherwise, make sure you've updated to the latest Jabref.


  I cannot do this because it requires openjfx and that's available for
only 64-bit processors. My desktop has a 32-bit CPU and this issue has come
up only in this document and with references (now 2) from only a single
author.


It has some tools to validate the bib(la)tex files (Menu Quality > Check
Integrity, and Menu Quality > Cleanup entries > Convert to biblatex), etc.


  Yes, so does version 3.8.2 that I use and none of the 'quality' checks do
anything.


But beware of the many warnings about small things like non-standard
author formatting which doesn't matter (the integrity check can produce a
lot of noise). I had a problem once with a badly encoded accented
character in the .bib file that caused LyX to just not finish; it took me
hours to find it (before I knew that Jabref had those tools).


  I've checked each journal title field for unprintable characters and
re-written them but nothing makes a difference.

Rich

Re: BibTeX issue: journal name not seen by LyX

[Cris Fuhrman]

Hi Rich,

If your JabRef format is biblatex, are you using LyX appropriately?
https://wiki.lyx.org/BibTeX/Biblatex

Otherwise, make sure you've updated to the latest Jabref. It has some tools
to validate the bib(la)tex files (Menu Quality > Check Integrity, and Menu
Quality >  Cleanup entries > Convert to biblatex), etc. But beware of the
many warnings about small things like non-standard author formatting which
doesn't matter (the integrity check can produce a lot of noise). I had a
problem once with a badly encoded accented character in the .bib file that
caused LyX to just not finish; it took me hours to find it (before I knew
that Jabref had those tools).

Cheers,

C. Fuhrman

On Thu, Feb 8, 2018 at 8:37 AM, Rich Shepard 
wrote:

> On Thu, 8 Feb 2018, Scott Kostyshak wrote:
>
>   journaltitle = {Chemosphere},
>>>
>>
>> I know nothing about this, but should this be "journal = " ?
>>
>
> Scott,
>
>   I wondered about this, but JabRef is set for bibtex, not biblatex, and
> all
> articles, including the other two Helsel's in that series, have the same
> form for the journal's name.
>
> Thanks,
>
> Rich
>

Re: BibTeX issue: journal name not seen by LyX

[Rich Shepard]

On Thu, 8 Feb 2018, Paul A. Rubin wrote:


I'm with Scott on this. I just checked a couple of .bib files from old
papers. One used "Journal = {...}" and the other used "journal = {...}".
I'm not sure why the capitalization was different, but I've never seen
"journaltitle = {...}".


Paul,

  If I remember correctly, 'journaltitle' is used with biblatex and
'journal' _should_ be used with bibtex.


Assuming you've exported your bibliography to a .bib file, try doing a
global search and replace to change all instances of "journaltitle" to
"journal", then see if the document compiles correctly.


  JabRef has a function (enabled by clicking on an icon) that inserts the
selected reference in the LyX document where the cursor is positioned. No
human action required.

  The frustrating point is that this is the only reference with this issue.
There are a dozen or so other references in this document, a couple of books
and the rest journal articles, and it is only this one that has the problem.

  If I can't fix it I'll just drop this one reference; the other two
certainly support the point I'm making.

Thanks,

Rich

Re: BibTeX issue: journal name not seen by LyX

[Jürgen Spitzmüller]

Am Donnerstag, den 08.02.2018, 10:09 -0500 schrieb Paul A. Rubin:
> I'm with Scott on this. I just checked a couple of .bib files from
> old 
> papers. One used "Journal = {...}" and the other used "journal =
> {...}". 
> I'm not sure why the capitalization was different, but I've never
> seen 
> "journaltitle = {...}".

"journaltitle" is biblatex jargon (in biblatex, "journaltitle" and
"journal" are synonyms, but there is also "journalsubtitle").

Jürgen

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Re: BibTeX issue: journal name not seen by LyX

[Paul A. Rubin]

On 02/08/2018 08:37 AM, Rich Shepard wrote:

On Thu, 8 Feb 2018, Scott Kostyshak wrote:


  journaltitle = {Chemosphere},


I know nothing about this, but should this be "journal = " ?


Scott,

  I wondered about this, but JabRef is set for bibtex, not biblatex, 
and all

articles, including the other two Helsel's in that series, have the same
form for the journal's name.

Thanks,

Rich
I'm with Scott on this. I just checked a couple of .bib files from old 
papers. One used "Journal = {...}" and the other used "journal = {...}". 
I'm not sure why the capitalization was different, but I've never seen 
"journaltitle = {...}".


Assuming you've exported your bibliography to a .bib file, try doing a 
global search and replace to change all instances of "journaltitle" to 
"journal", then see if the document compiles correctly.


Paul

Re: BibTeX issue: journal name not seen by LyX

[Rich Shepard]

On Thu, 8 Feb 2018, Scott Kostyshak wrote:


  journaltitle = {Chemosphere},


I know nothing about this, but should this be "journal = " ?


Scott,

  I wondered about this, but JabRef is set for bibtex, not biblatex, and all
articles, including the other two Helsel's in that series, have the same
form for the journal's name.

Thanks,

Rich