Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

Rob Oakes lyx-de...@oak-tree.us writes:
 Just one thought, make sure that there is a copy of Sweave.sty installed
 in your LaTeX path (and make sure that LyX can find it).  I was having
 some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
 what ultimately fixed it.

Are you sure? It should not be necessary on 2.0. What is needed though
is to have R installed and available in the path. The module tests the
availability of a Rnwtex converter (aka R CMD Sweave).

JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Hi Rob!

Rob Oakes wrote:

Hi Ricardo,

Just one thought, make sure that there is a copy of Sweave.sty installed
in your LaTeX path (and make sure that LyX can find it).  I was having
some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
what ultimately fixed it.

  


Nope, it is not! In fact Sweave.sty is no where in the path. It seems it 
looks for R! R was not installed in this box! Shame on me! Once 
installed, LyX 2.0 no longer crashes while loading Sweave module.


Thanks for your help!



But, to be honest, I haven't really played with LyX 2.0 on my Mac
recently.  I've been on a book deadline and it just felt to unstable to
any real work.  On Linux, though, it's been very reliable.

  
I will keep an eye on new releases and maintain this experimental 
installation on the MacPro running Mac OS X 10.6.3 and at the same time 
keep running a stable a 1.6.5 release in a 10.5.8 MacBook Pro. I have 
not two available boxes with the same SO. Please, let me know if I can 
be of any further help to debug this or any other issue. Thanks!


Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Oops!

Jean-Marc LASGOUTTES wrote:

Rob Oakes lyx-de...@oak-tree.us writes:
  

Just one thought, make sure that there is a copy of Sweave.sty installed
in your LaTeX path (and make sure that LyX can find it).  I was having
some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
what ultimately fixed it.



Are you sure? It should not be necessary on 2.0. What is needed though
is to have R installed and available in the path. The module tests the
availability of a Rnwtex converter (aka R CMD Sweave).
  


Sorry, I replied to Rob's message before reading this one! That's what 
I've found here: Sweave.sty as is is not longer in the path and LyX 
looks for R libraries instead. Is it ok this interpretation? Thanks!


Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[lyx-devel]

Hi JMarc,

Reasonably sure.  I was having the problems back in November.  And there
were two separate issues.  The first was getting LyX 2 to work, the second
was related to getting R + Sweave to work.

The problems that eventually required Sweave.sty were related to getting
documents to compile correctly.  Without it, the compilation would simply
terminate with There was an R error or some such.  After placing
Sweave.sty in the tex path, this resolved itself.

But then, I haven't really spent much time working on the Mac since then. 
Problems with PyQt (related to work stuff) have forced me over to my Linux
laptop, and that's what I've mostly been working with for the last seven
months.

It wasn't till this morning that sat down again to take a look at the
problem.  About the same time that it was reported solved ;)

If I have any problems, I'll be sure to file a bug report/send an email to
the developer list.

Cheers,

Rob

 Rob Oakes lyx-de...@oak-tree.us writes:
 Just one thought, make sure that there is a copy of Sweave.sty installed
 in your LaTeX path (and make sure that LyX can find it).  I was having
 some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
 what ultimately fixed it.

 Are you sure? It should not be necessary on 2.0. What is needed though
 is to have R installed and available in the path. The module tests the
 availability of a Rnwtex converter (aka R CMD Sweave).

 JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

[Ricardo Rodriguez] eBioTIC. ricardo.rodrig...@ebiotic.net writes:
 Sorry, I replied to Rob's message before reading this one! That's what
 I've found here: Sweave.sty as is is not longer in the path and LyX
 looks for R libraries instead. Is it ok this interpretation? Thanks!

Yes. But still it should not crash...

JMarc

Re: Trouble viewing DVI

[Paul Rubin]

Dean Chandler chandler at vvm.com writes:

 
 Yes,  Ghostscript  Imagemagick are installed.
 
 Also, I have qt4-dev installed.
 
 The problem occurs both with Lyx 1.5.3, from the Ubuntu repository and 
 with 1.6.5, which I downloaded from lyx.org and compiled. There were no 
 errors in the compilation. Could I be missing some file converter?
 

Unlikely. LyX uses a Python script to convert image formats; the Python script
by default uses ImageMagick; and when the result is EPS, I believe IM uses
Ghostscript.

The telling thing, though, is that you are getting an error message from
lyx2lyx, which is used to convert .lyx files from one format to another. You say
the error message indicates it is trying to convert a PNG file each time?  That
should not happen.

Do you have an older version of LyX installed on this machine?  The best guess I
can come up with for lyx2lyx errors would be an old version of lyx2lyx trying to
convert Tutorial.lyx to an earlier document version and thinking somehow that
the PNG files were child documents that needed to be converted (???).

If you do have multiple versions of LyX installed, I would suggest uninstalling
the old one(s) and then reinstalling a recent one.

/Paul

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Hi!

lyx-de...@oak-tree.us wrote:

Hi JMarc,

Reasonably sure.  I was having the problems back in November.  And there
were two separate issues.  The first was getting LyX 2 to work, the second
was related to getting R + Sweave to work.

The problems that eventually required Sweave.sty were related to getting
documents to compile correctly.  Without it, the compilation would simply
terminate with There was an R error or some such.  After placing
Sweave.sty in the tex path, this resolved itself.
  


Being truth what I've said before and what JMarc said about LyX checking 
R availability to load Sweave module, I'm facing the same problem Rob 
describes when trying to compile a new document including S/R 
expressions. I will try to describe the situation:



*1.* A LyX 2.0.0 alpha2 installation crashes when trying to load Sweave 
module if R is not installed in the same box. In this case, I guess it 
will be advisable to trigger a warning saying that R is required instead 
of causing an exception that crashes LyX. I'm sure developers are 
consciences of this and the only problem here is time to make the 
required changes! :-)


*2. *Once R is installed, Sweave module loads without a glitch.

*3.* If I try to compile a new document including S/R expressions, 
compilation fails throwing the following error:


! LaTeX Error: File `Sweave.sty' not found.

Here the full stack to further reference:

http://xen.net/onLyX/lyxSweaveStyNotFound.html

As stated in a previous message, the LaTeX environment here was created 
as per...


http://www.tug.org/mactex/2009/
[ approximately 1.3G - 12 March 2010 ]
MacTeX-2009.mpkg
MacTeX.mpkg.zip

*4. *Until I copy Sweave.sty to the TeX path and reconfigure LyX, 
compilation fails.


I copied Sweave.sty from a older box with a running LyX 1.6.5/Sweave/R 
installation.


GMXUX-Ricardo-Rodriguez:~ rrodriguez$ kpsewhich Sweave.sty
/Users/rrodriguez/Library/texmf/tex/latex/R/Sweave.sty



Please, provided its module is loaded, must Sweave work out of the box 
in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I 
guess a warning will be required some where to avoid the problem we are 
facing here! Thanks!


Let me know if I can be of any further help!

Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

[Ricardo Rodriguez] eBioTIC. ricardo.rodrig...@ebiotic.net writes:
 *3.* If I try to compile a new document including S/R expressions,
 compilation fails throwing the following error:

 ! LaTeX Error: File `Sweave.sty' not found.

 Here the full stack to further reference:

 http://xen.net/onLyX/lyxSweaveStyNotFound.html
 Please, provided its module is loaded, must Sweave work out of the box
 in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I
 guess a warning will be required some where to avoid the problem we
 are facing here! Thanks!

It is expected (by me at least) that either:

1/ the installation of R installs Sweave.sty at the right place (was
MaxTeX already installed when you installed R?)

or

2/ Sweave is set up in such a way that it puts the full path to the
Sweave.sty file in the \usepackage command.

If neither of those two conditions are fulfilled, I think this is a bug
in the way R installs itself...

JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[Rob Oakes]

This is clearly either a problem in the way that R installs itself, or
the way that LaTeX installs itself.  I'm not actually sure which though
and I don't know where to file the bug report.

When I just checked, I was not able to find a sweave package for R,
nor was I able to find one for TeXLive 2009 (don't know about MikTeX).
But I've experienced a similar problem on Mac OS X and on Linux, which
provides some evidence that it's not getting packaged.

Because out of the box support for Sweave is one of LyX 2's newest (and
IMHO, killer) features, it might make sense to include a copy of
Sweave.sty with the installation script and have it installed at the
time of LyX configuration.  LyX already does this with a few specialty
document classes anyway (broadway, hollywood).

Cheers,

Rob

Order of Tables and Figures

[rob]

Hi,

How do I fix the order in which tables and figures 
appear at the end of my document?  My paper must 
conform to an ordering of text, references, tables/figures.  
The problem is that the default order of the tables and 
figures is not what I want.  I tried changing the settings 
for each float by specifying ignore latex rules and 
then bottom or top, depending on what seemed to be 
necessary to get it right, but this didn't work.  
Selecting here definitely only created chaos. 

Also, how can I specify a \pdfbookmark[1]{} after 
references (for my figures)?  I use these elsewhere in 
my doc, but they won't work after the references section. 

Thanks very much.

Re: Order of Tables and Figures

[Rob Oakes]

Hi Rob,

I'm not sure that I follow what you're trying to accomplish.  Do you
need your figures to appear in text, or do you need them to appear at
the end of your document after the references section?  (The way that
many biomedical journals specify an article must be submitted.)

And what do you mean, by the default order isn't what I want.
Typically figures are printed in the order that they appear in the
document.  If you are doing fancy things with wrap-floats, that can
throw the ordering of the figures off; but otherwise, whatever order you
specify in your document should be the order they appear.

Which means, that if you need them at the end of your document, then
that is where I would place them (after the bibliography).  You can then
refer to them in the text by using a tag + cross-reference.

If you need them to appear in your text at a particular position, then
that is where you should place the float.  There are ways to make floats
go to the end of a document and arrange themselves into separate figures
and tables sections, but it involves resetting LaTeX values and some
ugly hackery.

Cheers,

Rob

Re: Order of Tables and Figures

[rob]

Rob Oakes lyx-devel at oak-tree.us writes:

 
 Hi Rob,
 
 I'm not sure that I follow what you're trying to accomplish.  Do you
 need your figures to appear in text, or do you need them to appear at
 the end of your document after the references section?  (The way that
 many biomedical journals specify an article must be submitted.)
 
 And what do you mean, by the default order isn't what I want.
 Typically figures are printed in the order that they appear in the
 document.  If you are doing fancy things with wrap-floats, that can
 throw the ordering of the figures off; but otherwise, whatever order you
 specify in your document should be the order they appear.
 
 Which means, that if you need them at the end of your document, then
 that is where I would place them (after the bibliography).  You can then
 refer to them in the text by using a tag + cross-reference.
 
 If you need them to appear in your text at a particular position, then
 that is where you should place the float.  There are ways to make floats
 go to the end of a document and arrange themselves into separate figures
 and tables sections, but it involves resetting LaTeX values and some
 ugly hackery.
 
 Cheers,
 
 Rob
 
 

Hi Rob,  Thanks for your reply.  Yes, I want all the figures/tables to 
appear at the end of my document, after the references. And I want them 
to appear in the order in which I make them in my .lyx file.  The 
problem is that the order in which they appear in my .pdf is not the 
order in which they appear in my .lyx. Yes, each figure is in the correct 
order with respect to all the other figures and each table is in the 
correct order w.r.t. all the other tables (and as they are listed in 
my .lyx), but each table is not in the correct order w.r.t. the figures 
and each figure is not in the correct order w.r.t. each table. 

I don't need them to appear in any particular position, only in a 
particular order.

Any idea how to use pdfbookmark after references?  I want to have a 
bookmark in my pdf that links to my figures.

Thanks.

Personal Dictionary - Hunspell - Linux

[Rob Oakes]

Dear LyX Users,

Does anyone happen to know where the personal dictionary for Hunspell
lives?  I've been trying to do a write-up of the new spell-checking
features in LyX 2, and have found that while I can add words to a
personal dictionary while I keep the program open, they aren't getting
stored between sessions (e.g., close the program and then re-open it).

The only explanation that I've been able to come up with is that my
system dictionaries are in a folder which my user account doesn't have
read/write permissions to.

Does anyone know if there is a hunspell user dictionary stored in
the /home/ folder that I should be using instead?  (I've already gotten
the same thing to work with aspell.)

Thanks,

Rob Oakes

Re: Problems with pdf conversion

[Uwe Stöhr]

Am 12.05.2010 00:19, schrieb Marcin Jurek:


I was looking for some solution to my problem and I found that it's a
recurrent one on other LaTeX-related sites too. I started writing my
degree dissertation in LyX and it was fine at the onset but then I
suddenly fonud out the file gets no longer compiled. I can produce
neither pdf nor dvi though no error messages are displayed. What could
be the reason for it?


If you send me a LyX file (If possible, I prefer short files of course), i will 
have a closer look.

regards Uwe

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

Rob Oakes lyx-de...@oak-tree.us writes:
 Just one thought, make sure that there is a copy of Sweave.sty installed
 in your LaTeX path (and make sure that LyX can find it).  I was having
 some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
 what ultimately fixed it.

Are you sure? It should not be necessary on 2.0. What is needed though
is to have R installed and available in the path. The module tests the
availability of a Rnwtex converter (aka R CMD Sweave).

JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Hi Rob!

Rob Oakes wrote:

Hi Ricardo,

Just one thought, make sure that there is a copy of Sweave.sty installed
in your LaTeX path (and make sure that LyX can find it).  I was having
some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
what ultimately fixed it.

  


Nope, it is not! In fact Sweave.sty is no where in the path. It seems it 
looks for R! R was not installed in this box! Shame on me! Once 
installed, LyX 2.0 no longer crashes while loading Sweave module.


Thanks for your help!



But, to be honest, I haven't really played with LyX 2.0 on my Mac
recently.  I've been on a book deadline and it just felt to unstable to
any real work.  On Linux, though, it's been very reliable.

  
I will keep an eye on new releases and maintain this experimental 
installation on the MacPro running Mac OS X 10.6.3 and at the same time 
keep running a stable a 1.6.5 release in a 10.5.8 MacBook Pro. I have 
not two available boxes with the same SO. Please, let me know if I can 
be of any further help to debug this or any other issue. Thanks!


Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Oops!

Jean-Marc LASGOUTTES wrote:

Rob Oakes lyx-de...@oak-tree.us writes:
  

Just one thought, make sure that there is a copy of Sweave.sty installed
in your LaTeX path (and make sure that LyX can find it).  I was having
some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
what ultimately fixed it.



Are you sure? It should not be necessary on 2.0. What is needed though
is to have R installed and available in the path. The module tests the
availability of a Rnwtex converter (aka R CMD Sweave).
  


Sorry, I replied to Rob's message before reading this one! That's what 
I've found here: Sweave.sty as is is not longer in the path and LyX 
looks for R libraries instead. Is it ok this interpretation? Thanks!


Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[lyx-devel]

Hi JMarc,

Reasonably sure.  I was having the problems back in November.  And there
were two separate issues.  The first was getting LyX 2 to work, the second
was related to getting R + Sweave to work.

The problems that eventually required Sweave.sty were related to getting
documents to compile correctly.  Without it, the compilation would simply
terminate with There was an R error or some such.  After placing
Sweave.sty in the tex path, this resolved itself.

But then, I haven't really spent much time working on the Mac since then. 
Problems with PyQt (related to work stuff) have forced me over to my Linux
laptop, and that's what I've mostly been working with for the last seven
months.

It wasn't till this morning that sat down again to take a look at the
problem.  About the same time that it was reported solved ;)

If I have any problems, I'll be sure to file a bug report/send an email to
the developer list.

Cheers,

Rob

 Rob Oakes lyx-de...@oak-tree.us writes:
 Just one thought, make sure that there is a copy of Sweave.sty installed
 in your LaTeX path (and make sure that LyX can find it).  I was having
 some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
 what ultimately fixed it.

 Are you sure? It should not be necessary on 2.0. What is needed though
 is to have R installed and available in the path. The module tests the
 availability of a Rnwtex converter (aka R CMD Sweave).

 JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

[Ricardo Rodriguez] eBioTIC. ricardo.rodrig...@ebiotic.net writes:
 Sorry, I replied to Rob's message before reading this one! That's what
 I've found here: Sweave.sty as is is not longer in the path and LyX
 looks for R libraries instead. Is it ok this interpretation? Thanks!

Yes. But still it should not crash...

JMarc

Re: Trouble viewing DVI

[Paul Rubin]

Dean Chandler chandler at vvm.com writes:

 
 Yes,  Ghostscript  Imagemagick are installed.
 
 Also, I have qt4-dev installed.
 
 The problem occurs both with Lyx 1.5.3, from the Ubuntu repository and 
 with 1.6.5, which I downloaded from lyx.org and compiled. There were no 
 errors in the compilation. Could I be missing some file converter?
 

Unlikely. LyX uses a Python script to convert image formats; the Python script
by default uses ImageMagick; and when the result is EPS, I believe IM uses
Ghostscript.

The telling thing, though, is that you are getting an error message from
lyx2lyx, which is used to convert .lyx files from one format to another. You say
the error message indicates it is trying to convert a PNG file each time?  That
should not happen.

Do you have an older version of LyX installed on this machine?  The best guess I
can come up with for lyx2lyx errors would be an old version of lyx2lyx trying to
convert Tutorial.lyx to an earlier document version and thinking somehow that
the PNG files were child documents that needed to be converted (???).

If you do have multiple versions of LyX installed, I would suggest uninstalling
the old one(s) and then reinstalling a recent one.

/Paul

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Hi!

lyx-de...@oak-tree.us wrote:

Hi JMarc,

Reasonably sure.  I was having the problems back in November.  And there
were two separate issues.  The first was getting LyX 2 to work, the second
was related to getting R + Sweave to work.

The problems that eventually required Sweave.sty were related to getting
documents to compile correctly.  Without it, the compilation would simply
terminate with There was an R error or some such.  After placing
Sweave.sty in the tex path, this resolved itself.
  


Being truth what I've said before and what JMarc said about LyX checking 
R availability to load Sweave module, I'm facing the same problem Rob 
describes when trying to compile a new document including S/R 
expressions. I will try to describe the situation:



*1.* A LyX 2.0.0 alpha2 installation crashes when trying to load Sweave 
module if R is not installed in the same box. In this case, I guess it 
will be advisable to trigger a warning saying that R is required instead 
of causing an exception that crashes LyX. I'm sure developers are 
consciences of this and the only problem here is time to make the 
required changes! :-)


*2. *Once R is installed, Sweave module loads without a glitch.

*3.* If I try to compile a new document including S/R expressions, 
compilation fails throwing the following error:


! LaTeX Error: File `Sweave.sty' not found.

Here the full stack to further reference:

http://xen.net/onLyX/lyxSweaveStyNotFound.html

As stated in a previous message, the LaTeX environment here was created 
as per...


http://www.tug.org/mactex/2009/
[ approximately 1.3G - 12 March 2010 ]
MacTeX-2009.mpkg
MacTeX.mpkg.zip

*4. *Until I copy Sweave.sty to the TeX path and reconfigure LyX, 
compilation fails.


I copied Sweave.sty from a older box with a running LyX 1.6.5/Sweave/R 
installation.


GMXUX-Ricardo-Rodriguez:~ rrodriguez$ kpsewhich Sweave.sty
/Users/rrodriguez/Library/texmf/tex/latex/R/Sweave.sty



Please, provided its module is loaded, must Sweave work out of the box 
in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I 
guess a warning will be required some where to avoid the problem we are 
facing here! Thanks!


Let me know if I can be of any further help!

Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

[Ricardo Rodriguez] eBioTIC. ricardo.rodrig...@ebiotic.net writes:
 *3.* If I try to compile a new document including S/R expressions,
 compilation fails throwing the following error:

 ! LaTeX Error: File `Sweave.sty' not found.

 Here the full stack to further reference:

 http://xen.net/onLyX/lyxSweaveStyNotFound.html
 Please, provided its module is loaded, must Sweave work out of the box
 in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I
 guess a warning will be required some where to avoid the problem we
 are facing here! Thanks!

It is expected (by me at least) that either:

1/ the installation of R installs Sweave.sty at the right place (was
MaxTeX already installed when you installed R?)

or

2/ Sweave is set up in such a way that it puts the full path to the
Sweave.sty file in the \usepackage command.

If neither of those two conditions are fulfilled, I think this is a bug
in the way R installs itself...

JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[Rob Oakes]

This is clearly either a problem in the way that R installs itself, or
the way that LaTeX installs itself.  I'm not actually sure which though
and I don't know where to file the bug report.

When I just checked, I was not able to find a sweave package for R,
nor was I able to find one for TeXLive 2009 (don't know about MikTeX).
But I've experienced a similar problem on Mac OS X and on Linux, which
provides some evidence that it's not getting packaged.

Because out of the box support for Sweave is one of LyX 2's newest (and
IMHO, killer) features, it might make sense to include a copy of
Sweave.sty with the installation script and have it installed at the
time of LyX configuration.  LyX already does this with a few specialty
document classes anyway (broadway, hollywood).

Cheers,

Rob

Order of Tables and Figures

[rob]

Hi,

How do I fix the order in which tables and figures 
appear at the end of my document?  My paper must 
conform to an ordering of text, references, tables/figures.  
The problem is that the default order of the tables and 
figures is not what I want.  I tried changing the settings 
for each float by specifying ignore latex rules and 
then bottom or top, depending on what seemed to be 
necessary to get it right, but this didn't work.  
Selecting here definitely only created chaos. 

Also, how can I specify a \pdfbookmark[1]{} after 
references (for my figures)?  I use these elsewhere in 
my doc, but they won't work after the references section. 

Thanks very much.

Re: Order of Tables and Figures

[Rob Oakes]

Hi Rob,

I'm not sure that I follow what you're trying to accomplish.  Do you
need your figures to appear in text, or do you need them to appear at
the end of your document after the references section?  (The way that
many biomedical journals specify an article must be submitted.)

And what do you mean, by the default order isn't what I want.
Typically figures are printed in the order that they appear in the
document.  If you are doing fancy things with wrap-floats, that can
throw the ordering of the figures off; but otherwise, whatever order you
specify in your document should be the order they appear.

Which means, that if you need them at the end of your document, then
that is where I would place them (after the bibliography).  You can then
refer to them in the text by using a tag + cross-reference.

If you need them to appear in your text at a particular position, then
that is where you should place the float.  There are ways to make floats
go to the end of a document and arrange themselves into separate figures
and tables sections, but it involves resetting LaTeX values and some
ugly hackery.

Cheers,

Rob

Re: Order of Tables and Figures

[rob]

Rob Oakes lyx-devel at oak-tree.us writes:

 
 Hi Rob,
 
 I'm not sure that I follow what you're trying to accomplish.  Do you
 need your figures to appear in text, or do you need them to appear at
 the end of your document after the references section?  (The way that
 many biomedical journals specify an article must be submitted.)
 
 And what do you mean, by the default order isn't what I want.
 Typically figures are printed in the order that they appear in the
 document.  If you are doing fancy things with wrap-floats, that can
 throw the ordering of the figures off; but otherwise, whatever order you
 specify in your document should be the order they appear.
 
 Which means, that if you need them at the end of your document, then
 that is where I would place them (after the bibliography).  You can then
 refer to them in the text by using a tag + cross-reference.
 
 If you need them to appear in your text at a particular position, then
 that is where you should place the float.  There are ways to make floats
 go to the end of a document and arrange themselves into separate figures
 and tables sections, but it involves resetting LaTeX values and some
 ugly hackery.
 
 Cheers,
 
 Rob
 
 

Hi Rob,  Thanks for your reply.  Yes, I want all the figures/tables to 
appear at the end of my document, after the references. And I want them 
to appear in the order in which I make them in my .lyx file.  The 
problem is that the order in which they appear in my .pdf is not the 
order in which they appear in my .lyx. Yes, each figure is in the correct 
order with respect to all the other figures and each table is in the 
correct order w.r.t. all the other tables (and as they are listed in 
my .lyx), but each table is not in the correct order w.r.t. the figures 
and each figure is not in the correct order w.r.t. each table. 

I don't need them to appear in any particular position, only in a 
particular order.

Any idea how to use pdfbookmark after references?  I want to have a 
bookmark in my pdf that links to my figures.

Thanks.

Personal Dictionary - Hunspell - Linux

[Rob Oakes]

Dear LyX Users,

Does anyone happen to know where the personal dictionary for Hunspell
lives?  I've been trying to do a write-up of the new spell-checking
features in LyX 2, and have found that while I can add words to a
personal dictionary while I keep the program open, they aren't getting
stored between sessions (e.g., close the program and then re-open it).

The only explanation that I've been able to come up with is that my
system dictionaries are in a folder which my user account doesn't have
read/write permissions to.

Does anyone know if there is a hunspell user dictionary stored in
the /home/ folder that I should be using instead?  (I've already gotten
the same thing to work with aspell.)

Thanks,

Rob Oakes

Re: Problems with pdf conversion

[Uwe Stöhr]

Am 12.05.2010 00:19, schrieb Marcin Jurek:


I was looking for some solution to my problem and I found that it's a
recurrent one on other LaTeX-related sites too. I started writing my
degree dissertation in LyX and it was fine at the onset but then I
suddenly fonud out the file gets no longer compiled. I can produce
neither pdf nor dvi though no error messages are displayed. What could
be the reason for it?


If you send me a LyX file (If possible, I prefer short files of course), i will 
have a closer look.

regards Uwe

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

Rob Oakes  writes:
> Just one thought, make sure that there is a copy of Sweave.sty installed
> in your LaTeX path (and make sure that LyX can find it).  I was having
> some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
> what ultimately fixed it.

Are you sure? It should not be necessary on 2.0. What is needed though
is to have R installed and available in the path. The module tests the
availability of a Rnw>tex converter (aka R CMD Sweave).

JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Hi Rob!

Rob Oakes wrote:

Hi Ricardo,

Just one thought, make sure that there is a copy of Sweave.sty installed
in your LaTeX path (and make sure that LyX can find it).  I was having
some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
what ultimately fixed it.

  


Nope, it is not! In fact Sweave.sty is no where in the path. It seems it 
looks for R! R was not installed in this box! Shame on me! Once 
installed, LyX 2.0 no longer crashes while loading Sweave module.


Thanks for your help!



But, to be honest, I haven't really played with LyX 2.0 on my Mac
recently.  I've been on a book deadline and it just felt to unstable to
any real work.  On Linux, though, it's been very reliable.

  
I will keep an eye on new releases and maintain this experimental 
installation on the MacPro running Mac OS X 10.6.3 and at the same time 
keep running a stable a 1.6.5 release in a 10.5.8 MacBook Pro. I have 
not two available boxes with the same SO. Please, let me know if I can 
be of any further help to debug this or any other issue. Thanks!


Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Oops!

Jean-Marc LASGOUTTES wrote:

Rob Oakes  writes:
  

Just one thought, make sure that there is a copy of Sweave.sty installed
in your LaTeX path (and make sure that LyX can find it).  I was having
some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
what ultimately fixed it.



Are you sure? It should not be necessary on 2.0. What is needed though
is to have R installed and available in the path. The module tests the
availability of a Rnw>tex converter (aka R CMD Sweave).
  


Sorry, I replied to Rob's message before reading this one! That's what 
I've found here: Sweave.sty as is is not longer in the path and LyX 
looks for R libraries instead. Is it ok this interpretation? Thanks!


Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[lyx-devel]

Hi JMarc,

Reasonably sure.  I was having the problems back in November.  And there
were two separate issues.  The first was getting LyX 2 to work, the second
was related to getting R + Sweave to work.

The problems that eventually required Sweave.sty were related to getting
documents to compile correctly.  Without it, the compilation would simply
terminate with "There was an R error" or some such.  After placing
Sweave.sty in the tex path, this resolved itself.

But then, I haven't really spent much time working on the Mac since then. 
Problems with PyQt (related to work stuff) have forced me over to my Linux
laptop, and that's what I've mostly been working with for the last seven
months.

It wasn't till this morning that sat down again to take a look at the
problem.  About the same time that it was reported solved ;)

If I have any problems, I'll be sure to file a bug report/send an email to
the developer list.

Cheers,

Rob

> Rob Oakes  writes:
>> Just one thought, make sure that there is a copy of Sweave.sty installed
>> in your LaTeX path (and make sure that LyX can find it).  I was having
>> some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is
>> what ultimately fixed it.
>
> Are you sure? It should not be necessary on 2.0. What is needed though
> is to have R installed and available in the path. The module tests the
> availability of a Rnw>tex converter (aka R CMD Sweave).
>
> JMarc
>

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

"[Ricardo Rodriguez] eBioTIC."  writes:
> Sorry, I replied to Rob's message before reading this one! That's what
> I've found here: Sweave.sty as is is not longer in the path and LyX
> looks for R libraries instead. Is it ok this interpretation? Thanks!

Yes. But still it should not crash...

JMarc

Re: Trouble viewing DVI

[Paul Rubin]

Dean Chandler  vvm.com> writes:

> 
> Yes,  Ghostscript & Imagemagick are installed.
> 
> Also, I have qt4-dev installed.
> 
> The problem occurs both with Lyx 1.5.3, from the Ubuntu repository and 
> with 1.6.5, which I downloaded from lyx.org and compiled. There were no 
> errors in the compilation. Could I be missing some file converter?
> 

Unlikely. LyX uses a Python script to convert image formats; the Python script
by default uses ImageMagick; and when the result is EPS, I believe IM uses
Ghostscript.

The telling thing, though, is that you are getting an error message from
lyx2lyx, which is used to convert .lyx files from one format to another. You say
the error message indicates it is trying to convert a PNG file each time?  That
should not happen.

Do you have an older version of LyX installed on this machine?  The best guess I
can come up with for lyx2lyx errors would be an old version of lyx2lyx trying to
convert Tutorial.lyx to an earlier document version and thinking somehow that
the PNG files were child documents that needed to be converted (???).

If you do have multiple versions of LyX installed, I would suggest uninstalling
the old one(s) and then reinstalling a recent one.

/Paul

Re: including a Sweave/R code chunk in a LyX table cell

[[Ricardo Rodriguez] eBioTIC.]

Hi!

lyx-de...@oak-tree.us wrote:

Hi JMarc,

Reasonably sure.  I was having the problems back in November.  And there
were two separate issues.  The first was getting LyX 2 to work, the second
was related to getting R + Sweave to work.

The problems that eventually required Sweave.sty were related to getting
documents to compile correctly.  Without it, the compilation would simply
terminate with "There was an R error" or some such.  After placing
Sweave.sty in the tex path, this resolved itself.
  


Being truth what I've said before and what JMarc said about LyX checking 
R availability to load Sweave module, I'm facing the same problem Rob 
describes when trying to compile a new document including S/R 
expressions. I will try to describe the situation:



*1.* A LyX 2.0.0 alpha2 installation crashes when trying to load Sweave 
module if R is not installed in the same box. In this case, I guess it 
will be advisable to trigger a warning saying that R is required instead 
of causing an exception that crashes LyX. I'm sure developers are 
consciences of this and the only problem here is time to make the 
required changes! :-)


*2. *Once R is installed, Sweave module loads without a glitch.

*3.* If I try to compile a new document including S/R expressions, 
compilation fails throwing the following error:


! LaTeX Error: File `Sweave.sty' not found.

Here the full stack to further reference:

http://xen.net/onLyX/lyxSweaveStyNotFound.html

As stated in a previous message, the LaTeX environment here was created 
as per...


http://www.tug.org/mactex/2009/
[ approximately 1.3G - 12 March 2010 ]
MacTeX-2009.mpkg
MacTeX.mpkg.zip

*4. *Until I copy Sweave.sty to the TeX path and reconfigure LyX, 
compilation fails.


I copied Sweave.sty from a older box with a running LyX 1.6.5/Sweave/R 
installation.


GMXUX-Ricardo-Rodriguez:~ rrodriguez$ kpsewhich Sweave.sty
/Users/rrodriguez/Library/texmf/tex/latex/R/Sweave.sty



Please, provided its module is loaded, must Sweave work out of the box 
in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I 
guess a warning will be required some where to avoid the problem we are 
facing here! Thanks!


Let me know if I can be of any further help!

Greetings,

Ricardo

--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems

Re: including a Sweave/R code chunk in a LyX table cell

[Jean-Marc LASGOUTTES]

"[Ricardo Rodriguez] eBioTIC."  writes:
> *3.* If I try to compile a new document including S/R expressions,
> compilation fails throwing the following error:
>
> ! LaTeX Error: File `Sweave.sty' not found.
>
> Here the full stack to further reference:
>
> http://xen.net/onLyX/lyxSweaveStyNotFound.html
> Please, provided its module is loaded, must Sweave work out of the box
> in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I
> guess a warning will be required some where to avoid the problem we
> are facing here! Thanks!

It is expected (by me at least) that either:

1/ the installation of R installs Sweave.sty at the right place (was
MaxTeX already installed when you installed R?)

or

2/ Sweave is set up in such a way that it puts the full path to the
Sweave.sty file in the \usepackage command.

If neither of those two conditions are fulfilled, I think this is a bug
in the way R installs itself...

JMarc

Re: including a Sweave/R code chunk in a LyX table cell

[Rob Oakes]

This is clearly either a problem in the way that R installs itself, or
the way that LaTeX installs itself.  I'm not actually sure which though
and I don't know where to file the bug report.

When I just checked, I was not able to find a "sweave" package for R,
nor was I able to find one for TeXLive 2009 (don't know about MikTeX).
But I've experienced a similar problem on Mac OS X and on Linux, which
provides some evidence that it's not getting packaged.

Because out of the box support for Sweave is one of LyX 2's newest (and
IMHO, killer) features, it might make sense to include a copy of
Sweave.sty with the installation script and have it installed at the
time of LyX configuration.  LyX already does this with a few specialty
document classes anyway (broadway, hollywood).

Cheers,

Rob

Order of Tables and Figures

[rob]

Hi,

How do I fix the order in which tables and figures 
appear at the end of my document?  My paper must 
conform to an ordering of text, references, tables/figures.  
The problem is that the default order of the tables and 
figures is not what I want.  I tried changing the settings 
for each float by specifying "ignore latex rules" and 
then bottom or top, depending on what seemed to be 
necessary to get it right, but this didn't work.  
Selecting "here definitely" only created chaos. 

Also, how can I specify a \pdfbookmark[1]{} after 
references (for my figures)?  I use these elsewhere in 
my doc, but they won't work after the references section. 

Thanks very much.

Re: Order of Tables and Figures

[Rob Oakes]

Hi Rob,

I'm not sure that I follow what you're trying to accomplish.  Do you
need your figures to appear in text, or do you need them to appear at
the end of your document after the references section?  (The way that
many biomedical journals specify an article must be submitted.)

And what do you mean, by "the default order isn't what I want."
Typically figures are printed in the order that they appear in the
document.  If you are doing fancy things with wrap-floats, that can
throw the ordering of the figures off; but otherwise, whatever order you
specify in your document should be the order they appear.

Which means, that if you need them at the end of your document, then
that is where I would place them (after the bibliography).  You can then
refer to them in the text by using a tag + cross-reference.

If you need them to appear in your text at a particular position, then
that is where you should place the float.  There are ways to make floats
go to the end of a document and arrange themselves into separate figures
and tables sections, but it involves resetting LaTeX values and some
ugly hackery.

Cheers,

Rob

Re: Order of Tables and Figures

[rob]

Rob Oakes  oak-tree.us> writes:

> 
> Hi Rob,
> 
> I'm not sure that I follow what you're trying to accomplish.  Do you
> need your figures to appear in text, or do you need them to appear at
> the end of your document after the references section?  (The way that
> many biomedical journals specify an article must be submitted.)
> 
> And what do you mean, by "the default order isn't what I want."
> Typically figures are printed in the order that they appear in the
> document.  If you are doing fancy things with wrap-floats, that can
> throw the ordering of the figures off; but otherwise, whatever order you
> specify in your document should be the order they appear.
> 
> Which means, that if you need them at the end of your document, then
> that is where I would place them (after the bibliography).  You can then
> refer to them in the text by using a tag + cross-reference.
> 
> If you need them to appear in your text at a particular position, then
> that is where you should place the float.  There are ways to make floats
> go to the end of a document and arrange themselves into separate figures
> and tables sections, but it involves resetting LaTeX values and some
> ugly hackery.
> 
> Cheers,
> 
> Rob
> 
> 

Hi Rob,  Thanks for your reply.  Yes, I want all the figures/tables to 
appear at the end of my document, after the references. And I want them 
to appear in the order in which I make them in my .lyx file.  The 
problem is that the order in which they appear in my .pdf is not the 
order in which they appear in my .lyx. Yes, each figure is in the correct 
order with respect to all the other figures and each table is in the 
correct order w.r.t. all the other tables (and as they are listed in 
my .lyx), but each table is not in the correct order w.r.t. the figures 
and each figure is not in the correct order w.r.t. each table. 

I don't need them to appear in any particular position, only in a 
particular order.

Any idea how to use pdfbookmark after references?  I want to have a 
bookmark in my pdf that links to my figures.

Thanks.

Personal Dictionary - Hunspell - Linux

[Rob Oakes]

Dear LyX Users,

Does anyone happen to know where the personal dictionary for Hunspell
lives?  I've been trying to do a write-up of the new spell-checking
features in LyX 2, and have found that while I can add words to a
"personal dictionary" while I keep the program open, they aren't getting
stored between sessions (e.g., close the program and then re-open it).

The only explanation that I've been able to come up with is that my
system dictionaries are in a folder which my user account doesn't have
read/write permissions to.

Does anyone know if there is a hunspell user dictionary stored in
the /home/ folder that I should be using instead?  (I've already gotten
the same thing to work with aspell.)

Thanks,

Rob Oakes

Re: Problems with pdf conversion

[Uwe Stöhr]

Am 12.05.2010 00:19, schrieb Marcin Jurek:


I was looking for some solution to my problem and I found that it's a
recurrent one on other LaTeX-related sites too. I started writing my
degree dissertation in LyX and it was fine at the onset but then I
suddenly fonud out the file gets no longer compiled. I can produce
neither pdf nor dvi though no error messages are displayed. What could
be the reason for it?


If you send me a LyX file (If possible, I prefer short files of course), i will 
have a closer look.

regards Uwe