Re: Problem compiling document to Postscript

[Påvel Nicklasson]

I managed to get a postscript file once from Kubuntu, but then I tried
again LyX refused. I have converted images to .eps and sometimes back to
jpg when the log states that it stopped at those images and still no luck
converting to postscript.

In Windows I have done the conversion several times without any problems. I
am beginning to suspect that it is a bug in the software handling the
process or in how memory is handled by the different systems. The file is
rather big with many big images so perhaps this is the problem.

I must be content with the postscript file made in Windows and I don't
think that I am able to solve the problem on Kubuntu. As I said it is very
strange since I can convert other very similar big manuscripts that also
contain a lot of jpg images.

Re: Problem compiling document to Postscript

[Ingar Pareliussen]

Just a thought: could it be that your /tmp directory almost full? If lyx does 
not have enough space to copy and convert all the image files in the tmp 
directory strange things may happen.

Ingar

- Reply message -
From: Påvel Nicklasson pavel223...@gmail.com
To: lyx-users@lists.lyx.org lyx-users@lists.lyx.org
Subject: Problem compiling document to Postscript
Date: Wed, May 30, 2012 09:30



I managed to get a postscript file once from Kubuntu, but then I tried again 
LyX refused. I have converted images to .eps and sometimes back to jpg when the 
log states that it stopped at those images and still no luck converting to 
postscript.

In Windows I have done the conversion several times without any problems. I am 
beginning to suspect that it is a bug in the software handling the process or 
in how memory is handled by the different systems. The file is rather big with 
many big images so perhaps this is the problem.

I must be content with the postscript file made in Windows and I don't think 
that I am able to solve the problem on Kubuntu. As I said it is very strange 
since I can convert other very similar big manuscripts that also contain a lot 
of jpg images.

Re: Problem compiling document to Postscript

[Påvel Nicklasson]

2012/5/30 Ingar Pareliussen ingar.parelius...@dmmh.no

  Just a thought: could it be that your /tmp directory almost full? If lyx
 does not have enough space to copy and convert all the image files in the
 tmp directory strange things may happen.

 Ingar


I thought on that too. I moved the tmp folder in LyX temporarily to my
homefolder with more space, but the result was the same, no postscriptfile,
even if LyX worked noticeable faster.

Påvel

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

I've set up a repo on github for the program.

The code:
https://github.com/abarker/lyxNotebook

For a quick overview, see the first section of the documentation:
https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf

Re: Error with Lyx 2.0.3 and Knitr

[Eugene]

Hi

Running Lyx 2.0.3 on WinXP witn Knitr results in the following error

LyX: Cannot convert file

An error occurred while running:
Rscript --verbose --no-save --no-restore C:/Program 
Files/Lyx20/bin/../Resources/scripts/lyxknitr.R C:/Documents and 
Settings/me/Local Settings/Temp/lyx_tmpdir.Hp4948/lyx_tmpbuf2/Paper2.Rnw
C:/Documents and Settings/me/Local 
Settings/Temp/lyx_tmpdir.Hp4948/lyx_tmpbuf2/Paper2.tex ISO-8859-a5
M:/REPOSITORY/Lyx_Paper2/

Re: program to use Lyx as a code-evaluating notebook

[Pavel Sanda]

Allen Barker wrote:

 I've set up a repo on github for the program.

It maight be goo to add note to http://wiki.lyx.org/Tools/Tools
P

Re: program to use Lyx as a code-evaluating notebook

[Nico Williams]

On Wed, May 30, 2012 at 11:24 AM, Allen Barker allen.l.bar...@gmail.com wrote:
 I've set up a repo on github for the program.

 The code:
 https://github.com/abarker/lyxNotebook

 For a quick overview, see the first section of the documentation:
 https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf

I looked at the README and I get it.  This is very much like the
weaver tool, that lets you compile statistics using R right in the LyX
document.  But yours is more generic.  The idea is very cool.  I
second the sentiment that this should be added to the tools wiki page.

Nico

PS: I have no use for this right now, but I'll keep it in mind.  One
use that comes to mind is using this approach to automatically test
code samples in a book, but that would need a way to request that code
be tested but output not included in the document.

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

On 05/30/2012 04:06 PM, Pavel Sanda wrote:

Allen Barker wrote:


I've set up a repo on github for the program.


It maight be goo to add note to http://wiki.lyx.org/Tools/Tools
P


Thanks, I've added a note to that list.

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

On 05/30/2012 05:32 PM, Nico Williams wrote:

On Wed, May 30, 2012 at 11:24 AM, Allen Barkerallen.l.bar...@gmail.com  wrote:

I've set up a repo on github for the program.

The code:
https://github.com/abarker/lyxNotebook

For a quick overview, see the first section of the documentation:
https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf


I looked at the README and I get it.  This is very much like the
weaver tool, that lets you compile statistics using R right in the LyX
document.  But yours is more generic.  The idea is very cool.  I
second the sentiment that this should be added to the tools wiki page.

Nico

PS: I have no use for this right now, but I'll keep it in mind.  One
use that comes to mind is using this approach to automatically test
code samples in a book, but that would need a way to request that code
be tested but output not included in the document.


The printing of cells of various types can be suppressed
by including a Latex command in the preamble or in an ERT.
To suppress printing of output cells for Python 2, for
example, you would add \lyxNotebookPrintOffOutputPythonTwo.
(The current implementation then uses \let to redefine
those cells to be Verbatim comment blocks.)

LyX cannot handle '$' sign in Sweave code chunk

[Lam Phung Khanh]

Dear all,

I used document class 'article' with Sweave module added in LyX version 2.0.3 
to write a short Sweave document:

Hi !
=
a - c(1:10)
b - c(11:20)
d - cbind(a, b)
d$a
@

I got error: LyX: cannot convert file when compiled it. My suspect is LyX 
cannot handle the '$' sign in Sweave code chunk. When I used another way to 
write the last code line, it worked fine:

Hi !
=
a - c(1:10)
b - c(11:20)
d - cbind(a, b)
d[,a]
@

I haven't known how to overcome it yet. It is a bit pity because for R-users, 
'$' is one of the most common sign used in the analysis.

Please forgive me if this email disturbs you. 

Thank you very much

Lam Phung Khanh
PhD student
Centre for Tropical Medicine
Oxford University Clinical Research Unit
764 Vo Van Kiet Street (Old: 190 Ben Ham Tu), Ward 1, District 5, Ho Chi Minh 
City
Vietnam

Wellcome Trust Major Overseas Programme

In partnership with
Hospital for Tropical Diseases

Tel: 84 8 39237954
Fax: 84 8 39238904
Mob: 84 (0) 915333751
E-mail: la...@oucru.org
Website: http://www.oucru.org

RE: LyX cannot handle '$' sign in Sweave code chunk

[Scott Kostyshak]

From: Lam Phung Khanh [la...@oucru.org]
Sent: Wednesday, May 30, 2012 10:54 PM

Note that I used knitr to test this, not Sweave. knitr is newer, has more 
features, and can do everything that Sweave can and a lot more. To use it, add 
the module Rnw (knitr) instead of Sweave. Is there a reason you want to use 
Sweave?

I got error: LyX: cannot convert file when compiled it. My suspect is LyX 
cannot handle the '$' sign in Sweave code chunk. When I used another way to 
write the last code line, it worked fine:

I don't think this is a LyX or a knitr error but a problem with your R code. R 
gives me the following error:

a - c(1:10)
b - c(11:20)
d - cbind(a, b)
d$a
Error in d$a : $ operator is invalid for atomic vectors

The following runs fine for me in R and in LyX + knitr

a - c(1:10)
b - c(11:20)
d - data.frame(a, b)
d$a

Please forgive me if this email disturbs you.
Of course not! Feel free to ask any question about LyX + knitr.

Scott

Re: Problem compiling document to Postscript

[Påvel Nicklasson]

I managed to get a postscript file once from Kubuntu, but then I tried
again LyX refused. I have converted images to .eps and sometimes back to
jpg when the log states that it stopped at those images and still no luck
converting to postscript.

In Windows I have done the conversion several times without any problems. I
am beginning to suspect that it is a bug in the software handling the
process or in how memory is handled by the different systems. The file is
rather big with many big images so perhaps this is the problem.

I must be content with the postscript file made in Windows and I don't
think that I am able to solve the problem on Kubuntu. As I said it is very
strange since I can convert other very similar big manuscripts that also
contain a lot of jpg images.

Re: Problem compiling document to Postscript

[Ingar Pareliussen]

Just a thought: could it be that your /tmp directory almost full? If lyx does 
not have enough space to copy and convert all the image files in the tmp 
directory strange things may happen.

Ingar

- Reply message -
From: Påvel Nicklasson pavel223...@gmail.com
To: lyx-users@lists.lyx.org lyx-users@lists.lyx.org
Subject: Problem compiling document to Postscript
Date: Wed, May 30, 2012 09:30



I managed to get a postscript file once from Kubuntu, but then I tried again 
LyX refused. I have converted images to .eps and sometimes back to jpg when the 
log states that it stopped at those images and still no luck converting to 
postscript.

In Windows I have done the conversion several times without any problems. I am 
beginning to suspect that it is a bug in the software handling the process or 
in how memory is handled by the different systems. The file is rather big with 
many big images so perhaps this is the problem.

I must be content with the postscript file made in Windows and I don't think 
that I am able to solve the problem on Kubuntu. As I said it is very strange 
since I can convert other very similar big manuscripts that also contain a lot 
of jpg images.

Re: Problem compiling document to Postscript

[Påvel Nicklasson]

2012/5/30 Ingar Pareliussen ingar.parelius...@dmmh.no

  Just a thought: could it be that your /tmp directory almost full? If lyx
 does not have enough space to copy and convert all the image files in the
 tmp directory strange things may happen.

 Ingar


I thought on that too. I moved the tmp folder in LyX temporarily to my
homefolder with more space, but the result was the same, no postscriptfile,
even if LyX worked noticeable faster.

Påvel

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

I've set up a repo on github for the program.

The code:
https://github.com/abarker/lyxNotebook

For a quick overview, see the first section of the documentation:
https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf

Re: Error with Lyx 2.0.3 and Knitr

[Eugene]

Hi

Running Lyx 2.0.3 on WinXP witn Knitr results in the following error

LyX: Cannot convert file

An error occurred while running:
Rscript --verbose --no-save --no-restore C:/Program 
Files/Lyx20/bin/../Resources/scripts/lyxknitr.R C:/Documents and 
Settings/me/Local Settings/Temp/lyx_tmpdir.Hp4948/lyx_tmpbuf2/Paper2.Rnw
C:/Documents and Settings/me/Local 
Settings/Temp/lyx_tmpdir.Hp4948/lyx_tmpbuf2/Paper2.tex ISO-8859-a5
M:/REPOSITORY/Lyx_Paper2/

Re: program to use Lyx as a code-evaluating notebook

[Pavel Sanda]

Allen Barker wrote:

 I've set up a repo on github for the program.

It maight be goo to add note to http://wiki.lyx.org/Tools/Tools
P

Re: program to use Lyx as a code-evaluating notebook

[Nico Williams]

On Wed, May 30, 2012 at 11:24 AM, Allen Barker allen.l.bar...@gmail.com wrote:
 I've set up a repo on github for the program.

 The code:
 https://github.com/abarker/lyxNotebook

 For a quick overview, see the first section of the documentation:
 https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf

I looked at the README and I get it.  This is very much like the
weaver tool, that lets you compile statistics using R right in the LyX
document.  But yours is more generic.  The idea is very cool.  I
second the sentiment that this should be added to the tools wiki page.

Nico

PS: I have no use for this right now, but I'll keep it in mind.  One
use that comes to mind is using this approach to automatically test
code samples in a book, but that would need a way to request that code
be tested but output not included in the document.

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

On 05/30/2012 04:06 PM, Pavel Sanda wrote:

Allen Barker wrote:


I've set up a repo on github for the program.


It maight be goo to add note to http://wiki.lyx.org/Tools/Tools
P


Thanks, I've added a note to that list.

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

On 05/30/2012 05:32 PM, Nico Williams wrote:

On Wed, May 30, 2012 at 11:24 AM, Allen Barkerallen.l.bar...@gmail.com  wrote:

I've set up a repo on github for the program.

The code:
https://github.com/abarker/lyxNotebook

For a quick overview, see the first section of the documentation:
https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf


I looked at the README and I get it.  This is very much like the
weaver tool, that lets you compile statistics using R right in the LyX
document.  But yours is more generic.  The idea is very cool.  I
second the sentiment that this should be added to the tools wiki page.

Nico

PS: I have no use for this right now, but I'll keep it in mind.  One
use that comes to mind is using this approach to automatically test
code samples in a book, but that would need a way to request that code
be tested but output not included in the document.


The printing of cells of various types can be suppressed
by including a Latex command in the preamble or in an ERT.
To suppress printing of output cells for Python 2, for
example, you would add \lyxNotebookPrintOffOutputPythonTwo.
(The current implementation then uses \let to redefine
those cells to be Verbatim comment blocks.)

LyX cannot handle '$' sign in Sweave code chunk

[Lam Phung Khanh]

Dear all,

I used document class 'article' with Sweave module added in LyX version 2.0.3 
to write a short Sweave document:

Hi !
=
a - c(1:10)
b - c(11:20)
d - cbind(a, b)
d$a
@

I got error: LyX: cannot convert file when compiled it. My suspect is LyX 
cannot handle the '$' sign in Sweave code chunk. When I used another way to 
write the last code line, it worked fine:

Hi !
=
a - c(1:10)
b - c(11:20)
d - cbind(a, b)
d[,a]
@

I haven't known how to overcome it yet. It is a bit pity because for R-users, 
'$' is one of the most common sign used in the analysis.

Please forgive me if this email disturbs you. 

Thank you very much

Lam Phung Khanh
PhD student
Centre for Tropical Medicine
Oxford University Clinical Research Unit
764 Vo Van Kiet Street (Old: 190 Ben Ham Tu), Ward 1, District 5, Ho Chi Minh 
City
Vietnam

Wellcome Trust Major Overseas Programme

In partnership with
Hospital for Tropical Diseases

Tel: 84 8 39237954
Fax: 84 8 39238904
Mob: 84 (0) 915333751
E-mail: la...@oucru.org
Website: http://www.oucru.org

RE: LyX cannot handle '$' sign in Sweave code chunk

[Scott Kostyshak]

From: Lam Phung Khanh [la...@oucru.org]
Sent: Wednesday, May 30, 2012 10:54 PM

Note that I used knitr to test this, not Sweave. knitr is newer, has more 
features, and can do everything that Sweave can and a lot more. To use it, add 
the module Rnw (knitr) instead of Sweave. Is there a reason you want to use 
Sweave?

I got error: LyX: cannot convert file when compiled it. My suspect is LyX 
cannot handle the '$' sign in Sweave code chunk. When I used another way to 
write the last code line, it worked fine:

I don't think this is a LyX or a knitr error but a problem with your R code. R 
gives me the following error:

a - c(1:10)
b - c(11:20)
d - cbind(a, b)
d$a
Error in d$a : $ operator is invalid for atomic vectors

The following runs fine for me in R and in LyX + knitr

a - c(1:10)
b - c(11:20)
d - data.frame(a, b)
d$a

Please forgive me if this email disturbs you.
Of course not! Feel free to ask any question about LyX + knitr.

Scott

Re: Problem compiling document to Postscript

[Påvel Nicklasson]

I managed to get a postscript file once from Kubuntu, but then I tried
again LyX refused. I have converted images to .eps and sometimes back to
jpg when the log states that it stopped at those images and still no luck
converting to postscript.

In Windows I have done the conversion several times without any problems. I
am beginning to suspect that it is a bug in the software handling the
process or in how memory is handled by the different systems. The file is
rather big with many big images so perhaps this is the problem.

I must be content with the postscript file made in Windows and I don't
think that I am able to solve the problem on Kubuntu. As I said it is very
strange since I can convert other very similar big manuscripts that also
contain a lot of jpg images.

Re: Problem compiling document to Postscript

[Ingar Pareliussen]

Just a thought: could it be that your /tmp directory almost full? If lyx does 
not have enough space to copy and convert all the image files in the tmp 
directory strange things may happen.

Ingar

- Reply message -
From: "Påvel Nicklasson" 
To: "lyx-users@lists.lyx.org" 
Subject: Problem compiling document to Postscript
Date: Wed, May 30, 2012 09:30



I managed to get a postscript file once from Kubuntu, but then I tried again 
LyX refused. I have converted images to .eps and sometimes back to jpg when the 
log states that it stopped at those images and still no luck converting to 
postscript.

In Windows I have done the conversion several times without any problems. I am 
beginning to suspect that it is a bug in the software handling the process or 
in how memory is handled by the different systems. The file is rather big with 
many big images so perhaps this is the problem.

I must be content with the postscript file made in Windows and I don't think 
that I am able to solve the problem on Kubuntu. As I said it is very strange 
since I can convert other very similar big manuscripts that also contain a lot 
of jpg images.

Re: Problem compiling document to Postscript

[Påvel Nicklasson]

2012/5/30 Ingar Pareliussen 

>  Just a thought: could it be that your /tmp directory almost full? If lyx
> does not have enough space to copy and convert all the image files in the
> tmp directory strange things may happen.
>
> Ingar
>
>
I thought on that too. I moved the tmp folder in LyX temporarily to my
homefolder with more space, but the result was the same, no postscriptfile,
even if LyX worked noticeable faster.

Påvel

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

I've set up a repo on github for the program.

The code:
https://github.com/abarker/lyxNotebook

For a quick overview, see the first section of the documentation:
https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf

Re: Error with Lyx 2.0.3 and Knitr

[Eugene]

Hi

Running Lyx 2.0.3 on WinXP witn Knitr results in the following error

LyX: Cannot convert file

An error occurred while running:
Rscript --verbose --no-save --no-restore "C:/Program 
Files/Lyx20/bin/../Resources/scripts/lyxknitr.R" "C:/Documents and 
Settings/me/Local Settings/Temp/lyx_tmpdir.Hp4948/lyx_tmpbuf2/""Paper2.Rnw"
""C:/Documents and Settings/me/Local 
Settings/Temp/lyx_tmpdir.Hp4948/lyx_tmpbuf2/""Paper2.tex" ISO-8859-a5
"M:/REPOSITORY/Lyx_Paper2/"

Re: program to use Lyx as a code-evaluating notebook

[Pavel Sanda]

Allen Barker wrote:
>
> I've set up a repo on github for the program.

It maight be goo to add note to http://wiki.lyx.org/Tools/Tools
P

Re: program to use Lyx as a code-evaluating notebook

[Nico Williams]

On Wed, May 30, 2012 at 11:24 AM, Allen Barker  wrote:
> I've set up a repo on github for the program.
>
> The code:
> https://github.com/abarker/lyxNotebook
>
> For a quick overview, see the first section of the documentation:
> https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf

I looked at the README and I get it.  This is very much like the
weaver tool, that lets you compile statistics using R right in the LyX
document.  But yours is more generic.  The idea is very cool.  I
second the sentiment that this should be added to the tools wiki page.

Nico

PS: I have no use for this right now, but I'll keep it in mind.  One
use that comes to mind is using this approach to automatically test
code samples in a book, but that would need a way to request that code
be tested but output not included in the document.

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

On 05/30/2012 04:06 PM, Pavel Sanda wrote:

Allen Barker wrote:


I've set up a repo on github for the program.


It maight be goo to add note to http://wiki.lyx.org/Tools/Tools
P


Thanks, I've added a note to that list.

Re: program to use Lyx as a code-evaluating notebook

[Allen Barker]

On 05/30/2012 05:32 PM, Nico Williams wrote:

On Wed, May 30, 2012 at 11:24 AM, Allen Barker  wrote:

I've set up a repo on github for the program.

The code:
https://github.com/abarker/lyxNotebook

For a quick overview, see the first section of the documentation:
https://github.com/abarker/lyxNotebook/blob/master/lyxNotebookDocs.pdf


I looked at the README and I get it.  This is very much like the
weaver tool, that lets you compile statistics using R right in the LyX
document.  But yours is more generic.  The idea is very cool.  I
second the sentiment that this should be added to the tools wiki page.

Nico

PS: I have no use for this right now, but I'll keep it in mind.  One
use that comes to mind is using this approach to automatically test
code samples in a book, but that would need a way to request that code
be tested but output not included in the document.


The printing of cells of various types can be suppressed
by including a Latex command in the preamble or in an ERT.
To suppress printing of output cells for Python 2, for
example, you would add \lyxNotebookPrintOffOutputPythonTwo.
(The current implementation then uses \let to redefine
those cells to be Verbatim comment blocks.)

LyX cannot handle '$' sign in Sweave code chunk

[Lam Phung Khanh]

Dear all,

I used document class 'article' with Sweave module added in LyX version 2.0.3 
to write a short Sweave document:

Hi !
<<>>=
a <- c(1:10)
b <- c(11:20)
d <- cbind(a, b)
d$a
@

I got error: "LyX: cannot convert file" when compiled it. My suspect is LyX 
cannot handle the '$' sign in Sweave code chunk. When I used another way to 
write the last code line, it worked fine:

Hi !
<<>>=
a <- c(1:10)
b <- c(11:20)
d <- cbind(a, b)
d[,"a"]
@

I haven't known how to overcome it yet. It is a bit pity because for R-users, 
'$' is one of the most common sign used in the analysis.

Please forgive me if this email disturbs you. 

Thank you very much

Lam Phung Khanh
PhD student
Centre for Tropical Medicine
Oxford University Clinical Research Unit
764 Vo Van Kiet Street (Old: 190 Ben Ham Tu), Ward 1, District 5, Ho Chi Minh 
City
Vietnam

Wellcome Trust Major Overseas Programme

In partnership with
Hospital for Tropical Diseases

Tel: 84 8 39237954
Fax: 84 8 39238904
Mob: 84 (0) 915333751
E-mail: la...@oucru.org
Website: http://www.oucru.org

RE: LyX cannot handle '$' sign in Sweave code chunk

[Scott Kostyshak]

From: Lam Phung Khanh [la...@oucru.org]
Sent: Wednesday, May 30, 2012 10:54 PM

Note that I used knitr to test this, not Sweave. knitr is newer, has more 
features, and can do everything that Sweave can and a lot more. To use it, add 
the module Rnw (knitr) instead of Sweave. Is there a reason you want to use 
Sweave?

>I got error: "LyX: cannot convert file" when compiled it. My suspect is LyX 
>cannot handle the '$' sign in Sweave >code chunk. When I used another way to 
>write the last code line, it worked fine:

I don't think this is a LyX or a knitr error but a problem with your R code. R 
gives me the following error:

a <- c(1:10)
b <- c(11:20)
d <- cbind(a, b)
d$a
Error in d$a : $ operator is invalid for atomic vectors

The following runs fine for me in R and in LyX + knitr

a <- c(1:10)
b <- c(11:20)
d <- data.frame(a, b)
d$a

>Please forgive me if this email disturbs you.
Of course not! Feel free to ask any question about LyX + knitr.

Scott