dev=tikz doesn't work - fix in previous discussion doesn't work
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nicky
May 22, 2012, 3:27:36 PM5/22/12
to knitr
Hello all,
I'm running Yihui's knitr-manual.Rnw example (https://raw.github.com/
yihui/knitr/master/inst/examples/knitr-manual.Rnw). After typing
knit('knitr-manual.Rnw') in the R console, I get the following error:
Warning: running command 'C:\PROGRA~2\MIKTEX~1.9\miktex\bin
\pdflatex.exe "manual-cars-demo1.tikz"' had status 1
label: cars-demo (with options)
List of 6
$ dev : chr "tikz"
$ fig.width : num 4
$ fig.height: num 2.8
$ out.width : chr ".45\\textwidth"
$ message : logi FALSE
$ cache : logi TRUE
Error in process_file(text) :
Quitting from lines 82-88: Error : failed to compile figure/manual-
cars-demo1.tikz to PDF
I tried the fix mentioned in previous discussion at:
https://groups.google.com/group/knitr/browse_thread/thread/3f1393dcca036ba0/efb0994d2d084090?#efb0994d2d084090
Try 1: pdflatex manual-cars-demo1.tikz
this generates a file called manual-low-level-plots1.pdf.
However, this figure is a truncated version. The xlim is from 0 to 10
(supposed to be 0 to 25) and ylim is from 0 to 10 which should be from
0 to 120). Thus, the linear function in the original plot is not
shown.
Try 2:
> library(tikzDevice)
> getOption("tikzDefaultEngine")
[1] "pdftex"
> getOption('tikzLatex')
pdflatex
"C:\\PROGRA~2\\MIKTEX~1.9\\miktex\\bin\\pdflatex.exe"
Best regards,
nicky
I'm running Yihui's knitr-manual.Rnw example (https://raw.github.com/
yihui/knitr/master/inst/examples/knitr-manual.Rnw). After typing
knit('knitr-manual.Rnw') in the R console, I get the following error:
Warning: running command 'C:\PROGRA~2\MIKTEX~1.9\miktex\bin
\pdflatex.exe "manual-cars-demo1.tikz"' had status 1
label: cars-demo (with options)
List of 6
$ dev : chr "tikz"
$ fig.width : num 4
$ fig.height: num 2.8
$ out.width : chr ".45\\textwidth"
$ message : logi FALSE
$ cache : logi TRUE
Error in process_file(text) :
Quitting from lines 82-88: Error : failed to compile figure/manual-
cars-demo1.tikz to PDF
I tried the fix mentioned in previous discussion at:
https://groups.google.com/group/knitr/browse_thread/thread/3f1393dcca036ba0/efb0994d2d084090?#efb0994d2d084090
Try 1: pdflatex manual-cars-demo1.tikz
this generates a file called manual-low-level-plots1.pdf.
However, this figure is a truncated version. The xlim is from 0 to 10
(supposed to be 0 to 25) and ylim is from 0 to 10 which should be from
0 to 120). Thus, the linear function in the original plot is not
shown.
Try 2:
> library(tikzDevice)
> getOption("tikzDefaultEngine")
[1] "pdftex"
> getOption('tikzLatex')
pdflatex
"C:\\PROGRA~2\\MIKTEX~1.9\\miktex\\bin\\pdflatex.exe"
Best regards,
nicky
Yihui Xie
May 22, 2012, 4:55:56 PM5/22/12
to nicky, knitr
Can you check the LaTeX log file manual-cars-demo1.log and see what
exactly is the error there?
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
exactly is the error there?
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
nicky
May 22, 2012, 5:02:28 PM5/22/12
to knitr
since running knit('knitr-manual.Rnw') fails, I cannot even see a .tex
file generated ...
On May 22, 3:55 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> Can you check the LaTeX log file manual-cars-demo1.log and see what
> exactly is the error there?
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyi...@gmail.com>
file generated ...
On May 22, 3:55 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> Can you check the LaTeX log file manual-cars-demo1.log and see what
> exactly is the error there?
>
> Regards,
> Yihui
> --
> Phone: 515-294-2465 Web:http://yihui.name
> Department of Statistics, Iowa State University
> 2215 Snedecor Hall, Ames, IA
>
>
>
>
>
>
>
> On Tue, May 22, 2012 at 2:27 PM, nicky <nickyt...@gmail.com> wrote:
> > Hello all,
>
> > I'm running Yihui's knitr-manual.Rnw example (https://raw.github.com/
> > yihui/knitr/master/inst/examples/knitr-manual.Rnw). After typing
> > knit('knitr-manual.Rnw') in the R console, I get the following error:
>
> > Warning: running command 'C:\PROGRA~2\MIKTEX~1.9\miktex\bin
> > \pdflatex.exe "manual-cars-demo1.tikz"' had status 1
> > label: cars-demo (with options)
> > List of 6
> > $ dev : chr "tikz"
> > $ fig.width : num 4
> > $ fig.height: num 2.8
> > $ out.width : chr ".45\\textwidth"
> > $ message : logi FALSE
> > $ cache : logi TRUE
>
> > Error in process_file(text) :
> > Quitting from lines 82-88: Error : failed to compile figure/manual-
> > cars-demo1.tikz to PDF
>
> > I tried the fix mentioned in previous discussion at:
> >https://groups.google.com/group/knitr/browse_thread/thread/3f1393dcca...
> Department of Statistics, Iowa State University
> 2215 Snedecor Hall, Ames, IA
>
>
>
>
>
>
>
> On Tue, May 22, 2012 at 2:27 PM, nicky <nickyt...@gmail.com> wrote:
> > Hello all,
>
> > I'm running Yihui's knitr-manual.Rnw example (https://raw.github.com/
> > yihui/knitr/master/inst/examples/knitr-manual.Rnw). After typing
> > knit('knitr-manual.Rnw') in the R console, I get the following error:
>
> > Warning: running command 'C:\PROGRA~2\MIKTEX~1.9\miktex\bin
> > \pdflatex.exe "manual-cars-demo1.tikz"' had status 1
> > label: cars-demo (with options)
> > List of 6
> > $ dev : chr "tikz"
> > $ fig.width : num 4
> > $ fig.height: num 2.8
> > $ out.width : chr ".45\\textwidth"
> > $ message : logi FALSE
> > $ cache : logi TRUE
>
> > Error in process_file(text) :
> > Quitting from lines 82-88: Error : failed to compile figure/manual-
> > cars-demo1.tikz to PDF
>
> > I tried the fix mentioned in previous discussion at:
nicky
May 22, 2012, 5:05:02 PM5/22/12
to knitr
Perhaps the error message given by R is more informative (previous
error message is from Rstudio):
pdflatex.exe: Windows API error 161: The specified path is invalid.
pdflatex.exe: Data: \\mdadqsfs02\workspace\ptong1\TCGA\OV\Analysis
\tempRun\errorReport\figure\.:\\mdadqsfs02/workspace/ptong1/TCGA/OV/
Analysis/tempRun/errorReport:
cars-demo1.tikz to PDF
error message is from Rstudio):
pdflatex.exe: Windows API error 161: The specified path is invalid.
pdflatex.exe: Data: \\mdadqsfs02\workspace\ptong1\TCGA\OV\Analysis
\tempRun\errorReport\figure\.:\\mdadqsfs02/workspace/ptong1/TCGA/OV/
Analysis/tempRun/errorReport:
Warning: running command 'C:\PROGRA~2\MIKTEX~1.9\miktex\bin
\pdflatex.exe "manual-cars-demo1.tikz"' had status 1
label: cars-demo (with options)
List of 6
$ dev : chr "tikz"
$ fig.width : num 4
$ fig.height: num 2.8
$ out.width : chr ".45\\textwidth"
$ message : logi FALSE
$ cache : logi TRUE
Error in process_file(text) :
Quitting from lines 83-89: Error : failed to compile figure/manual-
\pdflatex.exe "manual-cars-demo1.tikz"' had status 1
label: cars-demo (with options)
List of 6
$ dev : chr "tikz"
$ fig.width : num 4
$ fig.height: num 2.8
$ out.width : chr ".45\\textwidth"
$ message : logi FALSE
$ cache : logi TRUE
Error in process_file(text) :
cars-demo1.tikz to PDF
Yihui Xie
May 22, 2012, 5:13:34 PM5/22/12
to nicky, knitr
OK, this is another case of LaTeX failure on a network drive under
Windows. It was reported a few weeks ago:
http://groups.google.com/group/knitr/browse_thread/thread/10d4043ecc88cbc5
Similarly, can you try the latest version on Github?
https://github.com/yihui/knitr Thanks!
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Windows. It was reported a few weeks ago:
http://groups.google.com/group/knitr/browse_thread/thread/10d4043ecc88cbc5
Similarly, can you try the latest version on Github?
https://github.com/yihui/knitr Thanks!
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
nicky
May 22, 2012, 10:23:03 PM5/22/12
to knitr
Yes! After installing the latest version of knitr from Gibhub,
the .tex file can be generated (both R console and Rstudio). However,
when I use Rstudio to compile pdf, I still get error message:
--------
output file: \\mdadqsfs02\workspace\ptong1\TCGA\OV\Analysis\tempRun
\errorReport\knitr-manual.tex
>
>
Running pdflatex.exe on knitr-manual.tex...failed
--------
Strange enough, knitr-manual.pdf is generated accompanying this error
message. However, the citations in pdf file becomes question marks. I
do have the knitr-manual.bib and knitr-packages.bib under the same
directory. I deleted the following command in the .Rnw file since I
cannot find homework1-xie.R file:
<<read-chunk, eval=FALSE>>=
read_chunk('homework1-xie.R')
@
I'm not sure whether this problem comes from knitr or Rstudio. I'm
copying the knitr-manual.log file below for your reference.
I really appreciate your help and efforts.
Best,
Nicky
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2.9/fonts/type1/public/amsfonts/cm/cmtt10.pfb><C:/Users/ptong1/
AppData/Roaming
/MiKTeX/2.9/fonts/type1/public/mathpazo/fplmri.pfb><C:/Program Files
(x86)/MiKT
eX 2.9/fonts/type1/public/lm/lmss10.pfb><C:/Program Files (x86)/MiKTeX
2.9/font
s/type1/public/lm/lmtk10.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/
type1/pub
lic/lm/lmtt10.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/
public/lm/lmtt
8.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/palatino/
uplb8a.pfb><C
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uplr8a.pfb><C:/Progra
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Output written on knitr-manual.pdf (11 pages, 754465 bytes).
PDF statistics:
427 PDF objects out of 1000 (max. 8388607)
47 named destinations out of 1000 (max. 500000)
465 words of extra memory for PDF output out of 10000 (max. 10000000)
On May 22, 4:13 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> OK, this is another case of LaTeX failure on a network drive under
> Windows. It was reported a few weeks ago:http://groups.google.com/group/knitr/browse_thread/thread/10d4043ecc8...
the .tex file can be generated (both R console and Rstudio). However,
when I use Rstudio to compile pdf, I still get error message:
--------
output file: \\mdadqsfs02\workspace\ptong1\TCGA\OV\Analysis\tempRun
\errorReport\knitr-manual.tex
>
>
Running pdflatex.exe on knitr-manual.tex...failed
--------
Strange enough, knitr-manual.pdf is generated accompanying this error
message. However, the citations in pdf file becomes question marks. I
do have the knitr-manual.bib and knitr-packages.bib under the same
directory. I deleted the following command in the .Rnw file since I
cannot find homework1-xie.R file:
<<read-chunk, eval=FALSE>>=
read_chunk('homework1-xie.R')
@
I'm not sure whether this problem comes from knitr or Rstudio. I'm
copying the knitr-manual.log file below for your reference.
I really appreciate your help and efforts.
Best,
Nicky
----------------------------------------------
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)
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eX 2.9/fonts/type1/public/lm/lmss10.pfb><C:/Program Files (x86)/MiKTeX
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s/type1/public/lm/lmtk10.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/
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lic/lm/lmtt10.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/
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8.pfb><C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw/palatino/
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Output written on knitr-manual.pdf (11 pages, 754465 bytes).
PDF statistics:
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On May 22, 4:13 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> OK, this is another case of LaTeX failure on a network drive under
>
> Similarly, can you try the latest version on Github?https://github.com/yihui/knitrThanks!
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyi...@gmail.com>
> Similarly, can you try the latest version on Github?https://github.com/yihui/knitrThanks!
>
> Regards,
> Yihui
> --
Yihui Xie
May 22, 2012, 11:05:50 PM5/22/12
to nicky, knitr
Weird. The LaTeX log says the compilation was successful.
The chunk containing read_chunk() was set to eval=FALSE, so it really
does not matter when the file does not exist.
Which version of RStudio are you using? The latest version is 0.96
(http://rstudio.org/download/desktop). Can you try to compile the
manual in a local hard drive?
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
The chunk containing read_chunk() was set to eval=FALSE, so it really
does not matter when the file does not exist.
Which version of RStudio are you using? The latest version is 0.96
(http://rstudio.org/download/desktop). Can you try to compile the
manual in a local hard drive?
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
nicky
May 22, 2012, 11:20:52 PM5/22/12
to knitr
My Rstudio version is: 0.96.122, the latest version. R is 2.15.0
Compiling it on local drive still failed:
------
output file: C:\Users\ptong1\Desktop\LocalErrorReport\knitr-manual.tex
>
>
Running pdflatex.exe on knitr-manual.tex...failed
-----
Best,
Nicky
On May 22, 10:05 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> Weird. The LaTeX log says the compilation was successful.
>
> The chunk containing read_chunk() was set to eval=FALSE, so it really
> does not matter when the file does not exist.
>
> Which version of RStudio are you using? The latest version is 0.96
> (http://rstudio.org/download/desktop). Can you try to compile the
> manual in a local hard drive?
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyi...@gmail.com>
Compiling it on local drive still failed:
------
output file: C:\Users\ptong1\Desktop\LocalErrorReport\knitr-manual.tex
>
>
Running pdflatex.exe on knitr-manual.tex...failed
-----
Nicky
On May 22, 10:05 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> Weird. The LaTeX log says the compilation was successful.
>
> The chunk containing read_chunk() was set to eval=FALSE, so it really
> does not matter when the file does not exist.
>
> Which version of RStudio are you using? The latest version is 0.96
> (http://rstudio.org/download/desktop). Can you try to compile the
> manual in a local hard drive?
>
> Regards,
> Yihui
> --
Yihui Xie
May 22, 2012, 11:32:02 PM5/22/12
to nicky, knitr
knitr-manual.Rnw is too big to diagnose the problem; you can cook up a
smaller Rnw document, e.g.
\documentclass{article}
\begin{document}
<<dev='tikz'>>=
plot(1)
@
\end{document}
If this does not work on your local or network drive but pdflatex
works separately, you probably need to report to RStudio developers.
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
smaller Rnw document, e.g.
\documentclass{article}
\begin{document}
<<dev='tikz'>>=
plot(1)
@
\end{document}
If this does not work on your local or network drive but pdflatex
works separately, you probably need to report to RStudio developers.
Regards,
Yihui
--
Yihui Xie <xiey...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
nicky
May 22, 2012, 11:37:33 PM5/22/12
to knitr
I can run this toy example both on local and server drive. This
persuades me knitr works properly on my machine. Thanks so much!
On May 22, 10:32 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> knitr-manual.Rnw is too big to diagnose the problem; you can cook up a
> smaller Rnw document, e.g.
>
> \documentclass{article}
> \begin{document}
> <<dev='tikz'>>=
> plot(1)
> @
> \end{document}
>
> If this does not work on your local or network drive but pdflatex
> works separately, you probably need to report to RStudio developers.
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyi...@gmail.com>
persuades me knitr works properly on my machine. Thanks so much!
On May 22, 10:32 pm, Yihui Xie <xieyi...@gmail.com> wrote:
> knitr-manual.Rnw is too big to diagnose the problem; you can cook up a
> smaller Rnw document, e.g.
>
> \documentclass{article}
> \begin{document}
> <<dev='tikz'>>=
> plot(1)
> @
> \end{document}
>
> If this does not work on your local or network drive but pdflatex
> works separately, you probably need to report to RStudio developers.
>
> Regards,
> Yihui
> --
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