Re: [R-pkg-devel] Unable to create manual

[Edward Wei]

Hello Ivan.

The Does list.files(pattern = 'utils|Rout\\.fail') gave me something like
an empty string.

So after getting some in-person help on this issue, the key to resolving
this error was explicitly defining the environmental variables in the
console as:

set
PDFLATEX=C:\Users\edmon\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex



set
MAKEINDEX=C:\Users\edmon\AppData\Local\Programs\MiKTeX\miktex\bin\x64\makeindex


The makeindex was a package I was apparently missing for MikTex and I had
to download it as part of generating the manual.


I would have to set up the environmental variables every time that R got
started in order for the R CMD check to run smoothly.


Best regards,




On Mon, Sep 26, 2022 at 12:01 PM Ivan Krylov  wrote:

> On Mon, 26 Sep 2022 10:50:01 -0700
> Edward Wei  wrote:
>
> > 1. Where do I run "make check"?
>
> In the directory where R is built from source. If you're using a binary
> build of R, this isn't applicable.
>
> > 3. I get this back when I run the "tools::testInstalledPackages(scope
> > = "base")" on my RGUI.
> >
> > Error: testing 'utils' failed
> >
> > Where may I find the error log for this?
>
> testInstalledPackages() creates output files in the current directory.
> Does list.files(pattern = 'utils|Rout\\.fail') give you anything useful?
>
> --
> Best regards,
> Ivan
>

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Re: [R-pkg-devel] Unable to create manual

[Ivan Krylov]

On Mon, 26 Sep 2022 10:50:01 -0700
Edward Wei  wrote:

> 1. Where do I run "make check"?

In the directory where R is built from source. If you're using a binary
build of R, this isn't applicable.

> 3. I get this back when I run the "tools::testInstalledPackages(scope
> = "base")" on my RGUI.
> 
> Error: testing 'utils' failed
> 
> Where may I find the error log for this?

testInstalledPackages() creates output files in the current directory.
Does list.files(pattern = 'utils|Rout\\.fail') give you anything useful?

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Unable to create manual

[Edward Wei]

So I am looking at the R Installation and Administration section,
specifically section 3 for windows. . I have some inquiries.

1. Where do I run "make check"?
2. I got this when I was running the make check:
C:\Users\edmon\Documents\R\RFIN> R CMD make check
make: *** No rule to make target 'check'.  Stop.

I'm guessing I'm running it incorrectly.

3. I get this back when I run the "tools::testInstalledPackages(scope =
"base")" on my RGUI.

Error: testing 'utils' failed

Where may I find the error log for this?


Best regards,


On Sat, Sep 17, 2022 at 3:27 AM Tomas Kalibera 
wrote:

>
> On 9/16/22 20:17, Edward Wei wrote:
> > That is an interesting thought. I don't think I have downloaded LaTex
> > explicitly, however, I do have MikTex and I added that file to PATH
> > manually.
> >
> > This is what my current PATH calls:
> >
> "c:/rtools42/x86_64-w64-mingw32.static.posix/bin;c:/rtools42/usr/bin;C:\\Program
> > Files\\R\\R-4.2.0\\bin\\x64;C:\\Program Files (x86)\\Common
> >
> Files\\Oracle\\Java\\javapath;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program
> > Files\\Wolfram Research\\WolframScript\\;C:\\Program
> >
> Files\\Git\\cmd;C:\\Users\\edmon\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\edmon\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\edmon\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:/Program
> > Files/RStudio/bin/quarto/bin"
> >
> > I have been able to generate a PDF of my package by entering :
> > tools::texi2pdf(file = "avfintools.Rcheck/avfintools-manual.tex")
> > on the console.
> >
> > Is there a way to submit the manual manually rather than have it
> compiled?
> > Or is it a requirement for the manual to be able to be compiled from the
> > package?
> >
> > Thanks for your help,
>
> MikTeX is fine and common choice and works with R.
>
> R Admin manual has "Installing R under Windows" with more details there
> and in the linked documents, including
> Howto: Building R 4.2 and packages on Windows.
>
> There must be something special set up on your system that probably only
> debugging could reveal. Possibly some customization in any of the R
> startup files. Or some conflicting tool on the PATH (e.g. in Git?).
>
> Tomas
>
> >
> > On Wed, Sep 14, 2022 at 3:14 PM Uwe Ligges <
> lig...@statistik.tu-dortmund.de>
> > wrote:
> >
> >>
> >> On 14.09.2022 23:54, Duncan Murdoch wrote:
> >>> On 12/09/2022 9:09 a.m., Edward Wei wrote:
>  This is the following error message I get from R CMD check:
> 
>  LaTeX errors when creating PDF version.
>  This typically indicates Rd problems.
>  * checking PDF version of manual without index ... ERROR
>  Re-running with no redirection of stdout/stderr.
>  Hmm ... looks like a package
>  Converting parsed Rd's to LaTeX ...
>  Creating pdf output from LaTeX ...
>  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
>  quiet,  :
>  pdflatex is not available
> >>> This looks like a problem in the way tools::texi2dvi detects pdflatex.
> >>> If you have a valid LaTeX file, try running
> >>>
> >>> tools::texi2dvi(filename, pdf = TRUE)
> >>>
> >>> If that gives the same message, then debug(tools::texi2dvi), and
> repeat,
> >>> single stepping through the function to see what test it uses, and
> >>> figure out why it fails on your system.
> >> Or the env var PATH is overwritten once R get started, perhaps you have
> >> it in one of the files R process it at startup?
> >> Does Sys.getenv("PATH") show the pat to the LaTeX binary?
> >>
> >> Best,
> >> Uwe Ligges
> >>
> >>
> >>> Duncan Murdoch
> >>>
> >>>
>  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
>  quiet,  :
>  pdflatex is not available
>  Error in running tools::texi2pdf()
>  You may want to clean up by 'rm -Rf
>  C:/Users/edmon/AppData/Local/Temp/RtmpWkD7Iy/Rd2pdf35d81e3e188c'
>  * DONE
> 
>  Status: 1 ERROR, 1 WARNING, 2 NOTEs
> 
> 
>  Then, I tried debugging by isolating errors from the Rd to PDF
>  conversion.
> 
> 
>  C:\Users\edmon\Documents\R\RFIN> R CMD Rd2pdf avfintools --no-clean
>  Hmm ... looks like a package
>  Converting Rd files to LaTeX ...
>  Creating pdf output from LaTeX ...
>  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
>  quiet,  :
>  pdflatex is not available
>  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
>  quiet,  :
>  pdflatex is not available
>  Error in running tools::texi2pdf()
>  You may want to clean up by 'rm -Rf .Rd2pdf27964'
> 
> 
>  In this folder is the file Rd2.tex which I tried to complie into a
>  pdf. But
>  this error returns and PDF cannot be compiled. :
> 
> 
>  LaTeX Error: File `Rd.sty' not found.
> 
>  Type X to quit or  to proceed,
>  or enter new name. (Default 

Re: [R-pkg-devel] Unable to create manual

[Uwe Ligges]

On 16.09.2022 20:17, Edward Wei wrote:
That is an interesting thought. I don't think I have downloaded LaTex 
explicitly, however, I do have MikTex and I added that file to PATH 
manually.


This is what my current PATH calls:
"c:/rtools42/x86_64-w64-mingw32.static.posix/bin;c:/rtools42/usr/bin;C:\\Program 
Files\\R\\R-4.2.0\\bin\\x64;C:\\Program Files (x86)\\Common 
Files\\Oracle\\Java\\javapath;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program 
Files\\Wolfram Research\\WolframScript\\;C:\\Program 
Files\\Git\\cmd;C:\\Users\\edmon\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\edmon\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\edmon\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:/Program 
Files/RStudio/bin/quarto/bin"


I have been able to generate a PDF of my package by entering :
tools::texi2pdf(file = "avfintools.Rcheck/avfintools-manual.tex")
on the console.

Is there a way to submit the manual manually rather than have it 
compiled? Or is it a requirement for the manual to be able to be 
compiled from the package?



The latter, but the mechanism works on  CRAN, so you do not ned to worry 
about that.


Best,
Uwe Ligges



Thanks for your help,


On Wed, Sep 14, 2022 at 3:14 PM Uwe Ligges 
> wrote:




On 14.09.2022 23:54, Duncan Murdoch wrote:
 > On 12/09/2022 9:09 a.m., Edward Wei wrote:
 >> This is the following error message I get from R CMD check:
 >>
 >> LaTeX errors when creating PDF version.
 >> This typically indicates Rd problems.
 >> * checking PDF version of manual without index ... ERROR
 >> Re-running with no redirection of stdout/stderr.
 >> Hmm ... looks like a package
 >> Converting parsed Rd's to LaTeX ...
 >> Creating pdf output from LaTeX ...
 >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
 >> quiet,  :
 >>    pdflatex is not available
 >
 > This looks like a problem in the way tools::texi2dvi detects
pdflatex.
 > If you have a valid LaTeX file, try running
 >
 > tools::texi2dvi(filename, pdf = TRUE)
 >
 > If that gives the same message, then debug(tools::texi2dvi), and
repeat,
 > single stepping through the function to see what test it uses, and
 > figure out why it fails on your system.

Or the env var PATH is overwritten once R get started, perhaps you have
it in one of the files R process it at startup?
Does Sys.getenv("PATH") show the pat to the LaTeX binary?

Best,
Uwe Ligges


 > Duncan Murdoch
 >
 >
 >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
 >> quiet,  :
 >>    pdflatex is not available
 >> Error in running tools::texi2pdf()
 >> You may want to clean up by 'rm -Rf
 >> C:/Users/edmon/AppData/Local/Temp/RtmpWkD7Iy/Rd2pdf35d81e3e188c'
 >> * DONE
 >>
 >> Status: 1 ERROR, 1 WARNING, 2 NOTEs
 >>
 >>
 >> Then, I tried debugging by isolating errors from the Rd to PDF
 >> conversion.
 >>
 >>
 >> C:\Users\edmon\Documents\R\RFIN> R CMD Rd2pdf avfintools --no-clean
 >> Hmm ... looks like a package
 >> Converting Rd files to LaTeX ...
 >> Creating pdf output from LaTeX ...
 >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
 >> quiet,  :
 >>    pdflatex is not available
 >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
 >> quiet,  :
 >>    pdflatex is not available
 >> Error in running tools::texi2pdf()
 >> You may want to clean up by 'rm -Rf .Rd2pdf27964'
 >>
 >>
 >> In this folder is the file Rd2.tex which I tried to complie into a
 >> pdf. But
 >> this error returns and PDF cannot be compiled. :
 >>
 >>
 >> LaTeX Error: File `Rd.sty' not found.
 >>
 >> Type X to quit or  to proceed,
 >> or enter new name. (Default extension: sty)
 >>
 >> Enter file name:
 >> ! Emergency stop.
 >> 
 >>
 >> l.4 \usepackage
 >>     {makeidx}^^M
 >> ==> Fatal error occurred, no output PDF file produced!
 >>
 >>
 >> Thanks for your help,
 >>
 >> [[alternative HTML version deleted]]
 >>
 >> __
 >> R-package-devel@r-project.org
 mailing list
 >> https://stat.ethz.ch/mailman/listinfo/r-package-devel

 >
 > __
 > R-package-devel@r-project.org
 mailing list
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Re: [R-pkg-devel] Unable to create manual

[Tomas Kalibera]

On 9/16/22 20:17, Edward Wei wrote:

That is an interesting thought. I don't think I have downloaded LaTex
explicitly, however, I do have MikTex and I added that file to PATH
manually.

This is what my current PATH calls:
"c:/rtools42/x86_64-w64-mingw32.static.posix/bin;c:/rtools42/usr/bin;C:\\Program
Files\\R\\R-4.2.0\\bin\\x64;C:\\Program Files (x86)\\Common
Files\\Oracle\\Java\\javapath;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program
Files\\Wolfram Research\\WolframScript\\;C:\\Program
Files\\Git\\cmd;C:\\Users\\edmon\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\edmon\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\edmon\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:/Program
Files/RStudio/bin/quarto/bin"

I have been able to generate a PDF of my package by entering :
tools::texi2pdf(file = "avfintools.Rcheck/avfintools-manual.tex")
on the console.

Is there a way to submit the manual manually rather than have it compiled?
Or is it a requirement for the manual to be able to be compiled from the
package?

Thanks for your help,


MikTeX is fine and common choice and works with R.

R Admin manual has "Installing R under Windows" with more details there 
and in the linked documents, including

Howto: Building R 4.2 and packages on Windows.

There must be something special set up on your system that probably only 
debugging could reveal. Possibly some customization in any of the R 
startup files. Or some conflicting tool on the PATH (e.g. in Git?).


Tomas



On Wed, Sep 14, 2022 at 3:14 PM Uwe Ligges 
wrote:



On 14.09.2022 23:54, Duncan Murdoch wrote:

On 12/09/2022 9:09 a.m., Edward Wei wrote:

This is the following error message I get from R CMD check:

LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Converting parsed Rd's to LaTeX ...
Creating pdf output from LaTeX ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
quiet,  :
pdflatex is not available

This looks like a problem in the way tools::texi2dvi detects pdflatex.
If you have a valid LaTeX file, try running

tools::texi2dvi(filename, pdf = TRUE)

If that gives the same message, then debug(tools::texi2dvi), and repeat,
single stepping through the function to see what test it uses, and
figure out why it fails on your system.

Or the env var PATH is overwritten once R get started, perhaps you have
it in one of the files R process it at startup?
Does Sys.getenv("PATH") show the pat to the LaTeX binary?

Best,
Uwe Ligges



Duncan Murdoch



Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
quiet,  :
pdflatex is not available
Error in running tools::texi2pdf()
You may want to clean up by 'rm -Rf
C:/Users/edmon/AppData/Local/Temp/RtmpWkD7Iy/Rd2pdf35d81e3e188c'
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs


Then, I tried debugging by isolating errors from the Rd to PDF
conversion.


C:\Users\edmon\Documents\R\RFIN> R CMD Rd2pdf avfintools --no-clean
Hmm ... looks like a package
Converting Rd files to LaTeX ...
Creating pdf output from LaTeX ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
quiet,  :
pdflatex is not available
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
quiet,  :
pdflatex is not available
Error in running tools::texi2pdf()
You may want to clean up by 'rm -Rf .Rd2pdf27964'


In this folder is the file Rd2.tex which I tried to complie into a
pdf. But
this error returns and PDF cannot be compiled. :


LaTeX Error: File `Rd.sty' not found.

Type X to quit or  to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.


l.4 \usepackage
 {makeidx}^^M
==> Fatal error occurred, no output PDF file produced!


Thanks for your help,

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Re: [R-pkg-devel] Unable to create manual

[Edward Wei]

My next steps in debugging this is:
1. make sure my latex CAN generate PDFs by editing .tex file
2. Run pdflatex as an Admin
3. Download "texinfo" externally (unable to do in R studio as it says it is
incompatible with this version of R)
4. Inspect Rd files

I have made no real progress on this bug...

What is interesting is that previously, before I changed my code for
feedback from manual review, this didn't happen.

On Wed, Sep 14, 2022 at 1:30 PM Matthias Gondan 
wrote:

> That’s interesting. I was just wondering if it is installed, given the
> message „pdflatex is not available“.
>
>
>
>
>
>
>
> *Von: *Edward Wei 
> *Gesendet: *Mittwoch, 14. September 2022 22:26
> *An: *Matthias Gondan 
> *Cc: *r-package-devel@r-project.org
> *Betreff: *Re: [R-pkg-devel] Unable to create manual
>
>
>
> Hello Matthias.
>
>
>
> This is what is returned when I try pdflatex on terminal
>
>
>
> This is pdfTeX, Version 3.141592653-2.6-1.40.24 (MiKTeX 22.8.28)
> (preloaded format=pdflatex.fmt)
>  restricted \write18 enabled.
> **
>
>
>
>
>
>
>
> On Mon, Sep 12, 2022 at 7:20 AM Matthias Gondan 
> wrote:
>
> You may wish to check first if pdflatex works from the folder, i.e.
>
>
>
> C:\Users\edmon\Documents\R\RFIN> pdflatex
>
>
>
> The problem with Rd.sty may be unrelated.
>
>
>
>
>
> *Von: *Edward Wei 
> *Gesendet: *Montag, 12. September 2022 15:09
> *An: *r-package-devel@r-project.org
> *Betreff: *[R-pkg-devel] Unable to create manual
>
>
>
> This is the following error message I get from R CMD check:
>
>
>
> LaTeX errors when creating PDF version.
>
> This typically indicates Rd problems.
>
> * checking PDF version of manual without index ... ERROR
>
> Re-running with no redirection of stdout/stderr.
>
> Hmm ... looks like a package
>
> Converting parsed Rd's to LaTeX ...
>
> Creating pdf output from LaTeX ...
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>
>   pdflatex is not available
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>
>   pdflatex is not available
>
> Error in running tools::texi2pdf()
>
> You may want to clean up by 'rm -Rf
>
> C:/Users/edmon/AppData/Local/Temp/RtmpWkD7Iy/Rd2pdf35d81e3e188c'
>
> * DONE
>
>
>
> Status: 1 ERROR, 1 WARNING, 2 NOTEs
>
>
>
>
>
> Then, I tried debugging by isolating errors from the Rd to PDF conversion.
>
>
>
>
>
> C:\Users\edmon\Documents\R\RFIN> R CMD Rd2pdf avfintools --no-clean
>
> Hmm ... looks like a package
>
> Converting Rd files to LaTeX ...
>
> Creating pdf output from LaTeX ...
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>
>   pdflatex is not available
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>
>   pdflatex is not available
>
> Error in running tools::texi2pdf()
>
> You may want to clean up by 'rm -Rf .Rd2pdf27964'
>
>
>
>
>
> In this folder is the file Rd2.tex which I tried to complie into a pdf. But
>
> this error returns and PDF cannot be compiled. :
>
>
>
>
>
> LaTeX Error: File `Rd.sty' not found.
>
>
>
> Type X to quit or  to proceed,
>
> or enter new name. (Default extension: sty)
>
>
>
> Enter file name:
>
> ! Emergency stop.
>
> 
>
>
>
> l.4 \usepackage
>
>{makeidx}^^M
>
> ==> Fatal error occurred, no output PDF file produced!
>
>
>
>
>
> Thanks for your help,
>
>
>
>  [[alternative HTML version deleted]]
>
>
>
> __
>
> R-package-devel@r-project.org mailing list
>
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
>
>

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Re: [R-pkg-devel] Unable to create manual

[Uwe Ligges]

On 12.09.2022 15:09, Edward Wei wrote:

This is the following error message I get from R CMD check:

LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Converting parsed Rd's to LaTeX ...
Creating pdf output from LaTeX ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
   pdflatex is not available




Install some LaTeX distribution?

Best,
Uwe Ligges




Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
   pdflatex is not available
Error in running tools::texi2pdf()
You may want to clean up by 'rm -Rf
C:/Users/edmon/AppData/Local/Temp/RtmpWkD7Iy/Rd2pdf35d81e3e188c'
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs


Then, I tried debugging by isolating errors from the Rd to PDF conversion.


C:\Users\edmon\Documents\R\RFIN> R CMD Rd2pdf avfintools --no-clean
Hmm ... looks like a package
Converting Rd files to LaTeX ...
Creating pdf output from LaTeX ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
   pdflatex is not available
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
   pdflatex is not available
Error in running tools::texi2pdf()
You may want to clean up by 'rm -Rf .Rd2pdf27964'


In this folder is the file Rd2.tex which I tried to complie into a pdf. But
this error returns and PDF cannot be compiled. :


LaTeX Error: File `Rd.sty' not found.

Type X to quit or  to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.


l.4 \usepackage
{makeidx}^^M
==> Fatal error occurred, no output PDF file produced!


Thanks for your help,

[[alternative HTML version deleted]]

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