Re: [Rd] Building a custom Windows installer
John, It is not clear to me what you actually did (and I am also assuming this is 32-bit R), but I surmise that you did not build R in your source directory. One of the first steps in doing so is to make src/gnuwin32/MkRules. (You are also likely to need to customize the file, possibly via a MkRules.local, to set ISDIR.) I've done a quick check, and in R 2.11.x AFAICS all that is needed is cd R_SOURCES/src/gnuwin32 make MkRules cd installer make myR IMAGEDIR=e:/temp/R-2.11.1 MDISDI=1 However, in 2.12.0 you will need to make R completely in the sources, as R is used for scripting. Brian On Tue, 13 Jul 2010, John Fox wrote: Dear r-devel list members, It's been several years since I last built a custom Windows installer for R, and despite my notes and the instructions in Sections 3.1.7 and D.4 of the R Installation and Administration Manual, I've run into a problem, receiving the following error message: --- snip --- C:\R\src\R-2.11.1\src\gnuwin32\installer>make myR IMAGEDIR=c:/temp/R-2.11.1 MDISDI=1 Makefile:3: ../MkRules: No such file or directory make: ../fixed/rwver.pl: Command not found make: ../fixed/rwver.pl: Command not found make: ../fixed/rwver.pl: Command not found make: ../fixed/rwver.pl: Command not found make: *** No rule to make target `../MkRules'. Stop. --- snip --- My path looks like this: --- snip --- C:\R\src\R-2.11.1\src\gnuwin32\installer>set path Path=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\Program Files\Commo n Files\Microsoft Shared\Windows Live;C:\GTK\bin;C:\Program Files\Insightful\spl us80\;C:\Program Files\ActiveState Komodo Edit 4\;.;c:\R\R-2.11.1\bin;C:\progra~ 1\miktex~1.7\miktex\bin;c:\progra~1\htmlhe~1;C:\Windows\system32;C:\Windows; C:\W indows\System32\Wbem;C:\Program Files\Common Files\Roxio Shared\DLLShared\;C:\Pr ogram Files\GnuWin32\bin;C:\Program Files\CollabNet Subversion;C:\Program Files\ MySQL\MySQL Server 5.1\bin;C:\Program Files\SAS\Shared Files\Formats;C:\Program Files\TortoiseSVN\bin;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Fil es\Smart Projects\IsoBuster;C:\Program Files\MiKTeX 2.7\miktex\bin\;C:\Program F iles\QuickTime\QTSystem\;C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files\SSH Communications Security\SSH Secure Shell;C:\Program Fi les\Bibtex2html;C:\Graphviz2.20\bin PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC --- snip --- The directory c:/temp/R-2.11.1 contains a complete customized installation of R, while C:\R\src\R-2.11.1 contains the unpacked R sources. This is on a Windows Vista system. I've updated Rtools to version 2.11. I can supply more information, but I'm not sure what's relevant. I don't think that I should have to place a MkRules file in the gnuwin32 directory, but I tried copying each the MkRules.dist and MkRules.rules files there in turn to MkRules. Neither worked; I apparently got farther copying MkRules.rules to MkRules, but eventually got another error: --- snip --- C:\R\src\R-2.11.1\src\gnuwin32\installer>make myR IMAGEDIR=c:/temp/R-2.11.1 MDISDI=1 echo "make.packages.html(.Library)" | c:/temp/R-2.11.1/bin/rterm --vanilla --sla ve LC_COLLATE=C Making packages.html ... done adding MD5 checksums perl JRins.pl R-2.11.1 c:/temp/R-2.11.1 1 1 0 R-core "/iscc" R.iss > myR.log /iscc: not found make: *** [myR] Error 127 --- snip --- Any help would be appreciated. John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Precompiled vignette on CRAN
Hello, my package passes R CMD check without any warnings on my local machine (Mac OS), as well as on Uwe Ligges' Winbuilder. On RForge, however, we sometimes run into problems building the Sweave vignettes. Now here's my question: is it necessary for a CRAN submission that the Sweave vignettes can be compiled on CRAN, or is it possible to provide the (locally compiled) pdf vignette to be included in the package? Best, Felix __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Building a custom Windows installer
Dear Brian, > -Original Message- > From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] > Sent: July-14-10 3:15 AM > To: John Fox > Cc: r-devel@r-project.org > Subject: Re: [Rd] Building a custom Windows installer > > John, > > It is not clear to me what you actually did (and I am also assuming > this is 32-bit R), but I surmise that you did not build R in your > source directory. Yes, that's right. It wasn't clear to me from the manual that it was necessary to build R (or as it turns out, just MkRules) when using IMAGEDIR. I guess that this has changed since I last built a custom installer, or my notes were incomplete. > One of the first steps in doing so is to make > src/gnuwin32/MkRules. (You are also likely to need to customize the > file, possibly via a MkRules.local, to set ISDIR.) Not necessary in my case, since Inno Setup is in the default location. > > I've done a quick check, and in R 2.11.x AFAICS all that is needed is > > cd R_SOURCES/src/gnuwin32 > make MkRules > cd installer > make myR IMAGEDIR=e:/temp/R-2.11.1 MDISDI=1 Yes, this works fine for me as well. Thank you very much. John > > However, in 2.12.0 you will need to make R completely in the sources, > as R is used for scripting. > > Brian > > On Tue, 13 Jul 2010, John Fox wrote: > > > Dear r-devel list members, > > > > It's been several years since I last built a custom Windows installer for > R, > > and despite my notes and the instructions in Sections 3.1.7 and D.4 of the > R > > Installation and Administration Manual, I've run into a problem, receiving > > the following error message: > > > > --- snip --- > > > > C:\R\src\R-2.11.1\src\gnuwin32\installer>make myR IMAGEDIR=c:/temp/R-2.11.1 > > MDISDI=1 > > Makefile:3: ../MkRules: No such file or directory > > make: ../fixed/rwver.pl: Command not found > > make: ../fixed/rwver.pl: Command not found > > make: ../fixed/rwver.pl: Command not found > > make: ../fixed/rwver.pl: Command not found > > make: *** No rule to make target `../MkRules'. Stop. > > > > --- snip --- > > > > My path looks like this: > > > > --- snip --- > > > > C:\R\src\R-2.11.1\src\gnuwin32\installer>set path > > Path=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\Program > > Files\Commo > > n Files\Microsoft Shared\Windows Live;C:\GTK\bin;C:\Program > > Files\Insightful\spl > > us80\;C:\Program Files\ActiveState Komodo Edit > > 4\;.;c:\R\R-2.11.1\bin;C:\progra~ > > > 1\miktex~1.7\miktex\bin;c:\progra~1\htmlhe~1;C:\Windows\system32;C:\Windows; > > C:\W > > indows\System32\Wbem;C:\Program Files\Common Files\Roxio > > Shared\DLLShared\;C:\Pr > > ogram Files\GnuWin32\bin;C:\Program Files\CollabNet Subversion;C:\Program > > Files\ > > MySQL\MySQL Server 5.1\bin;C:\Program Files\SAS\Shared > > Files\Formats;C:\Program > > > Files\TortoiseSVN\bin;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program > > Fil > > es\Smart Projects\IsoBuster;C:\Program Files\MiKTeX > > 2.7\miktex\bin\;C:\Program F > > iles\QuickTime\QTSystem\;C:\Program Files\Common Files\Microsoft > > Shared\Windows > > Live;C:\Program Files\SSH Communications Security\SSH Secure > > Shell;C:\Program Fi > > les\Bibtex2html;C:\Graphviz2.20\bin > > PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC > > > > --- snip --- > > > > The directory c:/temp/R-2.11.1 contains a complete customized installation > > of R, while C:\R\src\R-2.11.1 contains the unpacked R sources. This is on a > > Windows Vista system. I've updated Rtools to version 2.11. I can supply > > more information, but I'm not sure what's relevant. > > > > I don't think that I should have to place a MkRules file in the gnuwin32 > > directory, but I tried copying each the MkRules.dist and MkRules.rules > files > > there in turn to MkRules. Neither worked; I apparently got farther copying > > MkRules.rules to MkRules, but eventually got another error: > > > > --- snip --- > > > > C:\R\src\R-2.11.1\src\gnuwin32\installer>make myR IMAGEDIR=c:/temp/R-2.11.1 > > MDISDI=1 > > echo "make.packages.html(.Library)" | c:/temp/R-2.11.1/bin/rterm --vanilla > > --sla > > ve LC_COLLATE=C > > Making packages.html ... done > > adding MD5 checksums > > perl JRins.pl R-2.11.1 c:/temp/R-2.11.1 1 1 0 R-core > > "/iscc" R.iss > myR.log > > /iscc: not found > > make: *** [myR] Error 127 > > > > --- snip --- > > > > Any help would be appreciated. > > > > John > > > > > > John Fox > > Senator William McMaster > > Professor of Social Statistics > > Department of Sociology > > McMaster University > > Hamilton, Ontario, Canada > > web: socserv.mcmaster.ca/jfox > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University o
Re: [Rd] Precompiled vignette on CRAN
On Wed, 14 Jul 2010, Felix Schönbrodt wrote: Hello, my package passes R CMD check without any warnings on my local machine (Mac OS), as well as on Uwe Ligges' Winbuilder. On RForge, however, we sometimes run into problems building the Sweave vignettes. Just 'problems' is not helpful. Now here's my question: is it necessary for a CRAN submission that the Sweave vignettes can be compiled on CRAN, or is it possible to provide the (locally compiled) pdf vignette to be included in the package? This really is a question to ask the CRAN gatekeepers, but people are on vacation right now, so I've give some indication of my understanding. What does 'compiled' mean here? (Run through LaTeX? Run the R code?) There are examples on CRAN of packages which cannot re-make their vignettes without external files (e.g. LaTeX style files), or take hours (literally) to run the code. The source package should contain the PDF versions of the vignettes as made by the author. There is relevant advice in 'Writing R Extensions'. What the people who do the CRAN package checks do get unhappy about are packages which fail running the R code in their vignettes, since this often indicates a problem in the package which is not exercised by the examples nor tests. This gives a warning, as you will see in quite a few CRAN package checks. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Precompiled vignette on CRAN
On Jul 14, 2010, at 4:04 PM, Prof Brian Ripley wrote: > On Wed, 14 Jul 2010, Felix Schönbrodt wrote: > >> Hello, >> >> my package passes R CMD check without any warnings on my local machine (Mac >> OS), as well as on Uwe Ligges' Winbuilder. On RForge, however, we sometimes >> run into problems building the Sweave vignettes. > > Just 'problems' is not helpful. > FWIW I think it was a red herring - after bugfixes to the package and installing (unstated*) dependencies it works (possibly use of require instead of library in the vignette might help - I don't know what the best practice is). >> Now here's my question: is it necessary for a CRAN submission that the >> Sweave vignettes can be compiled on CRAN, or is it possible to provide the >> (locally compiled) pdf vignette to be included in the package? > > This really is a question to ask the CRAN gatekeepers, but people are on > vacation right now, so I've give some indication of my understanding. > > What does 'compiled' mean here? (Run through LaTeX? Run the R code?) There > are examples on CRAN of packages which cannot re-make their vignettes without > external files (e.g. LaTeX style files), or take hours (literally) to run the > code. The source package should contain the PDF versions of the vignettes as > made by the author. > > There is relevant advice in 'Writing R Extensions'. > > What the people who do the CRAN package checks do get unhappy about are > packages which fail running the R code in their vignettes, since this often > indicates a problem in the package which is not exercised by the examples nor > tests. This gives a warning, as you will see in quite a few CRAN package > checks. > In the case of TripleR R CMD check failed (i.e. error code != 0) because of the vignette. Cheers, Simon * - which reminds me -- what is the correct place to list vignette dependencies? "Suggests:" ? R CMD check simply fails in the vignette build when vignetts use unstated dependencies [via library()] - there is no explicit warning/error by check itself. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Precompiled vignette on CRAN
On 07/14/2010 01:04 PM, Prof Brian Ripley wrote:
> On Wed, 14 Jul 2010, Felix Schönbrodt wrote:
>
>> Hello,
>>
>> my package passes R CMD check without any warnings on my local machine
>> (Mac OS), as well as on Uwe Ligges' Winbuilder. On RForge, however, we
>> sometimes run into problems building the Sweave vignettes.
>
> Just 'problems' is not helpful.
>
>> Now here's my question: is it necessary for a CRAN submission that the
>> Sweave vignettes can be compiled on CRAN, or is it possible to provide
>> the (locally compiled) pdf vignette to be included in the package?
>
> This really is a question to ask the CRAN gatekeepers, but people are on
> vacation right now, so I've give some indication of my understanding.
>
> What does 'compiled' mean here? (Run through LaTeX? Run the R code?)
> There are examples on CRAN of packages which cannot re-make their
> vignettes without external files (e.g. LaTeX style files), or take hours
> (literally) to run the code. The source package should contain the PDF
> versions of the vignettes as made by the author.
>
> There is relevant advice in 'Writing R Extensions'.
While on this topic, how are non-Sweave files to be made accessible to
browseVignettes() and help(package=...)?
At one point 00Index.dcf files could be used to influence index
creation, and Writing R Extensions indicates that an inst/doc/index.html
file can also be used. The 00Index.dcf approach seems better (no need
for the user to track the appropriate html structure of R's help pages),
but regardless it seems 00Index.dcf is ignored (stronger than 'no longer
necessary' in Writing R Extensions) and index.html does not influence
what is displayed by help(package='...') or browseVignettes().
I'm basing this on the 'limma' package (which seems to have tried to be
a good citizen, with 00Index.dcf and index.html files) and running R in
a console with
> getOption('help_type')
NULL
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-07-14 r52526)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.5.12
Martin
>
> What the people who do the CRAN package checks do get unhappy about are
> packages which fail running the R code in their vignettes, since this
> often indicates a problem in the package which is not exercised by the
> examples nor tests. This gives a warning, as you will see in quite a
> few CRAN package checks.
>
>
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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