[Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
When I did install.packages(sqldf) on Windows and Mac OSX, it installed fine. However, when I did it on my Debian Squeeze box under R 2.14.0, it failed. I discovered that three of the dependent packages, chron, proto, and gsubfn, do not include a NAMESPACE file in their distribution tar.gz files. I contacted the developer, who told me that, for packages without a NAMESPACE file, R 2.14 (but not early versions of R) generates a NAMESPACE file. My workaround to get sqldf installed was to copy the generated NAMESPACE files from my Mac to my Debian squeeze box and use R CMD INSTALL to install the packages. Although I read As from R 2.14.0 all packages will be installed with a namespace: rather than relying on this mechanism authors are strongly encouraged to add a namespace for themselves. on http://cran.r-project.org/doc/manuals/R-exts.html#Package-namespaces it nevertheless appears to me that this behavior (not generating NAMESPACE files) is peculiar to my Debian installation (since it worked on the Windows and Mac machines). Please let me know if you need more details or further research. R totally ROCKS! [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. Uwe ligges On 08.11.2011 10:49, Art Eschenlauer wrote: When I did install.packages(sqldf) on Windows and Mac OSX, it installed fine. However, when I did it on my Debian Squeeze box under R 2.14.0, it failed. I discovered that three of the dependent packages, chron, proto, and gsubfn, do not include a NAMESPACE file in their distribution tar.gz files. I contacted the developer, who told me that, for packages without a NAMESPACE file, R 2.14 (but not early versions of R) generates a NAMESPACE file. My workaround to get sqldf installed was to copy the generated NAMESPACE files from my Mac to my Debian squeeze box and use R CMD INSTALL to install the packages. Although I read As from R 2.14.0 all packages will be installed with a namespace: rather than relying on this mechanism authors are strongly encouraged to add a namespace for themselves. on http://cran.r-project.org/doc/manuals/R-exts.html#Package-namespaces it nevertheless appears to me that this behavior (not generating NAMESPACE files) is peculiar to my Debian installation (since it worked on the Windows and Mac machines). Please let me know if you need more details or further research. R totally ROCKS! [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
2011/11/8 Uwe Ligges lig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
On Tue, Nov 8, 2011 at 10:31 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: 2011/11/8 Uwe Ligges lig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html HIt send by mistake. I understand that its being fixed already on CRAN for that platform. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. The essential part of the question was: However, when I did it on my Debian Squeeze box under R 2.14.0, it failed. and it does not fail under any R-2.14.0 if you look at the page you cited above. Best, Uwe Ligges __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
2011/11/8 Uwe Ligges lig...@statistik.tu-dortmund.de: On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. OK. One would have thought that the checks on CRAN would be consistent with the package pages which link to them. The summary table at check_results_sqldf.html does not actually give the version that is being tested so its only by clicking each of the links on the summary table that one would uncover this inconsistency. Regarding quoting, the mail server seems to reject posts from gmail for all sorts of unknown reasons and quoting large posts very well might be one of them so one has to be extremely careful. For a while (this is some time ago) I was unable to post at all but over time learned that if I was sure to bottom rather than top post and not quote too much then it would get through. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN: How to list a non-Sweave doc under Vignettes: on package page?
Hi,
here's what I do:
I have two vignettes that are actually proper .Rnw files but the size of
the data used is not acceptable for CRAN nor polite to any unsuspecting
user.
So
- (I provide the original .Rnw and the data for download at r-forge)
- produce a .pdf from there in a directory external to the package
- have a fake .Rnw in the vignettes directory (actually still
inst/doc) that provides the keywords for the vignette listing:
--- beginning of chondro.Rnw ---
% for the real source, see http://hyperspec.r-forge.r-project.org/
% \VignetteIndexEntry{Vignette on the chondro data set. Shows common
Preprocessing tasks for Raman spectra, principal component analysis
(PCA), and hierarchical cluster analysis.}
% \VignetteKeywords{chondro, hyperSpec, cluster analysis, preprocessing,
Raman, principal component analysis, PCA}
% \VignettePackage{hyperSpec}
--- end of chondro.Rnw ---
- and have a Makefile in the directory with the relevant parts:
chondro.pdf:
rm -f chondro.tex
%.pdf: %.Rnw
$(R_HOME)/bin/Rscript -e library (tools); Sweave(\$(F)\);
texi2dvi(\$(basename $(F)).tex\, pdf = TRUE, clean = TRUE);
gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen
-dAutoRotatePages=/None \
-dDownsampleColorImages=false -dNOPAUSE -dQUIET -dBATCH
-dDownsampleColorImages=false \
-sOutputFile=tmp.pdf $@ qpdf tmp.pdf $@
rm tmp.pdf
rm -rf fig
rm -f $(basename $(F)).tex
rm -f Rplots.pdf
It is important that the .Rnw actually works - the Makefile is used only
_after_ Sweaving. But the makefile ensures that the .pdf of
corresponding name is not destroyed during the attempt to build it from
the .Rnw.
You can find the complete directory at:
https://r-forge.r-project.org/scm/viewvc.php/src/hyperSpec/inst/doc/?root=hyperspec
This way the vignette is listed correctly and I ship the .pdf only once.
So in priciple, everything that is a pdf is not far from being first
class citizen. The second class solution for non-pdf documents would be
a pdf containing the link to the actual file.
I don't remember where I got the idea, but I think it was one of Dirk
Eddelbüttel's packages. So: thanks, Dirk!
Best,
Claudia
Am 08.11.2011 05:23, schrieb Hadley Wickham:
How CRAN behaves and how the help package system behaves may be two
different problems. My question is specifically on how CRAN works.
To have inst/doc/ documents to be listed on the package's help page,
you can add an inst/doc/index.html file, cf. Section 'Writing package
vignettes' in 'Writing R Extensions'. You can use the following
index.html file as a template:
But they still won't be listed under vignette() - I see this solution
as a temporary hack until non-Sweave vignettes become first class
citizens.
Hadley
--
Claudia Beleites
Spectroscopy/Imaging
Institute of Photonic Technology
Albert-Einstein-Str. 9
07745 Jena
Germany
email: claudia.belei...@ipht-jena.de
phone: +49 3641 206-133
fax: +49 2641 206-399
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Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
On 08.11.2011 17:04, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. OK. One would have thought that the checks on CRAN would be consistent with the package pages which link to them. I only see consistent information on that page. And it should be like that within few hours after a change. Syncing the logs from at least 4 different sources and regenerating the overview page has to happen sometime and you can always visit between two updates so you may have seen an inconsistency that is no longer there. The summary table at check_results_sqldf.html does not actually give the version that is being tested It does, that's what the Version column contains. And the R version is also reported in the first column. You see check fro R-devel, R-release and R-oldrelease. uwe so its only by clicking each of the links on the summary table that one would uncover this inconsistency. Regarding quoting, the mail server seems to reject posts from gmail for all sorts of unknown reasons and quoting large posts very well might be one of them so one has to be extremely careful. For a while (this is some time ago) I was unable to post at all but over time learned that if I was sure to bottom rather than top post and not quote too much then it would get through. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
2011/11/8 Uwe Ligges lig...@statistik.tu-dortmund.de: On 08.11.2011 17:04, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. OK. One would have thought that the checks on CRAN would be consistent with the package pages which link to them. I only see consistent information on that page. If you go to: http://cran.r-project.org/web/packages/sqldf/index.html then the tar.gz file was created using R-2.14.0 but if you then click on the check results link on the same page it takes you to this: http://cran.r-project.org/web/checks/check_results_sqldf.html On the last link on that page it says ERROR and if click on that it takes you to the output of the check which reveals that it was run with R 2.13.2. The Version column on check_results_sqldf.html page refers to the package's version, not the R version. To get the R version you must know to click on each link. If its feasible in terms of effort and run time to add the R version used in a column on the check_results_sqldf.html page then that would make the summary page more useful since it would be immediately apparent not only what version of the package is being used but also what version of R is being used in each case. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] NAMESPACES for data only packages
the NEWS file for R-devel says * Even data-only packages without *R* code need a namespace and so may need to be installed under *R* 2.14.0 or later. but what should this contain? Can it simply be an empty NAMESPACE file? I assume that data does not have to be exported. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
On 08.11.2011 17:56, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 17:04, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. OK. One would have thought that the checks on CRAN would be consistent with the package pages which link to them. I only see consistent information on that page. If you go to: http://cran.r-project.org/web/packages/sqldf/index.html then the tar.gz file was created using R-2.14.0 but if you then click on the check results link on the same page it takes you to this: Yes. the tar.gz was created with R-2.14.0. http://cran.r-project.org/web/checks/check_results_sqldf.html On the last link on that page it says ERROR and if click on that it takes you to the output of the check which reveals that it was run with R 2.13.2. Yes, ince it is checked with different flavors of R, R-oldrelease, R-release, R-devel. See the first column! A source package can be created with an version of R and checked under another version. There is onlyone source package on CRAN, but - just as an exmaple - binaries for R-2.13.x and R-2.14.x. Of course, the checks are applied with the versions stated on the check page. I think you haven't got the whole point of checking with different versions of R. The Version column on check_results_sqldf.html page refers to the package's version, not the R version. To get the R version you must know to click on each link. No, no, no, no! See the first column! It definitely states if R-olrelease, R-release, R-pacthed or R-devel is used! Uwe If its feasible in terms of effort and run time to add the R version used in a column on the check_results_sqldf.html page then that would make the summary page more useful since it would be immediately apparent not only what version of the package is being used but also what version of R is being used in each case. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACES for data only packages
Hi Michael, You are correct that data does not *have* to be exported. For example, here is the contents of NAMESPACE for the datasets package from a recent devel version: # This package exports nothing (it uses lazydata) # exportPattern(.) Cheers, Josh On Tue, Nov 8, 2011 at 9:11 AM, Michael Friendly frien...@yorku.ca wrote: the NEWS file for R-devel says * Even data-only packages without *R* code need a namespace and so may need to be installed under *R* 2.14.0 or later. but what should this contain? Can it simply be an empty NAMESPACE file? I assume that data does not have to be exported. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
2011/11/8 Uwe Ligges lig...@statistik.tu-dortmund.de: On 08.11.2011 17:56, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 17:04, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. OK. One would have thought that the checks on CRAN would be consistent with the package pages which link to them. I only see consistent information on that page. If you go to: http://cran.r-project.org/web/packages/sqldf/index.html then the tar.gz file was created using R-2.14.0 but if you then click on the check results link on the same page it takes you to this: Yes. the tar.gz was created with R-2.14.0. http://cran.r-project.org/web/checks/check_results_sqldf.html On the last link on that page it says ERROR and if click on that it takes you to the output of the check which reveals that it was run with R 2.13.2. Yes, ince it is checked with different flavors of R, R-oldrelease, R-release, R-devel. See the first column! A source package can be created with an version of R and checked under another version. There is onlyone source package on CRAN, but - just as an exmaple - binaries for R-2.13.x and R-2.14.x. Of course, the checks are applied with the versions stated on the check page. I think you haven't got the whole point of checking with different versions of R. The Version column on check_results_sqldf.html page refers to the package's version, not the R version. To get the R version you must know to click on each link. No, no, no, no! See the first column! It definitely states if R-olrelease, R-release, R-pacthed or R-devel is used! OK. That wasn't clear. It would be better if it actually identified the release as R 2.13.2, etc. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NAMESPACES for data only packages
Can we clarify: As the NEWS says, to install a data-only package under 2.14.0 you need a namespace. And if you do not give one installation will create one. However, you can use an already-installed data-only package without a namespace under 2.14.x, but not under R-devel. This is to allow a transition (e.g. many of the BioC 2.9 binary data-only packages did not have a namespace at the time). On Tue, 8 Nov 2011, Joshua Wiley wrote: Hi Michael, You are correct that data does not *have* to be exported. For example, here is the contents of NAMESPACE for the datasets package from a recent devel version: # This package exports nothing (it uses lazydata) # exportPattern(.) Cheers, Josh On Tue, Nov 8, 2011 at 9:11 AM, Michael Friendly frien...@yorku.ca wrote: the NEWS file for R-devel says * Even data-only packages without *R* code need a namespace and so may need to be installed under *R* 2.14.0 or later. but what should this contain? Can it simply be an empty NAMESPACE file? I assume that data does not have to be exported. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ 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
Re: [Rd] NAMESPACE file generation issue R 2.14.0 on Debian Squeeze
On 08.11.2011 19:08, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 17:56, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 17:04, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.11.2011 16:31, Gabor Grothendieck wrote: 2011/11/8 Uwe Liggeslig...@statistik.tu-dortmund.de: I think many people like to help, but we cannot: You say you are under R-2.14.0 and whn you R CMD INSTALL a package with that version of R, it does not have a NAMESPACE in the end? Then - your R installation is broken or - you are looking into a library where you have old versios of the packages or - you belive you are using R-2.14.0 but you are actually using an older version. This is even reproduced on CRAN. All platforms work except one: http://cran.r-project.org/web/checks/check_results_sqldf.html No, that one is completely unrelated (and already solved, but not yet synced to CRAN master) to the original question you have removed in your reply. OK. One would have thought that the checks on CRAN would be consistent with the package pages which link to them. I only see consistent information on that page. If you go to: http://cran.r-project.org/web/packages/sqldf/index.html then the tar.gz file was created using R-2.14.0 but if you then click on the check results link on the same page it takes you to this: Yes. the tar.gz was created with R-2.14.0. http://cran.r-project.org/web/checks/check_results_sqldf.html On the last link on that page it says ERROR and if click on that it takes you to the output of the check which reveals that it was run with R 2.13.2. Yes, ince it is checked with different flavors of R, R-oldrelease, R-release, R-devel. See the first column! A source package can be created with an version of R and checked under another version. There is onlyone source package on CRAN, but - just as an exmaple - binaries for R-2.13.x and R-2.14.x. Of course, the checks are applied with the versions stated on the check page. I think you haven't got the whole point of checking with different versions of R. The Version column on check_results_sqldf.html page refers to the package's version, not the R version. To get the R version you must know to click on each link. No, no, no, no! See the first column! It definitely states if R-olrelease, R-release, R-pacthed or R-devel is used! OK. That wasn't clear. It would be better if it actually identified the release as R 2.13.2, etc. We do not want to change those fields daily: R-devel and R-patched typically change from day to day - and then things will really become inconsistent in some place. Uwe __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Question on parsing R code from C
Hi all, I am facing the necessity to parse R code from C-side. As a first approximation the goal would be a re-implementation of the R shell (not Rgui). I read the document at http://cran.r-project.org/doc/manuals/R-exts.html section 5.12, and the related source code example. I have some questions: 1. I need to declare the types and function signatures that I am going to use for this task without having to actually include the R headers. Can I safely declare SEXP according to the following ? typedef struct SEXP *unknwn_handle; More in general, is there a reference document for the C API (listing function signatures, and type definitions) ? 2. If the parsed R code of the working implementation contain commands like plot(), will the opportune windows pop-up as if I were using the R shell (on both windows and unix systems) ? 3. What initialization do I need to perform to be in exactly the same starting state as if I had executed the R shell with the --vanilla option? Any help or feedback is appreciated. Thank you. Kind regard __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question on parsing R code from C
On Nov 8, 2011, at 2:42 PM, KR wrote: Hi all, I am facing the necessity to parse R code from C-side. As a first approximation the goal would be a re-implementation of the R shell (not Rgui). I read the document at http://cran.r-project.org/doc/manuals/R-exts.html section 5.12, and the related source code example. I have some questions: 1. I need to declare the types and function signatures that I am going to use for this task without having to actually include the R headers. Can I safely declare SEXP according to the following ? typedef struct SEXP *unknwn_handle; I'm not sure I understand this really - it doesn't define SEXP. I would expect something like typedef void *SEXP; Which may work for declarations. Note, however, that for the actual code you'll need to include the headers anyway. More in general, is there a reference document for the C API (listing function signatures, and type definitions) ? http://r.research.att.com/man/R-exts.html is the documentation and the headers (Rinternals.h mainly) is the canonical reference. 2. If the parsed R code of the working implementation contain commands like plot(), will the opportune windows pop-up as if I were using the R shell (on both windows and unix systems) ? It depends on your settings - plot() uses whatever graphics device you tell it to use, so plot() doesn't decide about that. If you use the proper interactive graphics device *and* make sure you're serving the REPL then it may work. Beware of interactions with your other parts, though, since you are responsible for ensuring that it works. 3. What initialization do I need to perform to be in exactly the same starting state as if I had executed the R shell with the --vanilla option? It depends on the OS and the way you are initializing R. In the simple case pass the --vanilla as the argument when initializing R. Please read the section about embedding, it has examples. Also see the other R GUIs to understand the complexities involved. BTW: you subject has absolutely nothing to do with your question - your'e asking about embedding R ;) Cheers, Simon Any help or feedback is appreciated. Thank you. Kind regard __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question on parsing R code from C
Simon Urbanek simon.urbanek at r-project.org writes: I'm not sure I understand this really - it doesn't define SEXP. I would expect something like typedef void *SEXP; Which may work for declarations. Note, however, that for the actual code you'll need to include the headers anyway. Thanks for the prompt reply! It's my understanding that using opaque pointers to hide implementation is fine (as long as they are not de-referenced nor the size of the actual struct is needed). I actually come out with the tentative typedef by looking at the sources, but I got confused by some conditional pre-processor directives so I was searching for confirmation. For the actual code I can just declare the types (even opaques depending on the use) and function signatures that I strictly need by hand as long as I am doing it correctly (after all that's what is inside the headers, among with the stuff I don't need). http://r.research.att.com/man/R-exts.html is the documentation and the headers (Rinternals.h mainly) is the canonical reference. Understood, thanks. 2. If the parsed R code of the working implementation contain commands like plot(), will the opportune windows pop-up as if I were using the R shell (on both windows and unix systems) ? It depends on your settings - plot() uses whatever graphics device you tell it to use, so plot() doesn't decide about that. If you use the proper interactive graphics device *and* make sure you're serving the REPL then it may work. Beware of interactions with your other parts, though, since you are responsible for ensuring that it works. I admit I am quite lost here, is there any code I can look at for examples? :P BTW: you subject has absolutely nothing to do with your question - your'e asking about embedding R ;) H I may be excused because I copy and pasted the title of section 5.12 (which seemed most relevant for what I wanted to achieve) :-) Cheers __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question on parsing R code from C
On Nov 8, 2011, at 4:57 PM, KR wrote: Simon Urbanek simon.urbanek at r-project.org writes: I'm not sure I understand this really - it doesn't define SEXP. I would expect something like typedef void *SEXP; Which may work for declarations. Note, however, that for the actual code you'll need to include the headers anyway. Thanks for the prompt reply! It's my understanding that using opaque pointers to hide implementation is fine Except that you don't know what are macros, inlined functions and actual functions. If you are careful you can possibly fall back to external functions but, obviously, your code will be less efficient. I would still prefer including Rinternals.h - you must have a *really* good reason to not do so ;). (as long as they are not de-referenced nor the size of the actual struct is needed). I actually come out with the tentative typedef by looking at the sources, but I got confused by some conditional pre-processor directives so I was searching for confirmation. For the actual code I can just declare the types (even opaques depending on the use) and function signatures that I strictly need by hand as long as I am doing it correctly (after all that's what is inside the headers, among with the stuff I don't need). http://r.research.att.com/man/R-exts.html is the documentation and the headers (Rinternals.h mainly) is the canonical reference. Understood, thanks. 2. If the parsed R code of the working implementation contain commands like plot(), will the opportune windows pop-up as if I were using the R shell (on both windows and unix systems) ? It depends on your settings - plot() uses whatever graphics device you tell it to use, so plot() doesn't decide about that. If you use the proper interactive graphics device *and* make sure you're serving the REPL then it may work. Beware of interactions with your other parts, though, since you are responsible for ensuring that it works. I admit I am quite lost here, is there any code I can look at for examples? :P The embedding code examples and existing GUIs. It's not a trivial topic and you should be really familiar with R in order to venture there. Embedding R to perform computations is reasonably easy, but the moment you want to run it interactively like console R, you have to implement a bunch of callbacks and run the even loop (REPL). It is more tricky than it sounds, because you need to synchronize your app with the event loop, make sure you process system events etc. (Simple command line R is not that hard - there are examples in the R sources with stub implementations of the callbacks, but the complexity increases considerably the moment you start using any UI features in your app) BTW: you subject has absolutely nothing to do with your question - your'e asking about embedding R ;) H I may be excused because I copy and pasted the title of section 5.12 (which seemed most relevant for what I wanted to achieve) :-) ;) Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question on parsing R code from C
Simon Urbanek simon.urbanek at r-project.org writes: Except that you don't know what are macros, inlined functions and actual functions. If you are careful you can possibly fall back to external functions but, obviously, your code will be less efficient. I would still prefer including Rinternals.h - you must have a *really* good reason to not do so ;) Hmmm yes there are good motives (I am not completely unreasonable, yet :P) but I could probably cope with it if there is no other way. Regarding the rest of the e-mail, please let me be clearer on what my goal is. I would need a function to create and initialize an R state, a function to close the state, and a function (R_ParseVector?) that takes as input the R state and a string (containing R code), evaluates the code and return an error code (error, incomplete, done) plus (eventually) a string containing the output of the computation. In my application I do not have any UI elements (it's console based), but I would like calls to plot in R (and other functions using the graphic device) to function as they would under R.exe (on windows), i.e. have persistent windows popped up which you can resize ecc ecc. I naively thought that these graphic capabilities came automatically with the R_ParseVector via some threading techniques. Thanks for all your comments! Cheers __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question on parsing R code from C
Hi, With respect to initializing R state and parsing, you might want to look at the Linking GUI's and other front-ends to R section in Writing R Extensions http://cran.r-project.org/doc/manuals/R-exts.pdf. Once the initialization is done, you can use mkString() function to get an input SEXP from a C character buffer(your R code). Calling R_ParseVector() with this SEXP as input will give you the parsed output. It works for me. Thanks, Rob On Tue, Nov 8, 2011 at 6:53 PM, KR krunal.ra...@gmail.com wrote: Simon Urbanek simon.urbanek at r-project.org writes: Except that you don't know what are macros, inlined functions and actual functions. If you are careful you can possibly fall back to external functions but, obviously, your code will be less efficient. I would still prefer including Rinternals.h - you must have a *really* good reason to not do so ;) Hmmm yes there are good motives (I am not completely unreasonable, yet :P) but I could probably cope with it if there is no other way. Regarding the rest of the e-mail, please let me be clearer on what my goal is. I would need a function to create and initialize an R state, a function to close the state, and a function (R_ParseVector?) that takes as input the R state and a string (containing R code), evaluates the code and return an error code (error, incomplete, done) plus (eventually) a string containing the output of the computation. In my application I do not have any UI elements (it's console based), but I would like calls to plot in R (and other functions using the graphic device) to function as they would under R.exe (on windows), i.e. have persistent windows popped up which you can resize ecc ecc. I naively thought that these graphic capabilities came automatically with the R_ParseVector via some threading techniques. Thanks for all your comments! Cheers __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Accessing ENVSXP and CLOSXP while processing parsed R code
Thanks! that was useful
Rob
On Mon, Nov 7, 2011 at 6:49 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote:
On 11-11-07 5:24 AM, Rob Anderson wrote:
Hello Guys,
Following up my earlier mail where I am trying to write an alternative
front-end for R, I had a question about accessing the closures and
environments in R code.
Here's the function taken and modified a little from *Lexical Scope and
Statistical Computing*
==**==**=
f-function(){
Rmlfun-function(x){
sumx- sum(x)
n- length(x)
function(mu)
n*log(mu)-mu*sumx
}
efun-Rmlfun(1:10)
y1- efun(3)
print(y1)
efun2- Rmlfun(20:30)
y2- efun2(3)
print(y2)
}
==**==**=
Now assignment efun-Rmlfun(1:10) creates a closure where
*function(mu) n*log(mu)-mu*sumx *is returned and *sumx* and *n *are added
to the existing environment.
That's not correct. When you call Rmlfun, an evaluation frame
(environment) is created. It contains the argument x. Then sumx and n are
added to it. Then the anonymous closure is created, with body
n*log(mu)-mu*sumx, and the closure's environment is the evaluation frame
from the call to Rmlfun.
I can parse the code using *PROTECT(e =
R_ParseVector(tmp,1,status,R_**NilValue));* where tmp is the buffer
containing the same source. I can walk the resultant parser output and
build and alternative Abstract syntax tree(AST).
I would like to include the information about closure/environments in my
AST so that I can possibly do some optimizations.
It's not there, except potentially. When you call the function function
to create the closure, that's when the closure is created. That doesn't
happen at parse time. Rmlfun is created when you evaluate f() and then the
anonymous function is created when you call Rmlfun() within it.
My question is, how can I get hold of this information?
One thing I noticed while 'walking' through the parser output, I never
encounter a CLOSXP (which I check using TYPEOF()) , even though in the
above code, closure is created. Is it the case that this information is
meant just for the internal eval* function and not exposed application
writers?
No, there's nothing hidden, it just didn't exist at the time you were
looking for it.
Duncan Murdoch
[[alternative HTML version deleted]]
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Re: [Rd] Question on parsing R code from C
On Nov 8, 2011, at 6:53 PM, KR wrote: Simon Urbanek simon.urbanek at r-project.org writes: Except that you don't know what are macros, inlined functions and actual functions. If you are careful you can possibly fall back to external functions but, obviously, your code will be less efficient. I would still prefer including Rinternals.h - you must have a *really* good reason to not do so ;) Hmmm yes there are good motives (I am not completely unreasonable, yet :P) but I could probably cope with it if there is no other way. Regarding the rest of the e-mail, please let me be clearer on what my goal is. I would need a function to create and initialize an R state, a function to close the state, and a function (R_ParseVector?) that takes as input the R state and a string (containing R code), evaluates the code and return an error code (error, incomplete, done) plus (eventually) a string containing the output of the computation. That itself is quite simple - there is an example in R-ext 5.12. In my application I do not have any UI elements (it's console based), but I would like calls to plot in R (and other functions using the graphic device) to function as they would under R.exe (on windows), i.e. have persistent windows popped up which you can resize ecc ecc. I naively thought that these graphic capabilities came automatically with the R_ParseVector via some threading techniques. R_ParseVector doesn't evaluate anything so it's innocent here. Rf_eval() will run the actual code and it will create a window (if you use an interactive device) but the window won't respond to anything, because the moment Rf_eval() returns R has lost control and everything is up to your code. R is not threaded* (and the R API is not thread-safe) so the only way to continue is for you to run the run loop, i.e. you have to return control back to R so it can process events. Now the hard part is that running the event loop is system-dependent. You will see it discussed in R-ext 8.1 (unix) and 8.2 (Windows). Cheers, Simon * - on unix R itself doesn't use threads because it's problematic (other than OpenMP); the Windows Rgui actually uses threads cautiously so that the UI stays responsive while R is busy, but this is not done by R but the GUI. Similarly R.app GUI uses threads to monitor I/O pipes but the system loop is meshed into R. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
