Re: [Rd] how to unbreak a circular package dependence (S4 class data)
]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] -- Claudia Beleites, Chemist 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] FOSS licence with BuildVignettes: false
Hi there, Am Tue, 17 Sep 2013 09:25:14 +0100 schrieb Prof Brian Ripley rip...@stats.ox.ac.uk: On 16/09/2013 15:49, Paul Gilbert wrote: On 13-09-16 05:19 AM, Uwe Ligges wrote: ... Yes, and I could see really rare circumstances where vignette building takes a long time and the maintainer decides not to build vignettes as part of the daily checks. ... I have two vignettes that I build externally because the required data sets are largish (20 and 40 MB zipped), so I provide them for download on hyperSpec's home page but do not want to burden CRAN with them. Instructions how to get that data to build the vignette yourself are one of the first points in the vignette. I do /not/ have BuildVignettes: FALSE but a Makefile that turns of pdflatex for these two only, and dummy .Rnw files that provide just the appropriate \VignetteIndex etc. entries. IMHO that is a perfectly reasonable option for FOSS packages, and while it makes it my responsibility to check the vignette building, a Makefile for preparing the package takes care of that as well. I can also make sure that both data and real vignette source are available there. For an upcoming spectral unmixing package, however, I'd like to include a vignette dealing with the cuprite AVIRIS data set (remote sensing data, a standard data set used on many publications for spectral unmixing) that can be downloaded from the NASA (http://aviris.jpl.nasa.gov/data/free_data.html). Is it acceptable to have a vignette that points to yet another data source (which is out of my control)? (I think this question goes mainly to Brian and the author of the part of the manual cited by Ben). Best, Claudia I thought 'BuildVignettes: FALSE' only turns of assembling the pdf, all the code is still run. I don't think that would affect the time very much. Am I wrong (again)? Yes, as the code is run again to re-build the vignettes. The main use of BuildVignettes: FALSE is when building the vignettes requires unusual facilities -- presumably not R ones as it does not turn off running the code. However, for a FOSS package, the means to re-build the vignettes has to available to others, and CRAN therefore tries it so see if all the sources are available. Almost every time we uncover some problem with the sources and stale vignette PDFs. -- Claudia Beleites, Chemist 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Contribution
Hi Parthasarathy, IMHO the easiest way to contribute to R is contributing to an R package. And one way to do that is to apply for a Google Summer of Code project. I guess activities about that will start soon, as the program was just announced, and they will take place at a separate email list: gso...@groups.google.com So I suggest you sign up for that list, and maybe explain a bit who you are, what experience you have in R programming (or other languages) and what your programming interests are. Best, Claudia I am Parthasarathy G , from IIT Maras ( India ). I am currently in third year of the undergraduate course. I would like to contribute to the R project. Can anyone guide me regarding this? Thanking you, Parthasarathy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] as.numeric and as.character with locale using comma as separator
Dear all, summary: My LC_NUMERIC is changed from C to de_DE by library (qtbase). [which shouldn't happen according to the warning when setting it back manually]. I posted an issue at their github repository, but maybe the behaviour is a bit more of general interest. However, if LC_NUMERIC is changed, as.character () uses the decimal separator that belongs to LC_NUMERIC (and not options ()$OutDec as I supposed). as.double () (= as.numeric ()) doesn't, though. That causes trouble with constructs like as.numeric (as.character (x)) long version: as.character seems to take into account my locale (de_DE) which uses comma as decimal separator: x - rnorm (3) x [1] -0,004238328 -0,919358537 -1,654543297 as.character(x) [1] -0,00423832753479965 -0,919358536523751 -1,65454329680873 whereas as.numeric () doesn't: as.numeric (as.character(x)) [1] NA NA NA Warnmeldung: NAs durch Umwandlung erzeugt as.numeric (gsub (,, ., as.character(x))) [1] -0,004238328 -0,919358537 -1,654543297 I did not see any mention in the help of as.numeric nor as.character of this. Note also the output of example (as.character): example (as.character) as.chr form - y ~ a + b + c as.chr as.character(form) ## length 3 [1] ~ y a + b + c as.chr deparse(form) ## like the input [1] y ~ a + b + c as.chr a0 - 11/999 # has a repeating decimal representation as.chr (a1 - as.character(a0)) [1] 0,011011011011011 as.chr format(a0, digits=16) # shows one more digit [1] 0,01101101101101101 as.chr a2 - as.numeric(a1) as.chr a2 - a0 # normally around -1e-17 [1] NA as.chr as.character(a2) # normally different from a1 [1] NA as.chr print(c(a0, a2), digits = 16) [1] 0,01101101101101101 NA Warnmeldung: In eval(expr, envir, enclos) : NAs durch Umwandlung erzeugt *session info* sessionInfo () R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] de_DE.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Hmisc_3.9-3 survival_2.36-14 plumbr_0.6.6 cranvas_0.8 [5] maps_2.2-6 scales_0.2.1 qtpaint_0.9.0qtbase_1.0.5 [9] idendro_1.0 loaded via a namespace (and not attached): [1] cluster_1.14.2 colorspace_1.1-1 dichromat_1.2-4 [4] grid_2.15.1labeling_0.1 lattice_0.20-6 [7] munsell_0.3objectProperties_0.6.5 objectSignals_0.10.2 [10] plyr_1.7.1 RColorBrewer_1.0-5 SearchTrees_0.5.1 [13] stringr_0.6tools_2.15.1 tourr_0.5.2 Note that options ()$OutDec [1] . In fresh R sessions I have locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C It seems qtbase is the culprit: x [1] -0.2290188 -0.1884703 0.2507179 library (qtbase) x [1] -0,2290188 -0,1884703 0,2507179 After setting the numeric locale back to C: Sys.setlocale (LC_NUMERIC, C) [1] C Warnmeldung: In Sys.setlocale(LC_NUMERIC, C) : das Setzen von 'LC_NUMERIC' kann bewirken, dass R sich komisch benimmt as.numeric (as.character (x)) works as supposed (also output has decimal points again) Best, Claudia -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] test suites for packages
I use svUnit, too. I put a kind of standard skeleton into my packages that has a packagename.unittest () function that will run all svUnit tests (if svUnit is available). This function returns NA if svUnit is not available, invisible (TRUE) if all tests are passed and stops otherwise. Which will cause R CMD check to fail. My test directory contains one single tests.R file with the two lines: library (packagename) packagename.unittest () which gives me e.g.: Running the tests in ‘tests/tests.R’ failed. Last 13 lines of output: only logical matrix subscripts are allowed in replacement * : ...) ... **ERROR** Error in `[-.data.frame`(`*tmp*`, x.na, value = NA) : only logical matrix subscripts are allowed in replacement kind timingtime unit msg test(kernelpls.fit)OK 0.009 2012-05-23 14:38:49 test(scale)OK 0.009 2012-05-23 14:38:49 test(.ldapreproc) **ERROR** 0.007 2012-05-23 14:38:49 test(pcalda) OK 0.003 2012-05-23 14:38:49 Error in errorLog(summarize = FALSE) : 0 failure(s) and 1 error(s) Calls: cbmodels.unittest - errorLog Execution halted While the 13 lines may not be enough if there are lots of tests, I can easily run packagename.unittest () in an interactive session and start tracking down the problem from there. Claudia Am 18.05.2012 17:28, schrieb Cook, Malcolm: svUnit - is Runit compatible and provides some IDE integration and report generation and easy syntax for defining tests. I find it works a treat, and fits very nicely with my R coding/packaging style (which also uses inlinedocs for easy package creation). --Malcolm Cook On 5/17/12 9:10 AM, Whit Armstrong armstrong.w...@gmail.com wrote: Can anyone share some opinions on test suites for R packages? I'm looking at testthat and RUnit. Does anyone have strong opinions on either of those. Any additional packages I should consider? Thanks, Whit __ 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 -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R datasets ownership(copyright) and license
Yaroslav, coming from an experimental field, I use options 4 and 4a: 4. I measure the data myself, so I am the copyright holder. 4a. I publish data sets that are given to me in order to publish by the person(s) who did the measurement. This is properly annotated in the authors field. So far, the data sets I put as example data into packages are small subsets of real studies or data collected in pre-tests, so they are not that sensitive/valuable. I plan to publish at least one real data set (as own package) eventually. But we're not yet there. Claudia Am 03.04.2012 00:06, schrieb Yaroslav Halchenko: Dear R Developers, Recently filed (and dismissed ;) ) law suit by Astrolabe against tz database developers caused a lot of media-press and discussions and created some kind of precedence in the USA [3]. But also it imho showed that similar attacks might happen in the future, and possibly against data sets which are not that obviously factual thus after all might fall under copyright or IP protection if not in the states then in some other jurisdictions. And 'data copyright/license' question comes over and over again, I just wanted to ask based on what policies or advisories datasets were selected to be shipped with R. From a very very brief look at the datasets, many of them appear to be factual data, thus at least at the moment probably are not copyrightable in the states -- but is there guarantee that they are not protected by copyright elsewhere if their origin abroad? But some seems to come from published works (still) under copyright with All rights reserved, e.g. datasets Harman23 and Harman74 [4]. Although similar question to mine was raised before [e.g. 1,2] I have not found a straight answer e.g. from a list above or a mix of them: 1. we simply did not look into it and adopted them with idea that if someone complains -- we remove corresponding pieces 2. we considered all datasets factual data thus not copyrightable (in USA? around the globe?) 3. for each (or some or majority) dataset we did collected information on possible copyright+license/IP holder and contacted them where unclear about the permission for reuse in a project under GPL license Thank you in advance for the clarification! P.S. Please do not take me wrong -- I am not trying to pick at anyone. I just wanted to get a better sense on the procedures/assumptions R developers use while adopting data for the R package, so that it could be of help for other projects. [1] https://stat.ethz.ch/pipermail/r-help/2007-April/130422.html [2] http://www.mail-archive.com/r-help@r-project.org/msg62486.html [3] http://en.wikipedia.org/wiki/Tz_database [4] it is interesting there that actual data comes from unpublished PhD thesis, but once again from the U of Chicago who holds copyright for the book itself. -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN policies
Paul, One of the things I have noticed with the R 2.15.0 RC and --as-cran is that the I have to bump the version number of the working copy of my [snip] I am curious how other developers approach this. Regardless of --as-cran I find it very useful to use the date as minor part of the version number (e.g. hyperSpec 0.98-20120320), which I set automatically. Claudia -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Command completion of the R binary / Ubuntu
Am 11.01.2012 19:53, schrieb Sharpie: The bash completion script is also used by the Homebrew package manager on OS X. There we go... good to know. -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Command completion of the R binary / Ubuntu
Dear Deepayan and dear list, I notice a small inconsistency with the command completion of the R CMD check. --no-latex is deprecated sincs R 2.12.0 and defunct since 2.13.0 but the command line completion still suggests it: cb@cbdesktop:~/r-devel$ bin/R CMD check --no-here I hit tab --no-clean --no-examples --no-latex --no-vignettes --no-codoc --no-install--no-tests cb@cbdesktop:~/r-devel$ bin/R CMD check --no-latex Fehler: '--no-latex' is defunct: use '--no-manual' instead I gather the command line options could be updated to current R CMD check in file /etc/bash_completion.d/R: cb@cbdesktop:~/tmp$ diff R /etc/bash_completion.d/R 244,247c244,245 --no-install --no-tests --no-vignettes --no-manual \ --no-rebuild-vignettes --install-args --check-subdirs \ --extra-arch --multiarch --no-multiarch --force-multiarch \ --timings --use-gct --use-valgrind --rcfile --- --no-install --no-tests --no-vignettes --no-latex \ --use-gct --use-valgrind --rcfile I gather from the mailing list archives, that the original is available at http://code.google.com/p/rcompletion/source/browse/trunk/bash_completion/R Should I suggest the patch there? Will changes propagate to the packaged linux distributions from there or should the updated file be brought to the attention somewhere else? Best regards, Claudia sessionInfo () R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- 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 206-399 244,247c244,245 --no-install --no-tests --no-vignettes --no-manual \ --no-rebuild-vignettes --install-args --check-subdirs \ --extra-arch --multiarch --no-multiarch --force-multiarch \ --timings --use-gct --use-valgrind --rcfile --- --no-install --no-tests --no-vignettes --no-latex \ --use-gct --use-valgrind --rcfile __ 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] Data package questions
Dear Paul, In process of creating data package from an existing one. The current package has both raw data files and the associated RData objects created from them. Currently, the data subdirectory is 1.5Mb and the extdata is 5.4Mb. Never having created a data package before, how is this best done? Should the data package contain only the raw data, or the RData objects too (tightly coupled)? If the later, what (if anything) is added to the DESCRIPTION meta-information to denote the dependency? Should both packages suggest each other? I have one data set that I ship as a few principal components and reconstruct it by a function. The result is then assigned to the exported variable by delayedAssign. That way, you'd need to ship the raw data only, but can provide a ready-to-use R object as well. For my example data, I don't ship the raw data as it is too big (30 MB toy example is really unpolite on CRAN), but I provide it at r-forge and give the link on the help page and in the vignette. Claudia -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] logos
Dear all, I'd like to link one of the logos in our Google Summer of Code Profile. If I remember correctly, behind the logo link at http://developer.r-project.org/ (i.e. http://developer.r-project.org/Logo) also small versions can be found. However, I'm not allowed to access that directory. I have no problem with putting a small version of the normal logo somewhere online, but I'm wondering whether the logo directory really isn't supposed to be accessed by the public. Thanks, Claudia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Sweave: multiple graphic formats, e.g. win.metafile
On 03/23/2011 01:05 PM, Prof Brian Ripley wrote: We are currently in the process of implementing PNG and JPEG for 2.13.0, and an extensible architecture is planned for 2.14.0. :-) this is really good news :-) Thank you! -- Claudia Beleites DI3 Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] X error on r-forge
Dear all, since a few days, my package hyperSpec does not build on r-forge. I have no idea whether this is due to my code or whether something is wrong with r-forge. It fails with an X server error: X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 73 (X_GetImage) Serial number of failed request: 806 Current serial number in output stream: 806 My guesstimate from the other output (http://r-forge.r-project.org/R/?group_id=366log=build_srcpkg=hyperSpecflavor=patched) is that it happens in the plotting vignette where I demonstrate plotting with rgl and try to save the image as png. It used to work, and the package builds and checks on my computer with both R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) and the current r-devel as well as on winbuilder. Any ideas? Thanks a lot, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] vignette question was: CRAN package sizes
Also I started doing my homework with regards to package size, and that is mainly cleaning leftovers from vignette generation and compressing the pdfs. For most of my vignettes, ghostscript (lossy) compression works very well: I use the /screen settings and -dDownsampleColorImages=false gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -dDownsampleColorImages=false -dAutoRotatePages=/None (DownsampleColorImages=false is important as I found otherwise that some .png become completely useless. However, the pngs are saved with carefully determined size and are pngs because the pdfs were too large: so I know that the bitmap images are already size-optimized) I wrote a inst/doc/makefile to do this and also clean up a few more leftovers from the vignette. BTW: while compressing the final .pdf achieves better total compression, it already helps a lot to compress the .pdf figures which can be done at the end of the .Rnw. qpdf didn't help for my vignettes. One question remains, though. I have two vignettes, where I cannot put the original data into the package (the very first thing in the vignette is the link to a zip file on r-forge that contains everything needed to reproduce the vignette, though. I think this is accessible enough for FOSS). I'd like to have these documents accessible via the usual vignette () mechanism (this question has come up before, but I found only that the 00Index.dcf does not work any longer). My second thought was to set up the Makefile so that instead of building the pdf a message is printed and the available pdf is used. This does not work, however: buildVignettes (which I guess does the work*) first Sweaves the .Rnw file and then replaces the texi2dvi () call by make. Is this intended behaviour? If so, how do I make my vignette accessible [obviously the dummy .Rnw that includes the pdf-technique doesn't look quite appropriate as it leads to unnecessarily large package size]? *I did not realise this from the Makefile discussion in the extensions manual (nor does the help page of buildVignettes mention anything about this). Also, I'd appreciate very much if the extension manual would mention buildVignettes - it took me quite a while to find out what code is used and why my Makefile didn't lead to the desired results. Thanks a lot for any ideas, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vignette question was: CRAN package sizes
Please excuse the noise about dummy .Rnw. On 02/15/2011 03:44 PM, Claudia Beleites wrote: Also I started doing my homework with regards to package size, and that is mainly cleaning leftovers from vignette generation and compressing the pdfs. For most of my vignettes, ghostscript (lossy) compression works very well: I use the /screen settings and -dDownsampleColorImages=false gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -dDownsampleColorImages=false -dAutoRotatePages=/None (DownsampleColorImages=false is important as I found otherwise that some .png become completely useless. However, the pngs are saved with carefully determined size and are pngs because the pdfs were too large: so I know that the bitmap images are already size-optimized) I wrote a inst/doc/makefile to do this and also clean up a few more leftovers from the vignette. BTW: while compressing the final .pdf achieves better total compression, it already helps a lot to compress the .pdf figures which can be done at the end of the .Rnw. qpdf didn't help for my vignettes. One question remains, though. I have two vignettes, where I cannot put the original data into the package (the very first thing in the vignette is the link to a zip file on r-forge that contains everything needed to reproduce the vignette, though. I think this is accessible enough for FOSS). I'd like to have these documents accessible via the usual vignette () mechanism (this question has come up before, but I found only that the 00Index.dcf does not work any longer). My second thought was to set up the Makefile so that instead of building the pdf a message is printed and the available pdf is used. This does not work, however: buildVignettes (which I guess does the work*) first Sweaves the .Rnw file and then replaces the texi2dvi () call by make. Is this intended behaviour? If so, how do I make my vignette accessible [obviously the dummy .Rnw that includes the pdf-technique doesn't look quite appropriate as it leads to unnecessarily large package size]? coffe break was helpful: of course I just need a dummy .Rnw that is processed to a .tex but (via Makefile) _not_ to pdf... *I did not realise this from the Makefile discussion in the extensions manual (nor does the help page of buildVignettes mention anything about this). Also, I'd appreciate very much if the extension manual would mention buildVignettes - it took me quite a while to find out what code is used and why my Makefile didn't lead to the desired results. Sorry, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] drop argument for apply, rowSums, etc.
Dear list, dear Henrik,
I find myself often reconstructing matrices from the result of rowSum (matrix)
etc. I therefore propose a new argument, drop, for these functions:
drop = TRUE (default) is the current behaviour. With
drop = FALSE length (dim (x)) and dimnames are preserved and the affected
dimensions are set to 1 (or whatever teh result length of the applied function is)
I modified the base functions in colSums.R accordingly, and provide the
respective methods (I did not yet have the time to look into apply.R).
I'm wondering whether these changes are of sufficient interest to the R public
that these methods should have a more obvious home than a spectroscopy
package. As I learned this morning of package matrixStats: Henrik, would you
like to include these modified functions?
Anyways, the code is in the attached file, so if someone needs the funcionality,
he can find it here.
Claudia
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
# From base/R/colSums.R
.colSums - function(x, na.rm = FALSE, dims = 1L, drop = TRUE)
{
if(is.data.frame(x)) x - as.matrix(x)
if(!is.array(x) || length(dn - dim(x)) 2L)
stop('x' must be an array of at least two dimensions)
if(dims 1L || dims length(dn) - 1L)
stop(invalid 'dims')
n - prod(dn[1L:dims])
dn [1L : dims] - 1L
z - if(is.complex(x))
.Internal(colSums(Re(x), n, prod(dn), na.rm)) +
1i * .Internal(colSums(Im(x), n, prod(dn), na.rm))
else .Internal(colSums(x, n, prod(dn), na.rm))
if (drop){
if(length(dn) dims + 1L) {
dim(z) - dn[-(1L:dims)]
dimnames(z) - dimnames(x)[-(1L:dims)]
} else names(z) - dimnames(x)[[dims+1]]
} else {
dim(z) - dn
dimnames(z) - dimnames(x)
}
z
}
.colMeans - function(x, na.rm = FALSE, dims = 1L, drop = TRUE)
{
if(is.data.frame(x)) x - as.matrix(x)
if(!is.array(x) || length(dn - dim(x)) 2L)
stop('x' must be an array of at least two dimensions)
if(dims 1L || dims length(dn) - 1L)
stop(invalid 'dims')
n - prod(dn[1L:dims])
dn [1L : dims] - 1L
z - if(is.complex(x))
.Internal(colMeans(Re(x), n, prod(dn), na.rm)) +
1i * .Internal(colMeans(Im(x), n, prod(dn), na.rm))
else .Internal(colMeans(x, n, prod(dn), na.rm))
if (drop){
if(length(dn) dims + 1L) {
dim(z) - dn[-(1L:dims)]
dimnames(z) - dimnames(x)[-(1L:dims)]
} else names(z) - dimnames(x)[[dims+1]]
} else {
dim(z) - dn
dimnames(z) - dimnames(x)
}
z
}
.rowSums - function(x, na.rm = FALSE, dims = 1L, drop = TRUE)
{
if(is.data.frame(x)) x - as.matrix(x)
if(!is.array(x) || length(dn - dim(x)) 2L)
stop('x' must be an array of at least two dimensions)
if(dims 1L || dims length(dn) - 1L)
stop(invalid 'dims')
p - prod(dn[-(1L:dims)])
dn [(dims + 1L) : length (dn)] - 1L
z - if(is.complex(x))
.Internal(rowSums(Re(x), prod(dn), p, na.rm)) +
1i * .Internal(rowSums(Im(x), prod(dn), p, na.rm))
else .Internal(rowSums(x, prod(dn), p, na.rm))
if (drop){
if(dims 1L) {
dim(z) - dn [1L:dims]
dimnames(z) - dimnames(x)[1L:dims]
} else names(z) - dimnames(x)[[1L]]
} else {
dim(z) - dn
dimnames(z) - dimnames(x)
}
z
}
.rowMeans - function(x, na.rm = FALSE, dims = 1L, drop = TRUE)
{
if(is.data.frame(x)) x - as.matrix(x)
if(!is.array(x) || length(dn - dim(x)) 2L)
stop('x' must be an array of at least two dimensions)
if(dims 1L || dims length(dn) - 1L)
stop(invalid 'dims')
p - prod(dn[-(1L:dims)])
dn [(dims + 1L) : length (dn)] - 1L
z - if(is.complex(x))
.Internal(rowMeans(Re(x), prod(dn), p, na.rm)) +
1i * .Internal(rowMeans(Im(x), prod(dn), p, na.rm))
else .Internal(rowMeans(x, prod(dn), p, na.rm))
if (drop){
if(dims 1L) {
dim(z) - dn [1L:dims]
dimnames(z) - dimnames(x)[1L:dims]
} else names(z) - dimnames(x)[[1L]]
} else {
dim(z) - dn
dimnames(z) - dimnames(x)
}
z
}
test (.rowSums) - function (){
a - array (1:24, 4:2)
for (d in 1 : 2){
default - base::rowSums (a, dims = d)
drop - rowSums (a, dims = d, drop = TRUE)
nodrop - rowSums (a, dims = d, drop = FALSE)
checkEquals (default, drop, sprintf (base version ./. drop = TRUE, dim =
%i, d))
checkEquals (c (default), c (nodrop), sprintf (drop = TRUE ./. FALSE, dim
= %i, d))
dd - dim (default)
if (is.null (dd)) dd - length (default)
checkEquals (dim (nodrop) [1 : d], dd, sprintf (result dimensions, d =
%i, d))
}
}
test (.rowMeans) - function (){
a - array (1:24, 4:2)
for (d in 1 : 2){
default - base::rowMeans (a, dims = d)
drop
Re: [Rd] dependencies on system packages
Dear all, From the writing extensions manual: Other dependencies (external to the R system) should be listed in the ‘SystemRequirements’ field, possibly amplified in a separate README file. I guess one problem is the user may not realize that the -dev version is needed, and just sees libxml2 installed but the R package installation stopping with the respective error. Giving the package name for specific distributions is of course polite (if the developer knows it). As developer you may also put into the README that the package's mailing list/forum/wiki/... contains information and ask the user to enter the package name on his distro if it is not already there. my 2 ct Claudia Am 04.02.2011 04:48, schrieb Simon Urbanek: Jeroen, On Feb 3, 2011, at 9:31 PM, Jeroen Ooms wrote: Many R packages depend on some unix libraries that are not part of most default installations. I often spend a significant amount of time figuring out where to get the appropriate libraries for compiling these packages, after they give some vague error of something missing. I was wondering why there is no formal system of specifying non-R dependencies in the DESCRIPTION file. If this would be the case, then during the installation of an R package, the user could be prompted to install required system packages (if they have appropriate privileges). So for example: Package: XML Version: 3.2-0 Depends: R (= 1.2.0), methods, utils Depends-debian: libxml2-dev Depends-ubuntu: libxml2-dev Depends-redhat: libxml2-devel Depends-suse: libxml2-devel etc. This might make life for many people just a little easier. If they are root and the package is in their system repositories, than it will install automatically. If not, at least they know for which package to look, or request their sys admin to install. Well, there is already such system in place and it is the corresponding descriptions in the distributions. Obviously as an author of the package I don't care what any particular Linux distribution uses as a name for the needed dependencies as the corresponding chaos is distribution-specific. The only person who can reasonably determine the dependencies is the maintainer of the distribution and that's what they do and as a user of the above mentioned distributions you should be thankful to them. Fortunately, normal users don't have to worry about it as major distributions already come with a large set of R packages resolving all dependencies. Hence I don't see any reason why this should have anything to do with the DESCRIPTION file. The improvements I could think of would be a parseable entry or a canonical pointer to dependency sources, but that's a whole another story. Cheers, Simon __ 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
[Rd] Google Summer of Code 2011
Dear all, I just saw that Google Summer of Code 2011 is announced: http://www.google-melange.com/ Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] plotmath indices: suggested addition to help file
Dear all,
after realizing yesterday that my suggestion was not yet quite ripe as the
character version is very limited, I decided to wait a bit before summarizing
the outcome to a better proposition instead of creating too much fuss.
Martin, thanks for your support systematic table :-)
My main point is that somehow I didn't at all expect plotmath to throw away
everything after the i of expression (x [i,j]). I think this trap deserves
either change (nice to have; I now believe that this may be quite easy, see
below) or at least an announcement.
I agree that one needs to learn dealing with plotmath. On the other hand, it is
nice if plotmath's output corresponds to the R meaning of the expression.
I guess the underlying problem is that we have three different possibilities
with indexing:
R --- how I'd write down the R meaning
(a) x [i, j] --- x_{i, j} or x_{i j} (not x_{ij})
(b) x [i [j]] --- x_i_j
(c) x [i][j] --- (x_i)_j
(b) works as expected, though a tiny little bit more default space would be
excellent.
(a) produces plotmath output x_i which is _very_ unexpected, and
(c) produces output that looks very similar to my expectation for (a) and can
thus be used to cheat around unexpected behaviour of (a).
I'd say the behaviour of (c) is fine, and it is up to me to write (x [i])[j].
Note that writing (x [i]) [j] does not change the R meaning of the expression.
BTW: I prefer a comma for (a) because i couldn't distinguish the output of
expression (x [i][j])
from
expression (x [ij])
.
I also vote for a comma for the future behaviour of (a) - even with some space
it's easier to distinguish two indices if they are separated by a comma (and no
comma can still be obtained by x[i][j]). Plus, it may be easier to implement it
that way.
I tried:
CDDR instead CADDR in RenderSub (plotmath.c) yields all indices given in the
square bracket. Now I prepended install (list) by LCONS, and it seems to work:
plot (1,1, type = n); text (1, 1, expression (x [i[a,b,c],j,k]*f(x)), cex = 3)
now looks as I expect.
Disclaimer: This is the first time ever I tried to do something with the R C
interface, and I didn't even properly read the maual and SoDa chapters. So I
have no idea whether I did something that will cause trouble.
Best regards have a nice weekend
Claudia
cb@cb:~/r-devel$ svn diff src/main/plotmath.c
Index: src/main/plotmath.c
===
--- src/main/plotmath.c (revision 54062)
+++ src/main/plotmath.c (working copy)
@@ -898,6 +898,7 @@
mathContext*, pGEcontext , pGEDevDesc);
static BBOX RenderExpression(SEXP, int, mathContext*, pGEcontext , pGEDevDesc);
static BBOX RenderSymbolChar(int, int, mathContext*, pGEcontext , pGEDevDesc);
+static BBOX RenderCommaList(SEXP, int, mathContext *, pGEcontext, pGEDevDesc);
/* Code to Generate Bounding Boxes and Draw Formulae. */
@@ -1396,7 +1397,8 @@
{
BBOX bodyBBox, subBBox;
SEXP body = CADR(expr);
-SEXP sub = CADDR(expr);
+SEXP sub = CDDR(expr);
+SEXP list = install (list);
STYLE style = GetStyle(mc);
double savedX = mc-CurrentX;
double savedY = mc-CurrentY;
@@ -1407,6 +1409,7 @@
s5 = TeX(sigma5, gc, dd);
s16 = TeX(sigma16, gc, dd);
SetSubStyle(style, mc, gc);
+sub = LCONS (list, sub);
subBBox = RenderElement(sub, 0, mc, gc, dd);
v = max(max(v, s16), bboxHeight(subBBox) - 0.8 * sigma5);
subBBox = RenderOffsetElement(sub, 0, -v, draw, mc, gc, dd);
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
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[Rd] plotmath indices: suggested addition to help file
Dear all,
I just stumbled over the fact that subsetting by square bracket will only output
the first given index. I guess the rest is thrown away by the CADDR in RenderSub
(plotmath.c l. 1399).
Maybe changing this could be considered as low-priority desired (would be nice
if the output works for ?
However, I suggest to announce the fact that only the first parameter is printed
in plotmath.Rd.
E.g. in the table l. 72
\code{x[i]} \tab x subscript i; escape further indices (\code{x [i, j]})\cr
Claudia
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
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Re: [Rd] R vs. C now rather: how to ease package checking
La version fran�aise suit le texte anglais. This email may contain privileged and/or confidential information, and the Bank of Canada does not waive any related rights. Any distribution, use, or copying of this email or the information it contains by other than the intended recipient is unauthorized. If you received this email in error please delete it immediately from your system and notify the sender promptly by email that you have done so. Le pr�sent courriel peut contenir de l'information privil�gi�e ou confidentielle. La Banque du Canada ne renonce pas aux droits qui s'y rapportent. Toute diffusion, utilisation ou copie de ce courriel ou des renseignements qu'il contient par une personne autre que le ou les destinataires d�sign�s est interdite. Si vous recevez ce courriel par erreur, veuillez le supprimer imm�diatement et envoyer sans d�lai � l'exp�diteur un message �lectronique pour l'aviser que vous avez �limin� de votre ordinateur toute copie du courriel re�u. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R vs. C
from R to C.
But, then again, I am working with scientists who are not
primarily, or
even
secondarily, coders...
Dave H
This makes sense, but I have seem some very transparent algorithms
turned
into vectorized R code
that is difficult to read (and thus to maintain or to change). These
chunks
of optimized R code are like
embedded assembly, in the sense that nobody is likely to want to mess
with
it. This could be addressed
by including pseudo code for the original (more transparent)
algorithm as a
comment, but I have never
seen this done in practice (perhaps it could be enforced by R CMD
check?!).
On the other hand, in principle a well-documented piece of C/C++ code
could
be much easier to understand,
without paying a performance penalty...but coders are not likely to
place
this high on their
list of priorities.
The bottom like is that R is an adaptor (glue) language like Lisp that
makes it easy to mix and
match functions (using classes and generic functions), many of which are
written in C (or C++
or Fortran) for performance reasons. Like any object-based system
there can
be a lot of
object copying, and like any functional programming system, there can
be a
lot of function
calls, resulting in poor performance for some applications.
If you can vectorize your R code then you have effectively found a
way to
benefit from
somebody else's C code, thus saving yourself some time. For
operations other
than pure
vector calculations you will have to do the C/C++ programming
yourself (or
call a library
that somebody else has written).
Dominick
- Original Message
From: Dirk Eddelbuettele...@debian.org
To: Patrick Leyshockngkbr...@gmail.com
Cc: r-devel@r-project.org
Sent: Mon, January 17, 2011 10:13:36 AM
Subject: Re: [Rd] R vs. C
On 17 January 2011 at 09:13, Patrick Leyshock wrote:
| A question, please about development of R packages:
|
| Are there any guidelines or best practices for deciding when and
why to
| implement an operation in R, vs. implementing it in C? The
Writing R
| Extensions recommends working in interpreted R code . . . this is
normally
| the best option. But we do write C-functions and access them in R -
the
| question is, when/why is this justified, and when/why is it NOT
justified?
|
| While I have identified helpful documents on R coding standards,
I have
not
| seen notes/discussions on when/why to implement in R, vs. when to
implement
| in C.
The (still fairly recent) book 'Software for Data Analysis:
Programming
with
R' by John Chambers (Springer, 2008) has a lot to say about this. John
also
gave a talk in November which stressed 'multilanguage' approaches; see
e.g.
http://blog.revolutionanalytics.com/2010/11/john-chambers-on-r-and-multilingualism.html
In short, it all depends, and it is unlikely that you will get a
coherent
answer that is valid for all circumstances. We all love R for how
expressive
and powerful it is, yet there are times when something else is
called for.
Exactly when that time is depends on a great many things and you
have not
mentioned a single metric in your question. So I'd start with John's
book.
Hope this helps, Dirk
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--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
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[Rd] Vignette Questions
Dear List,
I recently stumbled over the possibility and need to specifiy
% \VignetteDepends{}
in my vignettes. I did not know about this, and I notice that it is not
mentioned in the R-extensions manual section Writing package vignettes.
I have some questions with regards to that:
- would it be possible to include into the section Writing package
vignettes some hint that besides \VignetteIndexEntry also
\VignetteDepends{}
\VignetteKeywords{}
\VignettePackage{}
exist (and should be used)?
Also a link to the R-News Paper Sweave, Part II: Package Vignettes may
be very helpful.
- Is the documentation of these somewhere else where I didn't find it?
- Are there more such commands?
- Is there a way to ask R CMD check to check whether all dependencies of
the vignettes are correctly specified?
Of course, on my computer all required packages are available...
- Which dependencies should go into \VignetteDepends{}?
Only those without Priority in the packageDescription, or also
recommended packages, or maybe even base packages?
Should I specify the package that the vignette belongs to itself?
- Related, but slightly different: is there a way to temporarily enforce
that specified packages should not be loaded (or that only specified
packages are allowed to be loaded)?
I have a few functions in my package that do use e.g. plotrix if it is
available but otherwise should work in a less fancy way.
Till now I test them on an old computer where I didn't install those
packages but that's quite a hassle.
Thank you very much for your kind help!
Claudia Beleites
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Valerio 2
I-34127 Trieste
ITALY
email: cbelei...@units.it
phone: +39 (0 40) 5 58-34 68
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Re: [Rd] SweaveInput + keep.source = TRUE trouble
Thank you - works fine for me now.
Claudia
Duncan Murdoch wrote:
This is fixed now in R-devel and the beta version. The fix isn't
perfect: if you use \SweaveInput, you lose the error reporting that
gives line numbers from the original file. It should be possible to
have both, but I think the changes to implement that are too large to
consider in a beta.
Duncan Murdoch
On 05/10/2010 5:38 AM, Claudia Beleites wrote:
Dear all,
I have trouble with R-beta sweaving files that include definitions with
\SweaveInput in combination with keep.source = TRUE
Symptom:
SInput is taken from too far down the input file (the shift is the
number of
lines of the included file). Is that known? Searching didn't turn up
anything,
yet I think there are more people than just me using keep.source.
Example:
$ ~/tmp/R-beta/bin/R CMD Sweave baseline.Rnw
mv baseline.tex baseline.devel.tex
R CMD Sweave baseline.Rnw
mv baseline.tex baseline.2.11.tex
diff -u baseline.2.11.tex baseline.devel.tex
gives:
--- baseline.2.11.tex2010-10-05 11:33:49.0 +0200
+++ baseline.devel.tex2010-10-05 11:33:49.0 +0200
@@ -83,7 +83,7 @@
\verb+\SweaveOpts{keep.source = TRUE}+
\begin{Schunk}
\begin{Sinput}
- 12
+ line 54
\end{Sinput}
\begin{Soutput}
[1] 12
@@ -106,7 +106,7 @@
line 63 chunk option keep.source = TRUE
\begin{Schunk}
\begin{Sinput}
- 14
+ line 67
\end{Sinput}
\begin{Soutput}
[1] 14
I used yesterday's R-beta, and my system is Ubuntu 9.10 64 bit (though
that
probably doesn't matter).
Building the example file I also found that \SweaveInput{} cannot be
followed by
anything else on the line(not even a LaTeX comment).
\SweaveInput{x}y
complains that file xy is not found.
Best regards,
Claudia Beleites
__
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--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
__
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Re: [Rd] SweaveInput + keep.source = TRUE trouble
Sorry, I forgot the sessionInfos:
devel:
R version 2.12.0 beta (2010-10-03 r53154)
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
2.11:
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu
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
Claudia Beleites wrote:
Dear all,
I have trouble with R-beta sweaving files that include definitions with
\SweaveInput in combination with keep.source = TRUE
Symptom:
SInput is taken from too far down the input file (the shift is the
number of
lines of the included file). Is that known? Searching didn't turn up
anything, yet I think there are more people than just me using keep.source.
Example:
$ ~/tmp/R-beta/bin/R CMD Sweave baseline.Rnw
mv baseline.tex baseline.devel.tex
R CMD Sweave baseline.Rnw
mv baseline.tex baseline.2.11.tex
diff -u baseline.2.11.tex baseline.devel.tex
gives:
--- baseline.2.11.tex2010-10-05 11:33:49.0 +0200
+++ baseline.devel.tex2010-10-05 11:33:49.0 +0200
@@ -83,7 +83,7 @@
\verb+\SweaveOpts{keep.source = TRUE}+
\begin{Schunk}
\begin{Sinput}
- 12
+ line 54
\end{Sinput}
\begin{Soutput}
[1] 12
@@ -106,7 +106,7 @@
line 63 chunk option keep.source = TRUE
\begin{Schunk}
\begin{Sinput}
- 14
+ line 67
\end{Sinput}
\begin{Soutput}
[1] 14
I used yesterday's R-beta, and my system is Ubuntu 9.10 64 bit (though
that probably doesn't matter).
Building the example file I also found that \SweaveInput{} cannot be
followed by anything else on the line(not even a LaTeX comment).
\SweaveInput{x}y
complains that file xy is not found.
Best regards,
Claudia Beleites
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbelei...@units.it
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I never used it. I got curious, though. What would be a situation that benefits of this option? Maybe a use case could be found by brute force (grep all .Rnw files on CRAN for the option? Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] cacheSweave / pgfSweave driver for package vignette
Dear all, Maybe we should move the discussion to r-devel? So please excuse the cross-posting, it is to tell people at r-help where to find the rest of the discussion (in case you agree with me). I've been wondering about that, too. Gabor, I use fake vignettes along your lines, too. In order to provide meaningful samples, I have both bulky data and bulky calculations (at least too long to have any fun in running R CMD check frequently). As I do not want to burden my package with lots ( 60 MB) of raw data in various file formats, two vignettes do their real work extra (and the source is available for separate download). So for the development work it would be good to have caching for speed-up. For the testing purposes of R CMD CHECK, however, the whole thing needs to be calculated: afaik the caching mechanism checks for changes in the respective chunks. Which is great for data-analysis work. However, in a package development scenario the changes are rather expected in the package. I suspect that the caching cannot check this. Thus a cached vignette does greatly reduce the calculation time, but also knocks out part of the testing. This would be without concern, if the package is well behaved and does its testing in the tests and has the vignettes as manuals. I have to admit, though, that my package is not (yet) at this point. So I personally find myself with a shell script that automatically builds all vignettes first, transfers some files into the package (the data sets coming with the package are constructed in vignettes), and then check and build the package. In the end, this dependency of the package on the results of its vignettes needs much more calculation. I'm talking of ca. 10 - 15 min for the whole process (i.e. 5 - 7 min for one check cycle). This is awkward for development, but I think it's OK for something to be done occasionally on a nightly check on the server. My conclusion is, that a cached Sweave driver should only be specified in certain situations. I.e. it would be very helpful for developing to do this at home, but I'm afraid it is not the best idea to reduce the work in checking the package in general (e.g. during nightly checks). I also say this because I have been running into trouble with the nighly build on r-forge (due to some LaTeX packages that I thought to be fairly standard, which they weren't). Another error I like to produce is to forget adding a new source file to the version control. Both cases are only found in checks during the nightly build on the server. There may be other mistakes that would be masked by the caching. Of course, it is also not nice to keep the servers calculating examples for hours. I presume, however, that this case is quite rare (compared to situations where the regular building and checking is too long for a fluent development cycle), and I'd say that in this case Gabor's procedure is OK. For my work it would be much more helpful, if R CMD CHECK had also positive flags (e.g. --tests as abbreviation for --no-codoc --no-examples --no-install --no-vignettes --no-latex) I know hardly anything about make files and never wrote one myself. I think they could be helpful here to switch between the development checks and a complete build check. So I'd be very curious to see some make files. HTH, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] rbind on data.frame that contains a column that is also a data.frame
Dear all, I also use matrices inside data.frames in my (S4) class hyperSpec. So, yes, it would be great if commands like apply would work as straightforward as e.g. rbind does on such data.frames. The problem here seems to me different, though: Is it possible that the relevant difference between matrices and data.frames is that the rownames of a matrix do not need to be unique? m - matrix (1:12, ncol = 3) rownames (m) - rep (1, 4) m df - as.data.frame (m) # seems to work, but: df # throws error: Fehler in data.frame(V1 = c(1, 2, 3, 4), V2 = c(5, 6, 7, : duplicate row.names: 1 dimnames (df) Greetings, Claudia Martin Maechler wrote: Heinz Tuechler tuech...@gmx.at on Sat, 07 Aug 2010 01:01:24 +0100 writes: Also Surv objects are matrices and they share the same problem when rbind-ing data.frames. If contained in a data.frame, Surv objects loose their class after rbind and therefore do not more represent Surv objects afterwards. Using rbind with Surv objects outside of data.frames shows a similar problem, but not the same column names. In conclusion, yes, matrices are common in data.frames, but not without problems. My understanding ( 20 yr long S and R experience) has been that a dataframe definitely can have matrix-like components, and as Bill Dunlap (with equal S R experience) has just explained, that's actually more common than you have thought. To have *data frame*s instead of simple matrices, should be much less common, I'm not sure if it's a good idea. But getting back to 'matrices', I think they should work without problems, at least for basic R operations such as rbind(). I don't have time to analyze the Surv - example below, but at the moment think, that we'd be interested in fixing the problems.. Martin Maechler, ETH Zurich Heinz ## example library(survival) ## create example data starttime - rep(0,5) stoptime - 1:5 event - c(1,0,1,1,1) group - c(1,1,1,2,2) ## build Surv object survobj - Surv(starttime, stoptime, event) ## build data.frame with Surv object df.test - data.frame(survobj, group) df.test ## rbind data.frames rbind(df.test, df.test) ## rbind Surv objects rbind(survobj, survobj) At 06.08.2010 09:34 -0700, William Dunlap wrote: -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Nicholas L Crookston Sent: Friday, August 06, 2010 8:35 AM To: Michael Lachmann Cc: r-devel-boun...@r-project.org; r-devel@r-project.org Subject: Re: [Rd] rbind on data.frame that contains a column that is also a data.frame OK...I'll put in my 2 cents worth. It seems to me that the problem is with this line: b$a=a , where s is something other than a vector with length equal to nrow(b). I had no idea that a dataframe could hold a dataframe. It is not just rbind(b,b) that fails, apply(b,1,sum) fails and so does plot(b). I'll bet other R commands fail as well. My point of view is that a dataframe is a list of vectors of equal length and various types (this is not exactly what the help page says, but it is what it suggests to me). Hum, I wonder how much code is based on the idea that a dataframe can hold a dataframe. I used to think that non-vectors in data.frames were pretty rare things but when I started looking into the details of the modelling code I discovered that matrices in data.frames are common. E.g., library(splines) sapply(model.frame(data=mtcars, mpg~ns(hp)+poly(disp,2)), class) $mpg [1] numeric $`ns(hp)` [1] ns basis matrix $`poly(disp, 2)` [1] poly matrix You may not see these things because you don't call model.frame() directly, but most modelling functions (e.g., lm() and glm()) do call it and use the grouping provided by the matrices to encode how the columns of the design matrix are related to one another. If matrices are allowed, shouldn't data.frames be allowed as well? Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com 15 years of using R just isn't enough! But, I can say that not one line of code I've written expects a dataframe to hold a dataframe. Hi, The following was already a topic on r-help, but after understanding what is going on, I think it fits better in r-devel. The problem is this: When a data.frame has another data.frame in it, rbind doesn't work well. Here is an example: -- a=data.frame(x=1:10,y=1:10) b=data.frame(z=1:10) b$a=a b z a.x a.y 1 1 1 1 2 2 2 2
[Rd] suggestion for sweep help page
Dear all, I stumbled over the fact that sweep in fact calls FUN with appropriate arrays. I used to think of it as apply-like to call a function with n-dimensional and n-1-dimensional arguments. I suggest to put a sentence like: sweep appropriately repeats STATS, and calls FUN with two arrays of the same size. into the help page to clarify what input FUN should expect. Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 dispatch for .DollarNames (utils)
Dear all, thank your for this discussion - I had been wondering how to get the completion with my S4 class, but it didn't bother me enough to dig into things. The workaround/hack that *does* work now, I believe, is to insert a dummy S3 class into the mix and define the S3 .DollarNames method for it. Example: setOldClass(foo3) .DollarNames.foo3 - function(x, pattern)bar My question here is: what is the dummy class needed for? I have a few S3 methods for my S4 class (rbind.hyperSpec, cbind.hyperSpec, and now .DollarNames.hyperSpec). They seem to work just fine without first setting up a dummy S3 class that is then used in the contains of the S4 definition. Any pitfalls with that? Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 dispatch for .DollarNames (utils)
John, Thank your for the explanation! Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] dots for sample -- implicitGeneric
Dear Martin, Martin Maechler wrote: CB == Claudia Beleites cbelei...@units.it on Sun, 28 Feb 2010 19:31:42 +0100 writes: CB Dear R-Developers, CB could 'sample' gain a ... argument? As you may know, adding '...' also has drawbacks, most notably that you lose automatic checking of correctly specified argument names (when the function is called). Yes, I'm aware of that - and was silently wondering whether one could do something against it (besides having nicely behaved functions without ... at the end of the call chain). OTOH, R has now (since 2.9.0) had sample.int() as a fast and robust alternative. Yes. I had a quick thought whether I should do sample (my.object) = new object with a subset of my.object's spectra and sample.int (my.object) = indices for use with my.object I decided that this is bad, as I would expect that a function somefun.int does *expect* rather than *return* the integer. The other thought was to have an additional function isample that returns indices. Which after rethinking seems the right thing to do. However this doesn't solve the implicitGeneric problem: if the object is returned I'd like to allow users to pass short messages that end up in the object's logbook. But this can easily be postponed until R 2.11 is released and sample has the implicit generic also for normal users (= my colleagues who already complain if I ask them to update their R to the official release). CB As a convenience function, I added a sample Method to my hyperSpec CB class. This function however has a flag indicating whether the results CB should be returned directly as a hyperSpec object or rather as indices CB that give a random sample. CB For the moment, I use SetGeneric to add the dots argument, but this of CB course gives a warning that the base function sample is overwritten (and CB my colleagues are almost as scared of warnings as of errors...) and they are not the only ones ... For a while now, we have (in 'methods') the possibility to make functions implicit generic, see ?implicitGeneric , exactly for purposes like (I think) you have here ( and notably to ensure that if *different* packages do this, they get compatible versions of the generic, and hence all the different method definitions will be attached to the same generic ) Yes, thank you - that's what I really wanted! I'll do my homework and reread the chaper in Chambers' book. Namely, you'd want to define S4 methods (and hence make 'sample' an S4 generic) with new arguments in your package. Exactly. So, yes, I now have added 'sample' to the list of functions that we make implicitGeneric in R. Thanks a lot. -- Get a version of R-devel, (svn revision = 51202) and try the following: setClass(foo, contains=vector) [1] foo setMethod(sample, foo, function(x, size, myArg, ...) sprintf(sample(foo, myArg=%s)\n,myArg)) Restoring the implicit generic function for ‘sample’ from package ‘base’ into package ‘.GlobalEnv’; the generic differs from the default conversion (Formal arguments differ: (x, size, replace, prob), (x, size, replace, prob, ...)) Creating a new generic function for sample in .GlobalEnv [1] sample sample(new(foo), myArg = 64) [1] sample(foo, myArg=64)\n Wonderful. Works like a charm. Thanks a lot. Thanks for your kind help, Claudia Best regards, Martin Maechler, ETH Zurich CB Thanks, CB Claudia CB -- CB Claudia Beleites CB Dipartimento dei Materiali e delle Risorse Naturali CB Università degli Studi di Trieste CB Via Valerio 2 CB I-34127 Trieste CB ITALY __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] dots for sample
Dear R-Developers, could 'sample' gain a ... argument? As a convenience function, I added a sample Method to my hyperSpec class. This function however has a flag indicating whether the results should be returned directly as a hyperSpec object or rather as indices that give a random sample. For the moment, I use SetGeneric to add the dots argument, but this of course gives a warning that the base function sample is overwritten (and my colleagues are almost as scared of warnings as of errors...) Thanks, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Valerio 2 I-34127 Trieste ITALY email: cbelei...@units.it phone: +39 (0 40) 5 58-34 68 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [SoC] R and Google Summer of Code 2010: Call for Proposals -
May I ask for a bit of help? I'd like to participate with my hyperSpec project. I set up a proposal page in the wiki [http://rwiki.sciviews.org/doku.php?id=developers:projects:gsoc2010:hyperspec]. hyperSpec is about handling spectroscopic (hyperspectral) data in R. It is thus a project that is aimed at a rather specific group of R users - far less broad audience than the other projects listed there. Is it OK if I have that project in that GSoC 2010 list? I'd really appreciate comments! Thanks, Claudia Dirk Eddelbuettel wrote: On 24 February 2010 at 11:09, Philippe Grosjean wrote: | I have created the projects subsection in developers. The Google | Summer of Code 2010 is at | http://rwiki.sciviews.org/doku.php?id=developers:projects:googlesummer2010 We dediced to make this http://rwiki.sciviews.org/doku.php?id=developers:projects:gsoc2010 to stick with the common 'GSoC' acronym. So go ahead and submit ideas! Dirk -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Sweave errors during package building
Dear all, I just spent quite a while fixing a weird error in my vignettes while doing R CMD build and R CMD check R CMD Sweave ran fine, though. The cause turned out to be: 1. I have a data set flu, 2. and a corresponding vignette explaining things one can do with that object. This vignette creates another object flu (which masks the packages one). 3. Now when the next vignette is processed, this object created by the first vignette still exists, and still masks the packaged data set. I was assuming that the building and checking processes are like R CMD Sweave, but this is not the case: they are like Sweave inside R, which will also change objects in the workspace (as I now know, see the example). Maybe I didn't enough RTFM, but I was completely unaware of that before. Would it be a good idea to have a few words about this in the FAQ and in the help page? Claudia file testsweave.Rnw: test= a - 3 b - 1 @ now in R: a - 4 a [1] 4 b Error: object 'b' not found Sweave (testsweave.Rnw) Writing to file testsweave.tex Processing code chunks ... 1 : echo term verbatim (label=test) You can now run LaTeX on 'testsweave.tex' a [1] 3 b [1] 1 -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] methods vs. functions
Dear Duncan and Oleg, thanks for your answers. For the moment, I'll use functions. Happy new year, Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] ... (dotMethods) and cbind/rbind: how to give the signature?
Dear Oleg, thanks a lot! I'll have S3 methods until the problems settle somehow. I wasn't aware that S3 despatch works for S4 classes as well. Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] ... (dotMethods) and cbind/rbind: how to give the signature?
Dear List,
I'm struggling with the signature writing cbind/rbind functions for a S4
class.
First of all, I'm very happy that it is now possible to dispatch on ...
I follow the example for paste in ?dotMethods, which works as far as this:
### start example
setClass (cbtest,
representation = representation (data = data.frame),
prototype = prototype (data = data.frame (spc = I (matrix (rnorm
(15) , 3, 5)))
)
)
a - new (cbtest)
a
setMethod(cbind2, signature (x = cbtest, y = cbtest),
function (x, y){
x...@data$spc - cbind (x...@data$spc, y...@data$spc)
x
}
)
setMethod(cbind2, signature (x = cbtest, y = missing), function (x, y)
x)
cb.cbind - function (..., deparse.level){
dots - list (...)
for (i in seq_along (dots)[-1])
dots[[1]] - cbind2 (dots[[1]], dots[[i]])
dots[[1]]
}
cbind2 (a, a)
cb.cbind (a, a, a)
cbind (a, a, a)
setGeneric (cbind, signature = signature(...))
setMethod (cbind, cbtest,
function (..., deparse.level) cb.cbind (...))
cbind (a, a, a)
cbind (a, a, a, deparse.level = 1)
### end example
However, I get the following message:
with setGeneric
Creating a generic for cbind in package .GlobalEnv
(the supplied definition differs from and overrides the implicit generic in
package base: Signatures differ: (...), (deparse.level))
How do I specify the correct signature?
Furthermore: as I do not want to do anything with deparse.level, I'd rather
specify it as missing in setMethod. But again, I don't get the signature
correct.
I tried
setGeneric (cbind, signature = signature (...=..., deparse.level =
integer))
and
setGeneric (cbind, signature = signature (..., deparse.level = integer))
both give:
Fehler in makeGeneric(name, fdef, fdeflt, group = group, valueClass =
valueClass, :
Nicht-Argumente in der Signatur: integer
What is my mistake?
Thanks a lot for your help!
Claudia
version
_
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major 2
minor 8.0
year 2008
month 10
day20
svn rev46754
language R
version.string R version 2.8.0 (2008-10-20)
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 (0 40) 5 58-34 47
email: cbelei...@units.it
__
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[Rd] methods vs. functions
Dear List, a second, more general, question concerning S4 classes. I have a bunch of functions/methods for my class. At the moment I have them as methods, because they work on objects of my S4 class and therefore belong to that class. On the other hand, it is comparably unlikely that someone else wants the same kind of method. And package.skeleton () produces the xzy-methods.Rds. But for the documentation I rather need normal function definitions. I know that I can write the Rd files just as if it was a normal function, but this got me to ask myself whether it is a good idea to have methods or whether I should rather use normal functions? If I understood the concept of namespace correctly, a package with a namespace avoids trouble with clashing function names - so I don't need to worry about that using functions (I anyways have some functions, that should not be methods of the class). Any comments? Thanks a lot! Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 (0 40) 5 58-34 47 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
