[Rd] Possible bug in edit(x) for editing matrices [tested on a Mac]
Hi, it seems there's a possible bug in edit(x) if x is a matrix filled with NA only. To reproduce please do the following: a - matrix() edit(a) change e.g. the cell value to 1 and close the GUI-based editor. edit(a) returns NA. This also happens for any dimension of the matrix as long as all cell values are NA. If at least one of the cell values is not NA it works correctly. The same behaviour I also get via fix(x). I tried this by using R via the Terminal (editing via X11 and Tcl/Tk) and the Mac R-GUI app. Here's my sessionInfo(): R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Any ideas? Or is this an undocumented behaviour? Best, --Hans __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possible bug in edit(x) for editing matrices [tested on a Mac]
On 19/12/2011 09:48, Hans-Jörg Bibiko wrote: Hi, it seems there's a possible bug in edit(x) if x is a matrix filled with NA only. It's as documented. Hint: look at mode(a) or str(a), and check what values are accepted for a logical matrix. To reproduce please do the following: a- matrix() edit(a) change e.g. the cell value to 1 and close the GUI-based editor. edit(a) returns NA. This also happens for any dimension of the matrix as long as all cell values are NA. If at least one of the cell values is not NA it works correctly. The same behaviour I also get via fix(x). I tried this by using R via the Terminal (editing via X11 and Tcl/Tk) and the Mac R-GUI app. Here's my sessionInfo(): R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Any ideas? Or is this an undocumented behaviour? Best, --Hans __ 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] Saving nothing with save()
Barry Rowlingson b.rowling...@lancaster.ac.uk on Sun, 18 Dec 2011 01:32:52 + writes: Scenario: Here I am working away in R. I've got results that prove global warming is anthropogenic and also the solution for producing limitless carbon-neutral energy from nuclear fusion. Its been a good day. So, I want to save my work. I don't want to overwrite my current .RData, so I save it to another file: save(file=prize.RData) # just need to email this to the Nobel committee q() Save workspace image? [y/n/c]: - no I don't want to save the workspace image, I just saved everything to prize.RData. But gee, it did seem to do that quite quickly considering the volume of evidential data in my work. My unix shell prompt returns. Uh oh. See what I did there? I typed 'save' when I meant 'save.image'. What does that give me? A 42 byte, empty, latest.RData, and because there was no warning or error I quit without saving it again. Oops. Massive Data Loss. Is there any reason why save(file=file.RData) couldn't warn or error if you try and save nothing? There's no obvious check in the R code for save. Barry PS the above scenario is fictional. really? ;-) well, after *not* save()ing all your findings, it wouldn't have been such a good day, would it? well, in spite of that. I agree that save() should warn or stop in that case. I have now committed a version -- to R-devel only -- which stop()s if 'pretest=TRUE' and uses warning() otherwise, e.g., in the case of save.image() when there's nothing to save. Thank you, Barry. for the suggestion! Martin When did I last have a good day? (I wish you more of those..) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possible bug in edit(x) for editing matrices [tested on a Mac]
On 19 Dec 2011, at 12:22, Prof Brian Ripley wrote: it seems there's a possible bug in edit(x) if x is a matrix filled with NA only. It's as documented. Hint: look at mode(a) or str(a), and check what values are accepted for a logical matrix. Thank you very much! I wasn't aware of the circumstance that mode(matrix()) of course returns 'logical'. Maybe one could warn the user in the function edit(x) that if (is.matrix(x) is.logical(x) == TRUE) that edit(x) doesn't work since my workaround was that I created a matrix of the dimension 10x20 via matrix(NA, nrow=10, ncol=20) and used the GUI data editor to fill the matrix's cells with values. Kind regards, --Hans __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Speed issue when writing to RGui console from tcl/tk GUI
It seems that there are speed issues when printing to the R console from a
tcl/tk GUI.
Here are functions to write a lot of output, and to display how long it
takes.
printsalot - function(n)
{
for(i in 1:n) cat(i, fill = TRUE)
}
timings - function(n = 1e3)
{
print(system.time(printsalot(n)))
}
Calling timings() from the console reveals a run time of a few hundredths
of a second.
The following GUI has two buttons. Clicking the slow buttons just calls
timings directly, and takes several seconds to run. However, if we request
input from the console, via readline (the fast button) then the timing
drops back down to hundredths of a second.
library(tcltk)
win - tktoplevel()
btn1 - ttkbutton(win, text = slow, command = function() timings())
btn2 - ttkbutton(win, text = fast, command = function() {readline(Press
ENTER ); timings()})
tkpack(btn1, btn2)
I've only observed this slow behaviour with RGui on Windows (XP) - it
doesn't happen with Rterminal or eclipse/StatET or RStudio.
I want a few people to run this code to see if it affects, for example,
other OSes, to narrow down the extent of the problem before I submit it as
a bug.
Also, if you have any insight as to what is happening or fixes, I'd be
interested to know.
Regards,
Richie.
[[alternative HTML version deleted]]
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Re: [Rd] R package BibTex entries: looking for a more general solution
On 12/19/2011 2:02 AM, Renaud Gaujoux wrote: Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (posted on r-help). Romain included it a couple of weeks ago into the bibtex package as function write.bib, and submitted the update to CRAN, but some NOTEs in the check delayed its availability on CRAN. You can still install and try out the new version with: install.packages(bibtex, repos=http://R-Forge.R-project.org;) Keys for multiple citations are generated as pkgname%i, which might not be ideal, but works ok though. It might be better not number the first (main) citation. Romain, I think I will submit a patch for this. Hope this helps. Thanks, Renaud I now have a working function, Rpackages.bib() that is roughly equivalent to your write.bib() and other related material at http://euclid.psych.yorku.ca/SCS/Private/Rbibs/ Also, see the document http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf which reports some problems perl fixes for the generated bibentries. These might be incorporated into the functions to make the resulting bibtex files directly usable. Your bibtex package seems the most natural place for this. Also, write.bib() doesn't seem to work unless you pass a list of package names. write.bib() Error in is(entry, bibentry) : argument entry is missing, with no default write.bib(NULL) Error in write.bib(NULL) : Invalid argument `entry`: expected a bibentry object or a character vector of package names. best, -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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
Indeed I broke the function when adding support for bibentry objects... By the way, let's give credits back to Ceasars: I am not the author of the bibtex package, Romain Francois is. I just contributed the write.bib function, mainly inspired by Achim's function. Romain, I will send a fix for this now. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 19/12/2011 15:56, Michael Friendly wrote: On 12/19/2011 2:02 AM, Renaud Gaujoux wrote: Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (posted on r-help). Romain included it a couple of weeks ago into the bibtex package as function write.bib, and submitted the update to CRAN, but some NOTEs in the check delayed its availability on CRAN. You can still install and try out the new version with: install.packages(bibtex, repos=http://R-Forge.R-project.org;) Keys for multiple citations are generated as pkgname%i, which might not be ideal, but works ok though. It might be better not number the first (main) citation. Romain, I think I will submit a patch for this. Hope this helps. Thanks, Renaud I now have a working function, Rpackages.bib() that is roughly equivalent to your write.bib() and other related material at http://euclid.psych.yorku.ca/SCS/Private/Rbibs/ Also, see the document http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf which reports some problems perl fixes for the generated bibentries. These might be incorporated into the functions to make the resulting bibtex files directly usable. Your bibtex package seems the most natural place for this. Also, write.bib() doesn't seem to work unless you pass a list of package names. write.bib() Error in is(entry, bibentry) : argument entry is missing, with no default write.bib(NULL) Error in write.bib(NULL) : Invalid argument `entry`: expected a bibentry object or a character vector of package names. best, -Michael __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Issues with building package with C src on windows [R CMD INSTALL ignoring makefile]
I've written a rather complex package that requires overriding the default compilation behavior for the C code component. In the src dir I have a Makefile that is used correctly on OSX and Linux builds of the package, but completely ignored on windows. R CMD INSTALL package on windows runs Makeconf instead of running make on my Makefile.If run make in the src directory manually on windows, the shared library compiles. How can I get the INSTALL command to look for the Makefile?I am building on R 2.14.0 on a win 7 vm. Thanks Jonathan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Saving nothing with save()
Martin, On Dec 19, 2011, at 6:39 AM, Martin Maechler wrote: Barry Rowlingson b.rowling...@lancaster.ac.uk on Sun, 18 Dec 2011 01:32:52 + writes: Scenario: Here I am working away in R. I've got results that prove global warming is anthropogenic and also the solution for producing limitless carbon-neutral energy from nuclear fusion. Its been a good day. So, I want to save my work. I don't want to overwrite my current .RData, so I save it to another file: save(file=prize.RData) # just need to email this to the Nobel committee q() Save workspace image? [y/n/c]: - no I don't want to save the workspace image, I just saved everything to prize.RData. But gee, it did seem to do that quite quickly considering the volume of evidential data in my work. My unix shell prompt returns. Uh oh. See what I did there? I typed 'save' when I meant 'save.image'. What does that give me? A 42 byte, empty, latest.RData, and because there was no warning or error I quit without saving it again. Oops. Massive Data Loss. Is there any reason why save(file=file.RData) couldn't warn or error if you try and save nothing? There's no obvious check in the R code for save. Barry PS the above scenario is fictional. really? ;-) well, after *not* save()ing all your findings, it wouldn't have been such a good day, would it? well, in spite of that. I agree that save() should warn or stop in that case. I have now committed a version -- to R-devel only -- which stop()s if 'pretest=TRUE' and uses warning() otherwise, I don't think I like that - why should it warn/stop in any case even when the use is absolutely legal? I think this is the wrong approach - the whole idea was to warn on unintended *interactive* use - breaking existing code in the process is IMHO not necessary. I don't think save(list=x, file=y) should fail even if x is empty - that makes it fail for completely legal code. What Barry was worried about was the interactive case of save(file=x) which should IMHO warn (there is a precedent for stopping as well - see tar - so I won't object). I really see no reason for adding the pretest flag - it makes no sense since is warns anyway so it doesn't help at all. I would propose changing *only* the behavior of save(file=x) (to warn or stop - personally I prefer former) and not anything else. e.g., in the case of save.image() when there's nothing to save. Why should save.image() warn? Again, it causes unnecessary trouble for automated saving... empty workspace is probably even more common that using save(file=foo) ... If save() was fixed as above, that would be a non-issue. Thank you, Barry. for the suggestion! Well, you did not follow his suggestion, though ;) Cheers, Simon Martin When did I last have a good day? (I wish you more of those..) __ 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] Issues with building package with C src on windows [R CMD INSTALL ignoring makefile]
On Dec 19, 2011, at 10:30 AM, Jonathan Shore wrote: I've written a rather complex package that requires overriding the default compilation behavior for the C code component. In the src dir I have a Makefile that is used correctly on OSX and Linux builds of the package, but completely ignored on windows. R CMD INSTALL package on windows runs Makeconf instead of running make on my Makefile.If run make in the src directory manually on windows, the shared library compiles. See R-ext - you probably need to create Makefile.win Note that in most cases it is unnecessary to use Makefile - you can add targets to Makevars which will supply you with the correct flags and give you flexibility whereas Makefile is very limited in that you need to write all rules by hand which is very error prone and likely to break with new R versions. Cheers, Simon How can I get the INSTALL command to look for the Makefile?I am building on R 2.14.0 on a win 7 vm. Thanks Jonathan __ 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] Issues with building package with C src on windows [R CMD INSTALL ignoring makefile]
If all else fails, read the manual: it is explicitly documented that you need a file src/Makefile.win . And very likely you should rather study the manual to resolve what issue you think 'requires' a Makefile: those who want to use R on other platforms (e.g. Solaris and AIX) are unlikely to thank you for taking that route. On 19/12/2011 15:30, Jonathan Shore wrote: I've written a rather complex package that requires overriding the default compilation behavior for the C code component. In the src dir I have a Makefile that is used correctly on OSX and Linux builds of the package, but completely ignored on windows. R CMD INSTALLpackage on windows runs Makeconf instead of running make on my Makefile.If run make in the src directory manually on windows, the shared library compiles. How can I get the INSTALL command to look for the Makefile?I am building on R 2.14.0 on a win 7 vm. Thanks Jonathan __ 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] error starting R-devel with --arch ppc -- an unusual circumstance has arisen
On Thu, Dec 15, 2011 at 4:46 PM, Simon Urbanek simon.urba...@r-project.org wrote: Dan, I don't know why, but something is off in the recent R-devel build for ppc. The result is that the installed binary ppc is older than the other ones, so it doesn't have paste0 while the others do. The really strange thing is that the build logs show success, but the build directory is old and the resulting tar ball is not updated. I'll keep you posted. It looks like this has been fixed. Thanks! Dan Cheers, Simon On Dec 15, 2011, at 4:56 PM, Dan Tenenbaum wrote: When I try and start R-devel as follows: R --vanilla --arch ppc I see this, over and over again, ^C does not interrupt it and I have to close the terminal window: Error in paste0(prefix, conditionMessage(e), \n) : not a BUILTIN function In addition: Warning message: An unusual circumstance has arisen in the nesting of readline input. Please report using bug.report() Error in paste0(prefix, conditionMessage(e), \n) : not a BUILTIN function In addition: Warning message: An unusual circumstance has arisen in the nesting of readline input. Please report using bug.report() I can't get to sessionInfo() but here is sessionInfo() of the same R invoked with no --arch argument: R Under development (unstable) (2011-12-14 r57899) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base This seems to be related to the issue I reported here previously: https://stat.ethz.ch/pipermail/r-devel/2011-December/062793.html Thanks, Dan __ 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] error starting R-devel with --arch ppc -- an unusual circumstance has arisen
On Dec 19, 2011, at 2:22 PM, Dan Tenenbaum wrote: On Thu, Dec 15, 2011 at 4:46 PM, Simon Urbanek simon.urba...@r-project.org wrote: Dan, I don't know why, but something is off in the recent R-devel build for ppc. The result is that the installed binary ppc is older than the other ones, so it doesn't have paste0 while the others do. The really strange thing is that the build logs show success, but the build directory is old and the resulting tar ball is not updated. I'll keep you posted. It looks like this has been fixed. Well, temporarily - I nudged the build manually (so the paste0 issues is gone), but the nightly builds behave very oddly - they create few files (like SVN-REVISION) but even Makefiles are not generated. I'll try to flush the whole tree and see how it goes ... Thanks, Simon Thanks! Dan Cheers, Simon On Dec 15, 2011, at 4:56 PM, Dan Tenenbaum wrote: When I try and start R-devel as follows: R --vanilla --arch ppc I see this, over and over again, ^C does not interrupt it and I have to close the terminal window: Error in paste0(prefix, conditionMessage(e), \n) : not a BUILTIN function In addition: Warning message: An unusual circumstance has arisen in the nesting of readline input. Please report using bug.report() Error in paste0(prefix, conditionMessage(e), \n) : not a BUILTIN function In addition: Warning message: An unusual circumstance has arisen in the nesting of readline input. Please report using bug.report() I can't get to sessionInfo() but here is sessionInfo() of the same R invoked with no --arch argument: R Under development (unstable) (2011-12-14 r57899) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base This seems to be related to the issue I reported here previously: https://stat.ethz.ch/pipermail/r-devel/2011-December/062793.html Thanks, Dan __ 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] Why is the 64bit Windows version of package RSVGTipsDevice not available on CRAN?
On CRAN, the package RSVGTipsDevice is only installed for 32bit Windows, and is not available as a 64bit package for Windows. The file linked to in the package check summary on CRAN says NB: this package is only installed for sub-architecture 'i386' . What do I need to do to make it available as both 64bit and 32bit on CRAN? (I am the maintainer of the package). It builds, checks and runs fine as a 64 bit package on my own Windows 64 bit (XP) machine. Has a flag has been set somewhere because some time in the past this package had problems running in 64 bit mode? Here's the truncated output from the link from CRAN package check page: http://www.r-project.org/nosvn/R.check/r-release-windows-ix86+x86_64/RSVGTipsDevice-00check.html * using R version 2.14.0 (2011-10-31) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'RSVGTipsDevice/DESCRIPTION' ... OK * this is package 'RSVGTipsDevice' version '1.0-4' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking whether package 'RSVGTipsDevice' can be installed ... OK * checking installed package size ... OK NB: this package is only installed for sub-architecture 'i386' * checking package directory ... OK * checking for portable file names ... OK * ... [truncated] Here's the output of R CMD check on my own machine: $ /cygdrive/c/R/R-2.14.0/bin/x64/R.exe CMD check RSVGTipsDevice_1.0-4.tar.gz * using log directory 'D:/tplate/R/rforge/rsvgtipsdevice/RSVGTipsDevice.Rcheck' * using R version 2.14.0 (2011-10-31) * using platform: x86_64-pc-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'RSVGTipsDevice/DESCRIPTION' ... OK * this is package 'RSVGTipsDevice' version '1.0-4' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking whether package 'RSVGTipsDevice' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking PDF version of manual ... OK [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] graphics device event handling
Hi All I run across the following situation quite frequently and was wondering if there exists a simple solution that I missed. Situation: I develop some graphical display using the nice basic R graphical functions (plots, lines, images, histogramm ...). Now I would like to add a few simple user interaction capabilities. Problem: There seems to be no simple callback type event handling for mouse/keyboard events for the basic graphics devices. The setGraphicsEventHandlers only work on X11 (on MAC) which doesn't look nearly as nice as the basic quartz device and doesn't support transparency. Question: Is there a way to add graphics event handling to the CairoX11 or quartz interface in a similar simple fashion as the setGraphicsEventHandlers framework without requiring packages such as Rgtk and deviceCairo which can get fairly large and seem somewhat overkill for adding few simple interactions to existing R plot compositions. Kind Regards Sam __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
