[Rd] segfault on functions with 'source' attribute set to a boolean or a number (PR#10437)
Full_Name: Karl Ove Hufthammer Version: 2.6.0 OS: Linux (Fedora 7) Submission from: (NULL) (129.177.61.84) When viewing a function that has its 'source' attribute set to a boolean or a numeric, R crashes with a segfault. (Setting 'source' to a character vector does not make R crash, however.) Steps to reproduce: > attr(lm,"source")=FALSE > lm *** caught segfault *** address 0x18, cause 'memory not mapped' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check in Windows
Hi all, R CMD check does not work for me under Windows. This is the error R CMD check mypackage.tar.gz * checking for working latex ... OK tar: and: Not found in archive tar: Settings/miguez/ ... /00_pkg_src: Not found in archive tar: Error exit delayed from previous errors Error: cannot untar mypackage.tar.gz I know tar is available because R CMD build created the tarball in the first place and man tar works. I'm mostly working in Linux but if I can fix this it would be nice. Ok now I'm thinking that I might have an old version of perl installed and this might be the problem. Any suggestions/explanations are welcome. Thanks! Fernando __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check in Windows
On 11/19/2007 10:37 AM, Fernando Miguez wrote: > Hi all, > > R CMD check does not work for me under Windows. This is the error > > R CMD check mypackage.tar.gz > * checking for working latex ... OK > tar: and: Not found in archive > tar: Settings/miguez/ ... /00_pkg_src: Not found in archive > tar: Error exit delayed from previous errors > Error: cannot untar mypackage.tar.gz > > I know tar is available because R CMD build created the tarball in the > first place and man tar works. > > I'm mostly working in Linux but if I can fix this it would be nice. Ok > now I'm thinking that I might have an old version of perl installed and > this might be the problem. Any suggestions/explanations are welcome. Old/bad versions of some utility are the likely cause. The Rtools collection contains a custom version of tar; if your PATH is finding a different one first, that could be the trouble. Take a look at the "Windows Toolset" section of the admin manual, and make sure you follow the instructions about path order (and the rest, too). It is possible to use a different PATH than the one in the manual, but there are many more choices that fail than there are that succeed. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] (PR#10437) segfault on functions with 'source' attribute
I am not sure why you would want to do that, but the C code does assume source attributes were put there by R, and changing tests from !isNull to isString in a few places will fix that. If there is a character vector "source" attribute it should be used: that is the point of such attributes. On Mon, 19 Nov 2007, [EMAIL PROTECTED] wrote: > Full_Name: Karl Ove Hufthammer > Version: 2.6.0 > OS: Linux (Fedora 7) > Submission from: (NULL) (129.177.61.84) > > > When viewing a function that has its 'source' attribute set to a boolean or a > numeric, R crashes with a segfault. (Setting 'source' to a character vector > does > not make R crash, however.) > > Steps to reproduce: > >> attr(lm,"source")=FALSE >> lm > > *** caught segfault *** > address 0x18, cause 'memory not mapped' > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] More Rgraphviz help needed (Was: package installation order)
On 14 November 2007 at 20:38, Seth Falcon wrote:
| Dirk Eddelbuettel <[EMAIL PROTECTED]> writes:
| > When trying to package the by-now-gargantuan Rmetrics for Debian (which is
| > still ongoing), I looked around for some Depends builders. Turns out that
| > BioC has this. E.g. the following worked for:
| >
| > ## > install.packages("Biobase", repo="http://www.bioconductor.org";)
| > ## > repos <- Biobase:::biocReposList()
| > ## > install.packages("pkgDepTools", repos=repos["bioc"])
| > ## > library(pkgDepTools)
| > ## Loading required package: graph
| > ## Loading required package: RBGL
| > ## > CRANdeps <- makeDepGraph(repos["cran"], type="source")
| > ## > getInstallOrder("Rmetrics", CRANdeps, needed.only=FALSE)
| >
| > worked for me. I meant to add some code for Graphviz visualization (or look
| > for it, Seth et al probably already wrote it) but what you get from
| > getInstallOrder() should suit your needs here.
|
| makeDepGraph returns a graphNEL instance and Rgraphviz knows how to
| plot those. The entire graph will likely not produce a particularly
| compelling visualization. But you can subset the graph according to a
| particular package's dependencies, etc.
Yes indeed!! That was pretty straightforward just by following some code
inside getInstallOrder. And using "twopi" is good enough for the 40-some
packages in the graph.
But now I need the icing on the cake: Given such a dependency graph, how can
I color further subgraphs according to some criterion: I'd love to select a
sub-list (of, say, new packages, or of packages that satisfy some other
criterion) and have their node plotted in a different color. The help pages
clearly indicate that this should be possible, but they are also a little
terse on how one would do this... Any pointers anywhere?
Dirk
--
Three out of two people have difficulties with fractions.
__
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Re: [Rd] R CMD check in Windows
My guess is the that problem is that the current directory is under c:\Documents and Settings\miguel, and that is not supported. Try using a directory without spaces in its name. On Mon, 19 Nov 2007, Duncan Murdoch wrote: > On 11/19/2007 10:37 AM, Fernando Miguez wrote: >> Hi all, >> >> R CMD check does not work for me under Windows. This is the error >> >> R CMD check mypackage.tar.gz >> * checking for working latex ... OK >> tar: and: Not found in archive >> tar: Settings/miguez/ ... /00_pkg_src: Not found in archive >> tar: Error exit delayed from previous errors >> Error: cannot untar mypackage.tar.gz >> >> I know tar is available because R CMD build created the tarball in the >> first place and man tar works. >> >> I'm mostly working in Linux but if I can fix this it would be nice. Ok >> now I'm thinking that I might have an old version of perl installed and >> this might be the problem. Any suggestions/explanations are welcome. > > Old/bad versions of some utility are the likely cause. The Rtools > collection contains a custom version of tar; if your PATH is finding a > different one first, that could be the trouble. > > Take a look at the "Windows Toolset" section of the admin manual, and > make sure you follow the instructions about path order (and the rest, too). > > It is possible to use a different PATH than the one in the manual, but > there are many more choices that fail than there are that succeed. > > Duncan Murdoch > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Cairo device in dev.copy2eps
Hi everybody, It would be nice to have Cairo device included in dev.copy2eps() in order to avoid RGtk2 developers to use a hacked version of the function. I was arealdy done in dev.print(). Best regards. Washington R 2.6.0 OS Kubuntu 7.10 kernel 2.6.22 -- Washington Leite Junger [EMAIL PROTECTED] Departamento de Epidemiologia Instituto de Medicina Social Universidade do Estado do Rio de Janeiro http://www.ims.uerj.br/ares-rio __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NEWS file (was faqs)
SU> On Nov 15, 2007, at 10:53 AM, Duncan Murdoch wrote: >> On 11/15/2007 9:57 AM, Simon Urbanek wrote: >>> On Nov 14, 2007, at 11:55 PM, Gabor Grothendieck wrote: inst/NEWS would have the advantage of consistency with R itself which also has a NEWS file. >>> I vote for NEWS for reasons above plus because that's >>> what I use in my packages already ;). IMHO it should be >>> installed automatically if present, i.e. it shouldn't be >>> necessary to have it in inst/NEWS, just plain NEWS >>> should suffice. >> >> And you're volunteering to make that change? >> SU> Yup, in R-devel now (43464). However, there are other candidate files SU> as well and we don't do anything with the NEWS file just SU> yet ... any further ideas? Yes, I think 'NEWS' and 'ChangeLog' are typically used a bit differently, and I would be very happy if we could install either (and both) if present... I'm sorry for coming this late to the thread... Martin SU> Cheers, Simon >> >>> Cheers, Simon On Nov 14, 2007 10:15 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 14/11/2007 8:53 PM, Gabor Grothendieck wrote: > Another possibility is to just place it at the end of the > vignette. > That is where it is in the proto package: >> > http://cran.r-project.org/doc/vignettes/proto/proto.pdf >> > Package documentation is already quite scattered and >> adding > a faq() command would add just one more thing one has > to do. Here are some places one might look already for > documentation: >> > package?mypackage > > Or just ?mypackage. Writing R Extensions recommends > package? mypackage, with ?mypackage also working if > that name isn't taken. However, the advice is ignored > more than it is followed. > > vignette(...) > library(help = mypackage) > ?mycommand > home page > WISHLIST file > NEWS file > THANKS file > svn log >> > I personally would give a much higher priority to a >> standardized > place to find change information. Some packages provide >> it. > Some don't which is very frustrating since you see a new >> version > and have no idea what has changed. If they do document it >> you > often have to download the source just to get at the >> change > information. > > Where do you put it? I put it in inst/ChangeLog, > which ends up installed in the package root as > ChangeLog. > > Whenever this has come up in the past, there have been > several proposals, but no consensus. So, to encourage > consensus, I've got a proposal: > > Why don't we vote on a location, with every voter > agreeing to follow the majority? The only condition > I'd put on it is that it should be something that gets > installed, hence somewhere in inst, but I'd be happy > to change the name if ChangeLog doesn't win. > > My vote is for inst/ChangeLog. > > Duncan Murdoch > > >> > > > On Nov 14, 2007 8:22 PM, roger koenker <[EMAIL PROTECTED] > > wrote: >> An extremely modest proposal: >> >> It would be nice if packages could have a FAQ and if >> >> faq(package.name) >> >> would produce this faq. And if, by default >> >> faq() >> FAQ() >> >> would produce the admirable R faq... Apologies in advance >> if there is already a mechanism like this, but help.search() >> didn't reveal anything. >> >> url:www.econ.uiuc.edu/~rogerRoger Koenker >> email [EMAIL PROTECTED] Department of >> Economics >> vox:217-333-4558University of >> Illinois >> fax:217-244-6678Champaign, IL >> 61820 >> >> __ >> 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 >>> >>> __ >>> 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] biocep project - R for the Web and the Virtual R Workbench
Dear all, I have been writing during last year at the European Bioinformatics Institute a general unified open source solution for R integration. This work is now available via this link: http://www.ebi.ac.uk/microarray-srv/frontendapp/ The different frameworks and tools of the biocep project are now robust enough for production use. The different APIs are finalized but the documentation is incomplete. the last version of the biocep README file can be found here : http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt Here are the major use cases I dealt with : - Generate java mappings for R Objects (Standard/S4). - Generate java mappings for selected packages' functions (Generic/TypeInfoed). - Use R and the R packages as a Java Toolkit via a Rich, High level, Object-Oriented API. - Deploy and use R as a remote component. - Expose automatically R packages and the R API as JAX-WS stateless or statefull Web Services. - Use R within a resource pooling infrastructure for scalable, web oriented, data analysis applications. - Use the Remote Resources Pooling framework (RPF) to deploy and use distributed computational resources (non R based, native libraries with JNI support or java code) - Use R for parallel computing via a Java API or Web Services. - Create and use Remote R Instances from within R (snow' like fucntions : makeCluster, clusterEvalQ, clusterExport, clusterApply, stopCluster ..) - Use the R API from within an applet (book, use and release a Remote R Instance via HTTP Tunneling) - Use R to generate Graphics on the fly for thin web clients - Use R from within a Workbench that includes an advanced script editor, a Spreadsheet View fully connected to R data and functions, an R Object Inspector, composable and dockable Views, interactive R devices, clonable R Graphics.. - Use the Workbench from within a browser or via Java Web Start to access a pool of Remote R Instances - Use the Workbench to control on demand any Remote R Instance - Provide a packaging for R Based Desktop applications that enables Web based, one click installation (Embedded R for Windows, detected R for other operating systems) This work uses extensively a large number of existing open source projects as is or patched. The public SVN url/login/pasword for the biocep project are in the README file You may want to try the Virtual R Workbench on your local machine, use the following link : http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp or type 'javaws http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp' from the command line. This is a one click installation process for Windows and Mac OS X. (You need to preinstall R on Mac OS X while on Widows an embedded R 2.6 can be deployed and used) The Java Web Start installer creates an RWorkbench directory in your home dir with all the files required. You may continue launching the application via the url (good for fetching updates automatically) or use the RWorkbench/VRWorkbench.txt to Run the application off line. rename it to VRWorkbench.bat on Windows or type 'source VRWorkbench.txt' on Mac OS X command line. use the sources of biocep to run the R Workbench on Unix-like operating systems. Best wishes, Karim __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
