Re: Technical papers was: Re: [Rd] documentation for 'open': some clarification?
I humbly suggest the Journal of Statistical Software (www.jstatsoft.org) which gives you peer-review, ISSN, directory of open access journals, Nelson Beebe's BibTeX repository, CODEN, and pretty soon CIS and official ASA status. -- Jan On Apr 14, 2005, at 13:42 , Detlef Steuer wrote: I for one want to support the idea of adding such technical papers to R-news. === Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] .mac: jdeleeuw ++ aim: deleeuwjan ++ skype: j_deleeuw homepages: http://gifi.stat.ucla.edu ++ http://www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 3.5 on Tiger
setenv CC gcc-3.5 setenv F77 gfortran setenv CXX g++-3.5 What I had to do. 1. Build a local zlib-1.2.1 2. Compile ppr.f in stats with g77-3.4 and not with gfortran-3.5 3. Change line 1581 in plot.c to double *aa = REAL(cex); if (R_FINITE(aa[i % ncex]) i.e. get the assignment out of the macro 4. Disable the DO_STR_DIM macro in plot.c (and thus the functions do_strheight and do_strwidth). This could be fixed by expanding the macros and pasting into the source. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R + OS X + gcc 3.5 = not quite there ..
I tried R-devel (07/31/04) with setenv CC gcc-3.5 setenv F77 gfortran setenv CXX g++-3.5 Here gfortran is g-95, version 3.5, from Gaurav's site. Configure goes fine, build goes fine, except for problems with macro-expansion in plot.c, similar to the one you mention in starma.c. After clobbering those, the compile is allright, the base package builds fine, and the binary runs. There is a problem with loading packages, however (see below). == [cabledoc70:Developer/R/R-devel] deleeuw% bin/R Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : internal error in decompress1 R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.0 Under development (unstable) (2004-07-30), ISBN 3-900051-00-3 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. library() Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : internal error in decompress1 == With R-patched (07/31/04) there are no problems with plot.c, but there is the problem with starma.c (I guess a cpp-3.5 bug). Even when fixing starma.c the package stats still refuses to build because of == gfortran -fno-common -g -O2 -c ppr.f -o ppr.o /var/tmp//ccSqEJAf.s:8241:FATAL:Symbol __BLOCK_DATA already defined. make[5]: *** [ppr.o] Error 1 make[4]: *** [all] Error 2 make[3]: *** [all] Error 1 make[2]: *** [R] Error 1 make[1]: *** [R] Error 1 make: *** [R] Error 1 and the bad restore file magic number errors are there as well. == [ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] OS X problem with DSTEIN in IGLS code
1. R-devel on OS X aborts when the code below is run after spitting out the message Loading required package: MASS Parameter 5 to routine DSTEIN was incorrect Mac OS BLAS parameter error in DSTEIN, parameter #0, (unavailable), is 0 2. I compiled R-patched using the included BLAS and Lapack, although Brian says this is impossible on OS X, because they are in FORTRAN (??). This version of R runs the code below just fine. 3. So there seems to be a difference between the implementation of DSTEIN in vecLib.framework and in other BLAS versions. The error message comes from vecLib. 4. To build libRlapack.dylib on OS X add the flags -flat_namespace -undefined suppress to the link. 5. I will post this version of R-1.9.1 (using the X11 version of Tcl/Tk 8.5 and the R version of BLAS and Lapack) on gifi. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] OS X problem with DSTEIN in IGLS code
[cabledoc110:~] deleeuw% gcc -v Reading specs from /usr/libexec/gcc/darwin/ppc/3.3/specs Thread model: posix gcc version 3.3 20030304 (Apple Computer, Inc. build 1660) [cabledoc110:~] deleeuw% g77 -v Reading specs from /usr/local/lib/gcc/powerpc-apple-darwin7.3.0/3.5.0/specs Configured with: ../gcc/configure --enable-threads=posix --enable-languages=f77 Thread model: posix gcc version 3.5.0 20040429 (experimental) I have tried xlf as well, but no success so far. On Jul 3, 2004, at 3:48, stefano iacus wrote: If I remember well, Jan is using g77 3.5(!) from KHanna page? I'm I right Jan? We have to solve this g77 issues on Mac OS X soon as many packages doesn't pass make check when they contain fortran code. I hope I can make some advance with xlf to see if I can manage to fix most of these. stefano On Jul 3, 2004, at 9:59 AM, Prof Brian Ripley wrote: On Sat, 3 Jul 2004, Jan de Leeuw wrote: 1. R-devel on OS X aborts when the code below is run after spitting out the message Loading required package: MASS Parameter 5 to routine DSTEIN was incorrect Mac OS BLAS parameter error in DSTEIN, parameter #0, (unavailable), is 0 2. I compiled R-patched using the included BLAS and Lapack, although Brian says this is impossible on OS X, because they are in FORTRAN (??). It depends on the compiler build. The version some (most?) people have of the gcc tools has a -lg2c that cannot be linked into a dylib. You seem to have one that does but no one else has reported success. Only a week ago someone reported being unable to build with the default configure settings on MacOS X for exactly this reason. This version of R runs the code below just fine. 3. So there seems to be a difference between the implementation of DSTEIN in vecLib.framework and in other BLAS versions. The error message comes from vecLib. Correction: DSTEIN is part of LAPACK, not BLAS In short, that is a MacOS error, for there is a reference implementation of LAPACK. It is compounded by an error in the error message. Have you reported it to `MacOS-bugs' yet? Please do so. 4. To build libRlapack.dylib on OS X add the flags -flat_namespace -undefined suppress to the link. That's not what works for other people. Why is is necessary for you? -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Packages of snippets? (was: A way to list only variables or functions?)
JSS does not have a code snippet section yet, but we have been in the process of trying to start one for a long time. We just haven't quite worked out how to define snippets. They need some documentation. I was thinking along the lines of the old JRSS-C or Applied Statistics code section. Publishing in JSS would have the advantage of a real journal publication, although a small one and easy access to the code on the jstatsoft site. Although we don't have the section yet, we do have some editors willing to handle it. So one possible strategy would be not to wait for precise instructions for authors, keep the JRSS-C model in mind, and just submit. JSS is working on TeX templates for articles, book reviews, software reviews, and code snippets. On Jun 23, 2004, at 18:31, Duncan Murdoch wrote: [Moved from r-help to r-devel] On Thu, 24 Jun 2004 09:29:12 +1200, Patrick Connolly [EMAIL PROTECTED] wrote: I made myself a function in the S-PLUS days which I've modified to work in R. It involved adding another few functions to add dates to objects. This isn't something I'd use, since I prefer to keep objects in source form, but I bet there are quite a few people who would use it if it were generally available. I've toyed with the idea of adding an object size column but it's not important enough for my use. Since I revisit projects over a period of years at times, the date is very useful information -- in fact, it's the main reason why I wrote it. My code is not elegant enough for an esteemed place on CRAN. I could make it a lot better myself if I spent the time on it, but it works well enough for me as it is, so in that sense, it ain't broke. However, if anyone is interested in having such functionality my code could be a good starting point. Inelegance is no excuse! However, I do understand the feeling of writing a nice little function, and not knowing exactly what to do with it: CRAN is crowded, and it does seem that an entire package just to support one or two simple functions is a bit of overkill. Can we work out a way to publish such things? Here's a proposal, with some serious flaws listed below. Can someone fix them? - It should be easy to publish a short article describing your nice little function, and making the code available to others. (I think this is already in place, either by publishing in RNews or Journal of Statistical Software, as a code snippet.) - It should be easy for users to get it, together with man pages, etc. This is not in place, unless you package your function and send it to CRAN. What I'd propose is that a volunteer should act as an editor of an RNews or JSS package, that contains *all* of the snippets that have been published in RNews or JSS. Some major flaws in this proposal are: - It needs a volunteer editor. - The editor would have to be organized, and willing to bug authors for updates whenever R changes and breaks their snippet (or makes it obsolete). If there's no one willing to do this, the editor should feel free to drop the snippet from the package. - There'd have to be a way for someone to see which snippets don't have maintainers so have been dropped, but could be resurrected. - If it's successful, there'll be name clashes. The editor should try to head these off from the start, by setting some rules for what kinds of names should be used for internal functions, and what public names should look like. - There aren't actually that many snippets being published, because it's hard work to convert something that works well enough for me to something we'd like others to see. Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Re: [R] Html help does not work in Mac OSX 10.3.4 (PR#7000)
sudo rm /usr/local/lib/libxml2.2.dylib and try again On Jun 21, 2004, at 17:35, [EMAIL PROTECTED] wrote: /usr/local/lib/libxml2.2.dylib === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] GUI from Terminal.app
If you start R from the terminal and then do non-X11 graphics, you get SetFrontProcess errors. For instance, I have a version of R configured without x11 and with the Aqua version of tcl/tk. If I start this, load tcltk, and do tkStartGUI() I cannot bring the window to the front, because clicking it gives SetFrontProcess errors. There is, however, a simple way to fix this. Make a copy of R.bin, call it RGUI, then say /Developer/Tools/Rez -t APPL Carbon.r -o RGUI and change the name of the R binary in the R startup script from R.bin to RGUI. Then this R will give a tkStartGUI window that you can interact with. The same is true for the tk demos, which now have nice aqua windows you can interact with. Also, starting quartz() and interacting with the quartz device works fine, and demos such as tkdensity now display two nicely interacting aqua windows. Also, you get a working version of Rcmdr in this way. Thus you have a version of RAqua which does not use the RAqua GUI but only the terminal. And we have a seemingly reliable way to use Aqua tcl/tk (and get rid of all of X11). It does not cost anything to add the Rez command above to the Makefile, and the benefits are huge. There does not seem to be a need to warn if quartz() is started from the terminal. Remains the fact that I have been looking for this solution for two years and it turns out to be this simple. Must be pretty well hidden. Observe the Rez command gives RGUI a resource fork and metafile info, also observe this would not work with Cocoa. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] Re: [R-SIG-Mac] GUI from Terminal.app
I was slightly too optimistic. If RGUI is started then .Device is the null device. If you say quartz() then you cannot interact with the graphics window (probably related to the quartz device warning). If you now say library(tcltk) the device is set to quartz and the window comes alive. If the first thing you say is library(tcltk), then the device is automatically set to quartz, and subsequent calls to quartz() are fine. On Feb 21, 2004, at 14:16, Jan de Leeuw wrote: If you start R from the terminal and then do non-X11 graphics, you get SetFrontProcess errors. For instance, I have a version of R configured without x11 and with the Aqua version of tcl/tk. If I start this, load tcltk, and do tkStartGUI() I cannot bring the window to the front, because clicking it gives SetFrontProcess errors. There is, however, a simple way to fix this. Make a copy of R.bin, call it RGUI, then say /Developer/Tools/Rez -t APPL Carbon.r -o RGUI and change the name of the R binary in the R startup script from R.bin to RGUI. Then this R will give a tkStartGUI window that you can interact with. The same is true for the tk demos, which now have nice aqua windows you can interact with. Also, starting quartz() and interacting with the quartz device works fine, and demos such as tkdensity now display two nicely interacting aqua windows. Also, you get a working version of Rcmdr in this way. Thus you have a version of RAqua which does not use the RAqua GUI but only the terminal. And we have a seemingly reliable way to use Aqua tcl/tk (and get rid of all of X11). It does not cost anything to add the Rez command above to the Makefile, and the benefits are huge. There does not seem to be a need to warn if quartz() is started from the terminal. Remains the fact that I have been looking for this solution for two years and it turns out to be this simple. Must be pretty well hidden. Observe the Rez command gives RGUI a resource fork and metafile info, also observe this would not work with Cocoa. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu --- -- No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au ___ R-SIG-Mac mailing list [EMAIL PROTECTED] https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] R with graphics from command line
I have made a regular R install, so that /Library/Frameworks/R.frameworks/Resources/bin/R.bin is now a Carbon APPL, using Rez in the way described before. We now have basically two R's -- one from Terminal.app and one from R.app. The first one works fine, except for the small glitch of not starting the default device properly. The second one does not work properly with Aqua Tcl/Tk, while the first one does. Both work with the quartz device. Also the first R works fine from the Carbon Emacs using ESS (while the standard build cannot use the quartz device from Emacs). This means that people who (a) prefer to run their R from the Terminal or from Emacs, and (b) who prefer Aqua to X11, should use the first R. Since I am one of these people, the next release of R on gifi will have no X11 and no R.app. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Macintosh (PR#6593)
http://www.economia.unimi.it/R/ On Feb 16, 2004, at 21:10, [EMAIL PROTECTED] wrote: Full_Name: David Steinsaltz Version: 1.8.1 OS: Mac 10.3.2 Submission from: (NULL) (216.175.92.195) A new installation of R on a new computer running OS 10.3.2 simply wouldn't start. When I tried to start it from the command line, I got the message dyld: /Applications/StartR.app/RAqua.app/Contents/MacOS/RAqua can't open library: /usr/local/lib/libreadline.4.3.dylib (No such file or directory, errno = 2) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Re: building R-devel on Panther
This is no problem. R does not use the Apple provided zlib, but the dynamic linker looks there first. The second warning would probably go away if you recompiled readline in /usr/local (because Apple did not provide ncurses until Panther). Anyway, there are no conflicts. On Feb 14, 2004, at 10:52, Roger Koenker wrote: ld: warning multiple definitions of symbol _zlibVersion /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion ../../../bin/libR.dylib(zutil.o) definition of _zlibVersion ld: warning multiple definitions of symbol _BC /usr/local/lib/libreadline.4.3.dylib(terminal.so) definition of _BC /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Developmental version of Matrix package for R-1.9.0
Builds OK on OS X, except for 1. The static archives foo.a are not ranlibbed, so you have to do that manually. 2. Cannot build Matrix.so because it uses flat namespaces and has multiple definitions of some symbols. I solved 2 by the usual hack, which is to add the -Xlinker -m flag to the link by the gcc driver, but the preferred solutions would be to use external in the code. Or, even better, to switch the Darwin build to two-level namespaces. On Jan 29, 2004, at 14:35, Douglas Bates wrote: I recently uploaded a developmental version of the Matrix package, Matrix_0.6-1.tar.gz, to CRAN where it is in the src/contrib/1.9.0/Other directory. It requires some of the packages that will appear in R-1.9.0. This version marks a major redesign of the Matrix package to use S4 classes and methods and to incorporate sparse matrix manipulations using routines from TAUCS (http://www.tau.ac.il/~stoledo/taucs/), Metis (http://www-users.cs.umn.edu/~karypis/metis/) and UMFPACK (http://www.cise.ufl.edu/research/sparse/umfpack). Although this package is very much a work in progress and the documentation is, shall we say, sketchy, there are two vignettes included with the package. One of these illustrates the performance of different ways of performing least squares calculations, using an example from Koenker and Ng's SparseM package. The results are, I think, impressive. Although not documented in this release, there are the beginnings of routines to represent large, sparse, pairwise crosstabulations as sparse matrices. I am using these in calculations for mixed-effects models and I understand that others may be interested in them for other applications. I would be happy to correspond off-list if you would like a preview of the capabilities. Metis is a package for partioning unstructured graphs, partitioning meshes, and computing fill-reducing orderings of sparse matrices. Although the entire source code for Metis is included in the Matrix package I am only using one of the functions for computing fill-reducing orderings. Perhaps those who are working on graphical models may want to look at some of the other capabilities of Metis. Certainly it provides standard ways of representing and manipulating unstructured graphs. I've only compiled and tested the package on Linux_x86 environments. I will be interested in whether Uwe is successful in building it for Windows and whether there are problems on 64-bit machines. -- Douglas Bates[EMAIL PROTECTED] Statistics Department608/262-2598 University of Wisconsin - Madison http://www.stat.wisc.edu/~bates/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help.start
I have a /usr/local/bin/netscape script with #!/bin/sh open /usr/local/lib/R/doc/html/index.html which means help.start() starts Safari. On Nov 11, 2003, at 13:17, Stefano Iacus wrote: Some user reported me that help.start() is no longer working on Panther under RAqua. I don't have this problem on my machine but a couple of users repoterd me this. Can you please make this small test an eventually tell me which is your system default browser? stefano __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] RAqua with X11 TclTk
That's a somewhat unfortunate step back, and a rather drastic hack to get around the eventloop problem. I make two versions of the tcltk package, one in RAqua, one in /usr/local/lib/R/library (the X11 version). I then make softlinks from all packages in /usr/local/lib/R/library to ~/Library/RAqua/library and then remove the softlinks to the packages that are already in RAqua (including tcltk). Now the Emacs and terminal versions use the X11 version and RAqua uses the Aqua version of tcltk. http://gifi.stat.ucla.edu/pub gives the deatils, including the ~/.emacs one needs. I have no build problems in Panther, except the problem with g77-3.4 when compiling tseries. Go back to g77-3.3 for this and you're fine. Panther fixes the pty bug in Darwin, and thus R now functions fine in Carbon, command line, and X11 Emacs using X11 graphics. See http://members.shaw.ca/akochoi-emacs/index.html On Nov 8, 2003, at 8:19, Stefano Iacus wrote: I've built a version of RAqua that uses X11 TclTk and NOT AquaTclTk. http://www.economia.unimi.it/R/RAquaX11.dmg (15 MB disk image) The idea is that you: launch RAqua, launch X application (the X Server), and from inside R type x11() # just tt set DISPLAY to :0.0. Eventually close this window device, we don't need this. load(tcltk) quartz() demo(tkdensity) It works on my Panther machine as well and it comes with three installers for: libreadline, tcltk (the X11 version) and the libxml2 in case you want to use the prebuilt XML package. Thomas Lumley has found oddities in configuring/building R on Panther so I built it on Jaguar and it works as well on panther. I would like to propose this version of RAqua for R-1.8.1, i.e. built only against X11/tcltk. This will allow one binary only for R that can run tcltk from Emacs or phyton for example. Could you please test it on Jaguar and Panther before the end of the next week? I've built this version with the following config ./configure --enable-R-shlib --with-blas='-framework vecLib' --with-lapack --with-aqua Of course, I have built from sources tck and tk 8.4.4. If you want to do this take care to configure and build the tcl/tk sources from inside the unix directory. stefano __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] what works and what not
r-devel, os x 10.3.1, tcl/tk 8.5 (unix and aqua), gifi setup === plot(1:10) library(tcltk) demo(tkdensity) works from Terminal, XTerm, and using ESS in Carbon Emacs, X11 Emacs, XTerm Emacs, Terminal Emacs, using X11 graphics throughout. === x11() plot(1:10) works from RAqua using X11. === library(tcltk) demo(tkdensity) in RAqua starts things, messes up the menus, and clobbers most of the mouse interaction. Not usable. === library(tcltk) tkStartGUI() demo(tkdensity) in tkStartGUI works OK in RAqua. Hack ! === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help.search in trouble with R-patched ?
This works fine in R-patched in Darwin. On Oct 14, 2003, at 23:02, Laurent Gautier wrote: help.search(prompt, agrep=F) === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] xlc/xlf on osx
I can now build most of R with XLC/XLF using optimization level O4 on OS X. I twice have to intervene and manually set optimization to O3 (for trees.c in zlib and util.c in main). But, more importantly, I cannot use the xlc/xlf compiler drivers for linking. They do not understand some of the gcc flags, which is no problem because they then pass them to ld, but more importantly they refuse to handle any file with name foo.lo. Is the lo a configure switch I can set to o ? Currently I am building everything by setting LD_MAIN and LD_SHLIB to gcc, i.e. xlc/xlf does the actual compilations and gcc drives the linking. This is not ideal, because it may include the wrong options and libraries, and it eventually breaks the methods package (which refuses to dump code after it compiles). Other things which I see is that the -framework Carbon flag gets lost when linking R.bin, and that I can only link libLapack.dylib by adding -flat_namespace -undefined suppress to the linker flags. These are somewhat mysterious. I am attaching config.site. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] IBM compilers on OS X
Although I still have to look into the various flags, the IBM vacpp (C and C++) and xlf (FORTRAN) compilers can be used to build at least R.bin. Of course libR.dylib and the various bundles are more complicated, but R.bin runs (in as far as it does not depend on any modules and packages). This is important, because people report speed increases of 100-200% compared to gcc/g77. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] building XML-0.95-1 on MacOS
This builds fine on Panther, using the libxml2 provided by Apple in /usr/lib. On Oct 9, 2003, at 9:02, Duncan Temple Lang wrote: Stefano asked me to post something along the following lines about the XML package. I have modified the configuration for the XML package so that it looks for libxml2 if instructed, or alternatively looks for libxml 1 and, if that is not present, then libxml 2. The new version: XML_0.95-4.tar.gz is on the Omegahat Web site: http://www.omegahat.org/RSXML So one should not have to set any environment variables or specify configuration arguments if you only have libxml2 on your machine. If you have both libxml and libxml2, you will get libxml 1 by default. Use --configure-args='--with-libxml2' or set the environment variable XML_CONFIG to xml2-config. At some point in the future, we will stop supporting old versions of libxml with no xml-config script, header files in odd places, ... This is what makes the configuration so complex. D. Duncan Temple Lang wrote: Hi Sean. Two things. There is a new version of the XML package now on the Omegahat web site: http://www.omegahat.org/RSXML/XML_0.95-3.tar.gz That uses a different approach to dealing with errors and avoids having to redefine the xmlParserError() routine. As a result, one should not need the -m flag. Secondly, unless there are good reasons for using libxml-1.8.*, it is preferrable to use the libxml2-2* series. The configuration for this version of the XML package has been upgraded, but may require some assistance. If it doesn't compile out of the box, please set the environment variable XML_CONFIG to the name of the xml-config or xml2-config script that provides the relevant information. I'll fix this up in the next release. D. Sean Davis wrote: I am trying to build the XML package on MacOS. I am using the fink installation of libxml-1.8.17. The configuration information is: Configuration information: Libxml settings libxml include directory: /sw/include/gnome-xml libxml library directory: -L/sw/lib -lxml -lz -lz -lxml libxml 2: no Compilation flags: -I/sw/include/gnome-xml -I/sw/include/gnome-xml/libxml -DLIBXML -I/sw/include/gnome-xml Link flags: -L/sw/lib -lxml -lz -lz -lxml Compiling produced the following error: gcc -bundle -flat_namespace -undefined suppress -L/sw/lib -L/usr/local/lib -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o RSDTD.o RUtils.o Utils.o XMLEventParse.o XMLTree.o -L/sw/lib -lxml -lz -lz -lxml -lcc_dynamic ld: multiple definitions of symbol _xmlParserError Utils.o definition of _xmlParserError in section (__TEXT,__text) /sw/lib/libxml.dylib(error.lo) definition of _xmlParserError make: *** [XML.so] Error 1 ERROR: compilation failed for package 'XML' I saw that back in September there was a discussion about fixing this problem that involved passing -m to the linker. My questions are (1) what do I need to modify (given that I am using R INSTALL to keep things simple for myself) to use the -Xlinker -m option when linking XML.so and (2) does this actually work despite the fact that there are then two definitions associated with the same symbol? I guess a third question follows from the second--are there other fixes that I can use to build the package? Thanks in advance, Sean __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel -- ___ Duncan Temple Lang[EMAIL PROTECTED] Bell Labs, Lucent Technologiesoffice: (908)582-3217 700 Mountain Avenue, Room 2C-259 fax:(908)582-3340 Murray Hill, NJ 07974-2070 http://cm.bell-labs.com/stat/duncan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel -- ___ Duncan Temple Lang[EMAIL PROTECTED] Bell Labs, Lucent Technologiesoffice: (908)582-3217 700 Mountain Avenue, Room 2C-259 fax:(908)582-3340 Murray Hill, NJ 07974-2070 http://cm.bell-labs.com/stat/duncan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https
Re: [Rd] tseries
If I compile dsumsl.f with the IBM xlf compiler then tseries builds and installs -- of course tseries.so does not load properly, because the rest of R is build with g77, but it suggests the problem is with g77. On Oct 3, 2003, at 8:02 , Stefano Iacus wrote: Has anyone successfully check/build tseries for MacOSX? It seems like there is the same problem with symbols duplications. The -m like option does not seem to help. stefano __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] darwin build with latest gcc from apple
This is on Panther B53 cabledoc92:Developer/R/R-devel] deleeuw% gcc -v Reading specs from /usr/libexec/gcc/darwin/ppc/3.3/specs Thread model: posix gcc version 3.3 20030304 (Apple Computer, Inc. build 1492) [cabledoc92:Developer/R/R-devel] deleeuw% g77 -v Reading specs from /usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/specs Configured with: '../gcc/configure' '--enable-threads=posix '--enable-languages=c,f77 Thread model: posix gcc version 3.4 20030828 (experimental) [cabledoc92:Developer/R/R-devel] deleeuw% uname -a Darwin cabledoc92.frazmtn.com 7.0.0 Darwin Kernel Version 7.0.0: Tue Aug 26 12:45:49 PDT 2003; root:xnu/xnu-493.obj~1/RELEASE_PPC Power Macintosh powerpc It seems I can get rid of FPICFLAGS -fno-common and CPPFLAGS -D__DEBUGGING__ If you do not use -lcc_dynamic as LDFLAGS it cannot find restFP and saveFP. /usr/lib/libcc_dynamic.a is a soft link to /usr/lib/gcc/darwin/3.3/libgcc.a which does contain these symbols. By the way, the symbols are not in /usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/libgcc.a Also, configure tests if saveFP is in libcc_dynamic.a, and says it isn't. On Sep 4, 2003, at 14:38 , Stefano Iacus wrote: we are trying to adapt the configure in order to work with latest gcc3.3 (from apple) and g77 3.4 (from http://gravity.psu.edu/~khanna/hpc.html ) At the moment there is no need to define the __DEBUGGING__ but there is still a problem with the -lcc_dynamic does any of you know how to check for this library and explain why we see -lcc_dynamic often passed as an ld flag. Where to find doc on this? stefano __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] R-devel on Panther
Both the command line version and the Aqua version build/install fine on Panther B44. Make checkruns fine as well. The configure flags are configure --enable-R-shlib --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh --with-blas='-framework vecLib' --with-lapack --with-aqua In the environment I have FPICFLAGS=-fno-common LDFLAGS=-lcc_dynamic CPPFLAGS=-D__DEBUGGING__ TCLTK_LIBS=-framework Tcl -framework Tk TCLTK_CPPFLAGS=-I/Library/Frameworks/Tcl.framework/Versions/Current/ Headers -I/Library/Frameworks/Tk.framework/Versions/Current/Headers I know that the two TCLTK variables (strangely enough), the DEBUGGING variable and the FPICFLAGS are necessary. I am using the g77-3.3 from fink -- not the one from Gaurav Khanna, the fink one comes with a patched assembler. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] (no subject)
RAqua now builds fine, but for some reason tcl/tk support cannot be compiled in. I get checking for /Library/Frameworks/Tcl.framework/tclConfig.sh... /Library/Frameworks/Tcl.framework/tclConfig.sh checking for /Library/Frameworks/Tk.framework/tkConfig.sh... /Library/Frameworks/Tk.framework/tkConfig.sh checking whether compiling/linking Tcl/Tk code works... no This is with configure --enable-R-shlib --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh --with-blas='-framework vecLib' --with-lapack --with-aqua and with in the environment FPICFLAGS=-fno-common LDFLAGS=-lcc_dynamic CPPFLAGS=-D__DEBUGGING__ TCLTK_LIBS=/Library/Frameworks/Tcl.framework/Versions/Current /Library/Frameworks/Tk.framework/Versions/Current TCLTK_CPPFLAGS=/Library/Frameworks/Tcl.framework/Versions/Current/ Headers /Library/Frameworks/Tk.framework/Versions/Current/Headers === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] R-devel problem
With the current version from rsync (8/16, 19:00) I get make[3]: *** No rule to make target `helpsearch.c', needed by `Makefile'. Stop. make[2]: *** [R] Error 1 make[1]: *** [R] Error 1 make: *** [R] Error 1 === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] RAqua
Some additional suggestions: If you install/update packages, the output can be viewed in the Console application. Is that really the place where we want it ? update.packages() without argument can be used from the RAqua console, but maybe the GUI should have an update.all button Quit from the menu requires you to respond to a question in the RAqua console. It would be more intuitive if Quit from the menu brought up a dialog window asking if you wanted to save the workspace. More inserted below, On Wednesday, August 13, 2003, at 7:24 AM, Thomas Lumley wrote: On Wed, 13 Aug 2003, Stefano Iacus wrote: 4. Input and output windows cannot be resized independently. I would still vote for two separate input and output windows. And I'd vote for a single combined window :) Compromise is my middle name: how about a resize bar in the middle of the single window, for relative resizing. 6. If you want to download from CRAN you select packages in a window, and the download starts if you close the window. it starts only if you check the item install, otherwise the R session continues giving you a prompt. That's not intuitive, there should be a separate download or go button. I don't find it intuitive, either, but isn't it fairly standard under Aqua/OSX that dialogs are `live' and changes happen without a separate confirmation button (eg in System Preferences)? If you change settings in Network, for instance, there is an Apply Now button. 7. I thought I saw somewhere that RAqua can now open X11 devices. Mine can't. you should start QuartzX and use x11(display=:0) You don't even need x11(display=:0), but you do need to start an X server. RAqua doesn't start an X server and I don't think it should. I agree (of course) it shouldn't start an X server. But I may have an older version of RAqua, because mine still says X11 module is not available under this GUI X display windows are still not resizable, which is a similar event-handling issue to the Tk one. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Re: [R-SIG-Mac] R version on gifi
Well, what happens if you say library(tcltk) and demo(tkdensity) in the R running in Xterm ? On Tuesday, Jun 17, 2003, at 11:25 US/Pacific, Stefano Iacus wrote: To be more explicit: the RAqua I have built it is built to run under X11 as well, just execute it in an xterm window without specifying --gui-aqua. Nothing has changed! === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] R version on gifi
Pretty soon, hopefully, the RAqua version will make the Darwin/X11 version unnecessary. In the meantime, for convergence, I'll modify the Gifi version in various ways. -- It's 1.7.1 -- It no longer supports gnome -- It still uses Tcl/Tk for X11 (using 8.5 from CVS) !! It no longer uses anything from fink (readline and dlcompat as on Stefano's site, jpeg and png and teTeX from Gerben Wierda's i-installer, Tcl/Tk from cvs, X11 from Apple) -- the package installer will put everything in /usr/local This means that all references to /sw in configure.ac can go. This next distribution will appear probably on wednesday. Undoubtedly some packages will break, because they still use stuff from /sw, but I'll fix those as we go along. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] cvs version of r-devel on darwin
No, but if you do not have dlcompat in /usr/local/lib, you also get link errors because it cannot find dlopen and friends. So one need a dlcompat somewhere where the linker can find it. Not finding environ must be due to some very recent change in the R code, it seems. On Sunday, Jun 15, 2003, at 08:47 US/Pacific, Stefano Iacus wrote: On Domenica, giu 15, 2003, at 02:39 Europe/Rome, Jan de Leeuw wrote: Does not use -L/sw/lib -dl anymore, so only works for those who have libdl in /usr/local/lib Cannot find _environ in linking libR.dylib (not sure where it normally gets it). Does not seem to need it in linking R.bin. I do not have /sw on my machine and I was able to build R till yesterday. So it should not be a problem related to fink. But today I get the same error of you ld: Undefined symbols: _environ /usr/bin/libtool: internal link edit command failed make[3]: *** [libR.dylib] Error 1 make[2]: *** [R] Error 2 make[1]: *** [R] Error 1 make: *** [R] Error 1 === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu -- --- No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] cvs version of r-devel on darwin
R-devel builds again from CVS if LDFLAGS is '-L/sw -lccc_dynamic'. I can't build RAqua.app, though. -- Jan On Sunday, Jun 15, 2003, at 15:20 US/Pacific, Stefano Iacus wrote: Yes, __APPLE_CC__ is for Darwin indeed. stefano On Domenica, giu 15, 2003, at 18:50 Europe/Rome, Luke Tierney wrote: On Sun, 15 Jun 2003, Jan de Leeuw wrote: No, but if you do not have dlcompat in /usr/local/lib, you also get link errors because it cannot find dlopen and friends. So one need a dlcompat somewhere where the linker can find it. Not finding environ must be due to some very recent change in the R code, it seems. Yes--a bit of overzealous code cleaning by someone who thought code conditionalized for __APPLE__ was for classic MacOS. Should be OK again in cvs. luke On Sunday, Jun 15, 2003, at 08:47 US/Pacific, Stefano Iacus wrote: On Domenica, giu 15, 2003, at 02:39 Europe/Rome, Jan de Leeuw wrote: Does not use -L/sw/lib -dl anymore, so only works for those who have libdl in /usr/local/lib Cannot find _environ in linking libR.dylib (not sure where it normally gets it). Does not seem to need it in linking R.bin. I do not have /sw on my machine and I was able to build R till yesterday. So it should not be a problem related to fink. But today I get the same error of you ld: Undefined symbols: _environ /usr/bin/libtool: internal link edit command failed make[3]: *** [libR.dylib] Error 1 make[2]: *** [R] Error 2 make[1]: *** [R] Error 1 make: *** [R] Error 1 === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu --- --- --- No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - --- - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] Re: [R-SIG-Mac] Darwin-Aqua R-devel
I made a script RAqua with #!/bin/sh exec /Applications/RAqua.app/Contents/MacOS/RAqua $@ and put it in /usr/local/bin. Now RAqua starts up the Aqua GUI, as expected, but library(tcltk) says there is no tcl/tk support (and I do have the frameworks). Also the menubar is blocked, and output from help() and library() is written to the Terminal window. But I guess you already new all this. Very exciting. In previous builds I used, by the way, configure --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh --enable-R-shlib --without-x --with-aqua --with-blas='-framework vecLib' --with-lapack TCLTK_LIBS='-framework Tcl -framework Tk' TCLTK_CPPFLAGS='-I/Library/Frameworks/Tcl.Framework/Headers -I/Library/Frameworks/Tk.Framework/Headers' to make absolutely sure that AquaTcl/Tk was used. On Thursday, Jun 12, 2003, at 18:29 US/Pacific, Stefano Iacus wrote: I've been able to build a very primitive Aqua GUI for Darwin R. This version as minimum event handler support but at least you can drag around the quartz device. You need to download the RAqua.app.sit archive from http://www.economia.unimi.it/R/ You need to unstuff it and put inside your system Applications folder (i.e. /Applications) If you click on the RAqua icon nothing will happen (in reality something happens if you have a look at the Console log window). To run this version of R you should type the following from a term window /Applications/RAqua.app/Contents/MacOS/RAqua If you want to build this version of R you should download tomorrow R-devel tgz as I have just committed the files via CVS. This version has been configured with ./configure --enable-R-shlib --with-blas='-framework vecLib' --with-lapack --with-aqua if you have aquatcl/tk it should work fine. I'll try it tomorrow as it is too late now :) stefano ___ R-SIG-Mac mailing list [EMAIL PROTECTED] https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] g77-3.3 on darwin
I would wait to see what Apple comes up with in the next installment of Developer Tools. --- J. On Sunday, Jun 1, 2003, at 03:07 US/Pacific, Kurt Hornik wrote: Jan de Leeuw writes: The new g77 in fink/unstable is 3.3. It fails to build R, unless I setenv LDFLAGS to -lcc_dynamic. Is this a temporary bug or something we should try to work around in the configure code? Best -k === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] all.rda again
After a clean download of R-devel, I do not get the same error anymore involving dataClass when dumping, but I do get dumping R code in package 'methods' initializing class and method definitions now ...make[1]: *** [../../../library/methods/R/all.rda] Error 139 make: *** [all] Error 2 If I move to src/library/methods and do setenv R_DEFAULT_PACKAGES NULL ../../../bin/R --vanilla --slave all.R I get initializing class and method definitions now ...Segmentation fault and the console tells me Thread 0 Crashed: #0 0x0185095c in Rf_install (names.c:1024) #1 0x01827d64 in R_execMethod (eval.c:721) #2 0x013d6c38 in R_standardGeneric (methods_list_dispatch.c:630) #3 0x00082d60 in do_standardGeneric (objects.c:1013) #4 0x00057188 in Rf_eval (eval.c:441) #5 0x00058f40 in do_set (eval.c:1281) #6 0x00056fcc in Rf_eval (eval.c:418) #7 0x00058810 in do_begin (eval.c:1055) #8 0x00056fcc in Rf_eval (eval.c:418) #9 0x00057614 in Rf_applyClosure (eval.c:609) #10 0x00057200 in Rf_eval (eval.c:453) #11 0x00058810 in do_begin (eval.c:1055) #12 0x00056fcc in Rf_eval (eval.c:418) #13 0x00057614 in Rf_applyClosure (eval.c:609) #14 0x00057200 in Rf_eval (eval.c:453) #15 0x00058810 in do_begin (eval.c:1055) #16 0x00056fcc in Rf_eval (eval.c:418) #17 0x00057614 in Rf_applyClosure (eval.c:609) #18 0x00057200 in Rf_eval (eval.c:453) #19 0x00058bcc in applydefine (eval.c:1178) #20 0x00056fcc in Rf_eval (eval.c:418) #21 0x00058810 in do_begin (eval.c:1055) #22 0x00056fcc in Rf_eval (eval.c:418) #23 0x0005832c in do_for (eval.c:950) #24 0x00056fcc in Rf_eval (eval.c:418) #25 0x00058810 in do_begin (eval.c:1055) #26 0x00056fcc in Rf_eval (eval.c:418) #27 0x00057614 in Rf_applyClosure (eval.c:609) #28 0x00057200 in Rf_eval (eval.c:453) #29 0x00058f40 in do_set (eval.c:1281) #30 0x00056fcc in Rf_eval (eval.c:418) #31 0x00058810 in do_begin (eval.c:1055) #32 0x00056fcc in Rf_eval (eval.c:418) #33 0x00056fcc in Rf_eval (eval.c:418) #34 0x00058810 in do_begin (eval.c:1055) #35 0x00056fcc in Rf_eval (eval.c:418) #36 0x00057614 in Rf_applyClosure (eval.c:609) #37 0x00057200 in Rf_eval (eval.c:453) #38 0x00058810 in do_begin (eval.c:1055) #39 0x00056fcc in Rf_eval (eval.c:418) #40 0x00057614 in Rf_applyClosure (eval.c:609) #41 0x00057200 in Rf_eval (eval.c:453) #42 0x00058810 in do_begin (eval.c:1055) #43 0x00056fcc in Rf_eval (eval.c:418) #44 0x00057614 in Rf_applyClosure (eval.c:609) #45 0x00057200 in Rf_eval (eval.c:453) #46 0x00058810 in do_begin (eval.c:1055) #47 0x00056fcc in Rf_eval (eval.c:418) #48 0x00056fcc in Rf_eval (eval.c:418) #49 0x00058810 in do_begin (eval.c:1055) #50 0x00056fcc in Rf_eval (eval.c:418) #51 0x00057614 in Rf_applyClosure (eval.c:609) #52 0x00057200 in Rf_eval (eval.c:453) #53 0x00072cfc in Rf_ReplIteration (main.c:237) #54 0x00072e5c in R_ReplConsole (main.c:285) #55 0x00073828 in run_Rmainloop (main.c:616) #56 0x000dc520 in main (system.c:102) #57 0x1a40 in _start (crt.c:267) #58 0x18c0 in start === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au -__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] R-devel uses flat namespaces again
And compiles, and passes make check. I will continue to experiment with two-level namespaces (and perhaps with weak linking) but in a private copy only. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] flat namespaces
The build works fine if I use -flat_namespace -undefined suppress for shlib_ldflags (which means R.bin and libR.dylib are still build with two-level namespaces, but all the module and library foo.so files have flat namespaces). This should probably be the way to do it, and I'll try to find out what goes on in a separate version of R-devel. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel problems
Number 3 below is fixed. Number 5 is a bootstrap problem, which
could be solved perhaps with
make bin; make install bin; make install modules packages
or by doing a real two stage build. But I agree that is a major
change in the build process.
This can also be hacked by doing a make install, wait until it breaks,
then do another make install. I am not suggesting this as an actual
solution.
It's not a problem if you have a version of R installed, at least not
if that R.bin has all the required symbols (but I think the R.bin from
1.6.2 misses one symbol needed by the 1.7.0 version of ctest,
for example). Again this does not provide a solution.
I'll see if the bundle_loader solution can be changed in any
way (for instance by using weak binding, so that the symbol
does not have to be there at link time, only at run time).
On Tuesday, Feb 25, 2003, at 23:57 US/Pacific, Kurt Hornik wrote:
Jan de Leeuw writes:
The OS X configure in R-devel has been changed to use two-level
namespaces. There are still some problems.
3. Configure does not pass the $(Rexecbindir) to the Makefiles in the
/src/library directory, so the links cannot find the bundle_loader. I
added them by hand for all package links.
I thought I had already fixed this, but maybe I am missing something
obvious. It seems to me that e.g. ctest/src/Makefile has
R_HOME = $(top_builddir)
...
include $(top_srcdir)/share/make/shlib.mk
where the latter has
include $(R_HOME)/etc/Makeconf
which in turn has
## As we currently use
## -bundle -bundle_loader $(Rexecbindir)/R.bin -undefined error
## for the default SHLIB_LDFLAGS on Darwin = 5 ...
rhome = @libdir@/R
Rexecbindir = $(rhome)/bin
(in the source). But I now see that on my system this gives
rhome = ${exec_prefix}/lib/R
for reasons maybe known to Autoconf wizards but not to me: so I will
add
substitutions for prefix and exec_prefix as well. Pls let me know if
this helps.
5. In order to link the bundles with -bundle -bundle_loader
/usr/local/lib/R/bin/R.bin the /usr/local/lib/R/bin/R.bin must exist,
and moreover must be an R-devel build. This is a little bootstrap
problem which can be easily hacked.
As I already tried to explain, I think there is a more substantial
problem here. We build in say, BUILDDIR and install to INSTALLDIR,
say,
and there no reason to assume for something to work in BUILDDIR that
something else has happened in INSTALLDIR. In fact, for typical users
we cannot even do something in the default INSTALLDIR as they will have
no write permissions in /usr/local.
The only thing guaranteed to work is to use a bundle loader path in
BUILDDIR when building, and change to one in INSTALLDIR when
installing. I assume this amounts to re-linking and hence a terrible
mess unless we use GNU libtool to provide an abstraction, and I hope we
will have this for R 2.0, but certainly not for 1.7. Or is there a way
to change the bundle loader?
Best
-k
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===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED]
homepage: http://gifi.stat.ucla.edu
-
No matter where you go, there you are. --- Buckaroo Banzai
http://gifi.stat.ucla.edu/sounds/nomatter.au
-
__
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[Rd] nice combo on os x
You need (a) a recent OS X framework build of python, which also installs IDLE (b) a recent OS X framework build of AquaTk (i.e. native Tcl/Tk) (c) a version of R compiled with AquaTk and without X11 (d) a recent version of Rpy Now you can open IDLE and say from rpy import * r.quartz() r.library(tcltk) r.demo(tkdensity) This all works. You get the Aqua Tk widgets and the plotting in the quartz device. Windows can be brought to the foreground, minimized to the dock, and widgets can be operated with the mouse. No X11 is required at all. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel problems
As for the tcl/tk, I actually configured without pointing to
tclConfig.sh
and tkConfig.sh at all, but putting TCLTK_LIBS and TCLTK_CPPFLAGS
in the environment.
I could try to use, in addition, --with-tclconfig and --with-tkconfig,
but I
thought that would not be necessary if location of headers and libs are
defined explicitly.
On Tuesday, February 25, 2003, at 12:06 AM, [EMAIL PROTECTED] wrote:
On Mon, 24 Feb 2003, Jan de Leeuw wrote:
The OS X configure in R-devel has been changed to use two-level
namespaces. There
are still some problems.
1. Trunmed.c in the modreg packages defines a function heapsort(),
while heapsort
is also defined (differently) in /usr/lib/stdlib.h. I (temporarily)
disabled the
definition in stdlib.h.
That's a very recent addition, and we do try to keep an eye on such
things. The R symbol has been changed now.
2. If R is configured with the --without-x flag, then CPPFLAGS does
not
include
/usr/X11R6/include, while the tk.h files still tries to include
X11/xlib.h (and
can't find it, obviously). I added -I /usr/X11R6/include to the
compile
of tcltk.o
This looks like a bug in your tkConfig.sh. For example on Solaris it
has
# -I switch(es) to use to make all of the X11 include files accessible:
TK_XINCLUDES='-I/usr/openwin/include'
and that is what R uses, specifically
if test -n ${TK_XINCLUDES}; then
TCLTK_CPPFLAGS=${TCLTK_CPPFLAGS} ${TK_XINCLUDES}
else
TCLTK_CPPFLAGS=${TCLTK_CPPFLAGS} ${X_CFLAGS}
fi
Or is tkConfig.sh not being found and you need to point configure at
it?
--
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
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Re: [Rd] R-devel problems
Indeed. But I was expecting it not to look for X includes. This has
nothing to
do with R, however, only with tk.h for AquaTk.
On Tuesday, Feb 25, 2003, at 09:18 US/Pacific, [EMAIL PROTECTED]
wrote:
If you
1) Tell configure not to look for X includes
2) Tell it a TCLTK_CPPFLAGS omitting X includes
then I think you should expect no X includes to be found, no?
Brian
On Thu, 1 Jan 1970, Jan de Leeuw wrote:
As for the tcl/tk, I actually configured without pointing to
tclConfig.sh
and tkConfig.sh at all, but putting TCLTK_LIBS and TCLTK_CPPFLAGS
in the environment.
I could try to use, in addition, --with-tclconfig and
--with-tkconfig,
but I
thought that would not be necessary if location of headers and libs
are
defined explicitly.
On Tuesday, February 25, 2003, at 12:06 AM, [EMAIL PROTECTED]
wrote:
On Mon, 24 Feb 2003, Jan de Leeuw wrote:
The OS X configure in R-devel has been changed to use two-level
namespaces. There
are still some problems.
1. Trunmed.c in the modreg packages defines a function heapsort(),
while heapsort
is also defined (differently) in /usr/lib/stdlib.h. I (temporarily)
disabled the
definition in stdlib.h.
That's a very recent addition, and we do try to keep an eye on such
things. The R symbol has been changed now.
2. If R is configured with the --without-x flag, then CPPFLAGS does
not
include
/usr/X11R6/include, while the tk.h files still tries to include
X11/xlib.h (and
can't find it, obviously). I added -I /usr/X11R6/include to the
compile
of tcltk.o
This looks like a bug in your tkConfig.sh. For example on Solaris it
has
# -I switch(es) to use to make all of the X11 include files
accessible:
TK_XINCLUDES='-I/usr/openwin/include'
and that is what R uses, specifically
if test -n ${TK_XINCLUDES}; then
TCLTK_CPPFLAGS=${TCLTK_CPPFLAGS} ${TK_XINCLUDES}
else
TCLTK_CPPFLAGS=${TCLTK_CPPFLAGS} ${X_CFLAGS}
fi
Or is tkConfig.sh not being found and you need to point configure at
it?
--
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
__
[EMAIL PROTECTED] mailing list
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--
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
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED]
homepage: http://gifi.stat.ucla.edu
-
No matter where you go, there you are. --- Buckaroo Banzai
http://gifi.stat.ucla.edu/sounds/nomatter.au
-
__
[EMAIL PROTECTED] mailing list
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[Rd] R-devel problems
The OS X configure in R-devel has been changed to use two-level namespaces. There are still some problems. 1. Trunmed.c in the modreg packages defines a function heapsort(), while heapsort is also defined (differently) in /usr/lib/stdlib.h. I (temporarily) disabled the definition in stdlib.h. 2. If R is configured with the --without-x flag, then CPPFLAGS does not include /usr/X11R6/include, while the tk.h files still tries to include X11/xlib.h (and can't find it, obviously). I added -I /usr/X11R6/include to the compile of tcltk.o 3. Configure does not pass the $(Rexecbindir) to the Makefiles in the /src/library directory, so the links cannot find the bundle_loader. I added them by hand for all package links. 4. The aqua module does not work with two-level namespaces. Since it does not work anyway, and Stefano will remove it soon, it may be better to remove it even sooner. 5. In order to link the bundles with -bundle -bundle_loader /usr/local/lib/R/bin/R.bin the /usr/local/lib/R/bin/R.bin must exist, and moreover must be an R-devel build. This is a little bootstrap problem which can be easily hacked. __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] Re: [R-SIG-Mac]4. Exit Gifi Gnome problem
Confirmed. It is not your version of R or environment or the window manager (happens in OroborOSX, sawfish, blackbox). So it must be R-gnome, or gnome from fink, or gnome itself. Would be good if it could be verified/falsified on other gnome systems. On Thursday, January 2, 2003, at 12:39 PM, Joseph Kunkel wrote: Following from R-Sig-Mac digest #238 ... I installed R as suggested in R.pdf 4. Exit Gifi. On starting R with R --gui=gnome The system works reasonably but demo(graph) plots several demo graphs and their labeling off its window and the problem can not be cured by simple resizing the screen. This is only a bug when using gnome. When using the regular Xterm invocation of R all demo(graphs) behave as they should. I assume this is a problem with gnome? Is this problem catalogued and solved yet? Joe - Joseph G. Kunkel, Professor Biology Department University of Massachusetts Amherst Amherst MA 01003 http://www.bio.umass.edu/biology/kunkel/ ___ R-SIG-Mac mailing list [EMAIL PROTECTED] http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-devel
