Re: [R-SIG-Mac] R2.12 for Mac
On 15-11-2010, at 20:45, steven mosher wrote: > I guess I've had the worst of it. > > With my last clean install I even killed my ability to run R from terminal > > R version 2.12.0 (2010-10-15) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > > 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. > > dyld: lazy symbol binding failed: Symbol not found: _iconv_open > Referenced from: /Library/Frameworks/R. > framework/Resources/lib/i386/libR.dylib > Expected in: /sw/lib/libiconv.2.dylib > > dyld: Symbol not found: _iconv_open > Referenced from: > /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib > Expected in: /sw/lib/libiconv.2.dylib > /sw/... is a Fink thing. Somewhere in your .profile Fink "things" are being set. When you open a terminal and do "set" what do you get? What does echo $PATH show? etc.,... I did an otool -L on /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib l and got this libR.dylib: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib (compatibility version 2.12.0, current version 2.12.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib (compatibility version 3.0.0, current version 3.0.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 476.19.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib (compatibility version 5.0.0, current version 5.2.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 36.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.5) /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R2.12 for Mac
On 15-11-2010, at 11:24, Ivan Calandra wrote: > Dear users, > > I've seen a few problems on this list related to R2.12 on Mac. It looks to me > that the Mac release is not really stable yet, or is it? Maybe it's just a > few instances and most of you have no problems at all with it. > > Therefore, I've kept my R2.11 on my Mac. Would you advise to upgrade or to > wait some time? And if I should/can upgrade, do you have any recommendations > regarding how to do it correctly (that are not included in the FAQ)? Installing R and updating installed packages went smoothly on both computers (iMac,MacBook Pro). I haven't encountered any problems using R. I use both the GUI and the R bundle of TextMate (latest version is 1.5.10 and all is well). Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Rcartogram build failind
On 10-06-2010, at 22:00, Erich Neuwirth wrote: > I tried to build Rcartogram from Omegahat > It requires fftw3 (available from www.fftw.org) to be built and installed on > the machine > before Rcartogram can be built. > the usual configure/make/sudo install worked without problems on my Mac (OSX > 10.6.3, Xcode 3.2.1, 64bit version) > R CMD INSTALL Rcartogram then gave the following message: > You should have compiled with the same architecture you intended to compile Rcartogram with. > gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names > -undefined dynamic_lookup -single_module -multiply_defined suppress > -L/usr/local/lib -o Rcartogram.so Rcart.o cart.o -L/usr/local/lib -lfftw3 > -lfftw3 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > -Wl,CoreFoundation > ld: warning: in /usr/local/lib/libfftw3.a, file is not of required > architecture > > I have no experience building with Xcode on OSX, but I assume the the problem > comes from the fact > that Xcode is the 64bit version. > Is there a switch I can set so that libfftw3 is compiled in a way R can use > it? > Is there a way to build both the 32bit and the 64bit version of the library? > What else can I do do make it work? Go to R for Mac OS X - developer's page at http://r.research.att.com/ Section Other binaries and tools and then /libs/ ==> http://r.research.att.com/libs/ You'll find fftw there in required architectures. If this doesn't work, you'll have to wait for the experts. Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R texteditor for mac OS
I use TextMate as main editor and the R/R Console/ R Daemon bundles. Especially the R bundle. Furthermore R.app and R64.app for interactive use. Berend On 02-06-2010, at 19:31, Bunny, lautloscrew.com wrote: > Dear all, > > i really have some issues using the standard R editor on Snow Leopard. On > several occasions lines were cut off horizontally. Plus, there are problems > with line breaks after copy pasting code from one window to another. Is there > any quality editor or IDE for R? What do y´all use ? > > thx in advance > > matt > ___ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Oops --- still have problems building R from source.
On 27-05-2010, at 01:20, Rolf Turner wrote: > > On 27/05/2010, at 12:37 AM, Simon Urbanek wrote: > > > mv /sw /sw.notused and edit your Bash .profile to NOT source the init script of Fink (If I remember correctly). Because that's how the Fink include and lib paths are activated and how Fink modifies your PATH. (I think). >>> >>> >>> Tried that. And I get >>> >>> make[3]: *** No rule to make target `/sw/include/iconv.h', needed by >>> `sysutils.o'. Stop. >>> make[2]: *** [R] Error 2 >>> make[1]: *** [R] Error 1 >>> make: *** [R] Error 1 >>> >>> So somehow it is still looking for /sw even though I moved /sw aside and >>> took the call to >>> the init script out (of my .cshrc, actually). >>> >>> Any other ideas? Sorry for all the bother. >>> >> >> Are sure you cleaned up your build (i.e. removed the whole build directory) >> before configuring? > > I'm not sure of *anything* since I don't understand the subtleties of the > procedure @ all. > > What I did was *remove* the directory created by untarring the R tarball. I > then > unpacked the tarball again, made the requisite edits to config.site, moved > /sw aside, took the line referring to /sw/bin/init.csh out of my .cshrc file, > did ./configure (that worked!) and then did ``make''. > > Wound up getting: > >> . >> . >> . >> gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names >> -undefined dynamic_lookup -single_module -multiply_defined suppress >> -L/usr/local/lib -o R_X11.so dataentry.o devX11.o rotated.o rbitmap.o -lSM >> -lICE -lX11 -lXt -lXmu -L../../../lib -lR -Wl,-framework >> -Wl,CoreFoundation >> ld: library not found for -lSM >> collect2: ld returned 1 exit status >> make[4]: *** [R_X11.so] Error 1 >> make[3]: *** [R] Error 2 >> make[2]: *** [make.X11] Error 2 >> make[1]: *** [R] Error 1 >> make: *** [R] Error 1 > > What is the ``-lSM'' business all about? What is ``SM''? How do > I get the missing library? Psigh! :-( You had the same thing some iterations ago. -lSM tells the linker to link against libSM.dylib (in this case; because of the -dynamiclib if i am correct). This .dylib is in /usr/X11/lib You may have forgotten to put the line LIBS=-L/usr/X11/lib into the config.site file. I can't think of anything else. Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Oops --- still have problems building R from source.
On 25-05-2010, at 06:30, Rolf Turner wrote: > > On 25/05/2010, at 4:24 PM, Berend Hasselman wrote: > >> >> On 25-05-2010, at 05:54, Rolf Turner wrote: >> >>> . >>> . >>> . >>>> gcc -arch x86_64 -std=gnu99 -I. -I../../../src/include >>>> -I../../../src/include -I/sw/include -I/usr/local/include >>>> -DHAVE_CONFIG_H -fPIC -g -O2 -c dataentry.c -o dataentry.o >>>> gcc -arch x86_64 -std=gnu99 -I. -I../../../src/include >>>> -I../../../src/include -I/sw/include -I/usr/local/include >>>> -DHAVE_CONFIG_H -fPIC -g -O2 -c devX11.c -o devX11.o >>>> gcc -arch x86_64 -std=gnu99 -I. -I../../../src/include >>>> -I../../../src/include -I/sw/include -I/usr/local/include >>>> -DHAVE_CONFIG_H -fPIC -g -O2 -c rotated.c -o rotated.o >>>> gcc -arch x86_64 -std=gnu99 -I. -I../../../src/include >>>> -I../../../src/include -I/sw/include -I/usr/local/include >>>> -DHAVE_CONFIG_H -fPIC -g -O2 -c rbitmap.c -o rbitmap.o >>>> gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names >>>> -undefined dynamic_lookup -single_module -multiply_defined suppress >>>> -L/sw/lib -L/usr/local/lib -o R_X11.so dataentry.o devX11.o rotated.o >>>> rbitmap.o -lSM -lICE -lX11 -lXt -lXmu -L../../../lib -lR >>>> -Wl,-framework -Wl,CoreFoundation >>>> ld: library not found for -lSM >>>> collect2: ld returned 1 exit status >>>> make[4]: *** [R_X11.so] Error 1 >>>> make[3]: *** [R] Error 2 >>>> make[2]: *** [make.X11] Error 2 >>>> make[1]: *** [R] Error 1 >>>> make: *** [R] Error 1 >>> >>> Anyone have any ideas as to what I need to do to o'erleap *this* hurdle? >> >> You still seem to have /sw/include and /sw/lib active. >> >> On my Snow Leopard 10.6.3 libSM.dylib is in /usr/X11/lib. > > > Not ``still'' actually; ``again''. I found that when I had /sw moved > aside there were a couple or three utilities (dos2unix; aspell) that I > like to use, that were gone. > > So I reinstalled fink, thinking that it was a ***broken*** fink that was > causing problems, so if I reinstalled it, it wouldn't be broken any more > and all would be well. > > And things went well up to this point > > Is there any way that I can keep /sw around and tell ``make'' not to use it? > Or something like that. (Please be monosyllabic!!! :-) ) > mv /sw /sw.notused and edit your Bash .profile to NOT source the init script of Fink (If I remember correctly). Because that's how the Fink include and lib paths are activated and how Fink modifies your PATH. (I think). Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with readline when building R from source.
On 21-05-2010, at 04:20, Rolf Turner wrote: > > On 21/05/2010, at 1:46 PM, Simon Urbanek wrote: > >> Rolf, >> >> you have broken fink is /sw -- remove it (or move aside) and all should be >> well :) > > > Psigh. I'm sure this is getting tedious for you ... but where else can > I turn? > > I did: > > cd /sw > sudo mv fink fink.broken > > Then I tried the ./configure trick again. Same error message as before. > > Any other ideas? :-( I believe Simon meant: remove or rename /sw and get rid of references to /sw/... in PATH Berend Hasselman ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] building R package on Mac OS: R CMD build yields empty directories
On 19-05-2010, at 16:19, Carsten Dormann wrote: > > My problem: although "R CMD build bipartite" works, it produces a nicely > packed set of EMPTY directories: > > cle09:~ dormann$ R CMD build bipartite > * checking for file 'bipartite/DESCRIPTION' ... OK > * preparing 'bipartite': > * checking DESCRIPTION meta-information ... OK > * cleaning src > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > WARNING: directory 'bipartite/data' is empty > WARNING: directory 'bipartite/inst/doc' is empty > WARNING: directory 'bipartite/man' is empty > WARNING: directory 'bipartite/R' is empty > WARNING: directory 'bipartite/src' is empty > * building 'bipartite_1.12.tar.gz' I have just downloaded the source of bipartite. I ran R CMD build bipartite in the directory containing bipartite. No error message. It generated a perfectly correct .tar.gz with no error messages. By the way, R CMD build <...> does not produce directories; it produces a <...>.tar.gz So it would seem that your bipartite directory is empty. Try downloading the source package from CRAN and then run R CMD check. Berend Hasselman ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] problems with X11 in R 2.11.0
If it's not part of the standard Mac OS X system, it comes in Apple Developer Tools. You'll have to register in the Apple Developer program and download Xcode. And I'm not sure if you can use the latest Xcode 3.2.2 on Snow Leopard. It's probably a good idea to wait for a reaction from Simon who is the expert in these matters. Which version of Mac OS X and X11 do you have? Neither of you have provided that information. Berend On 03-05-2010, at 20:27, steven mosher wrote: > hmm. where did u get otool? > > On Mon, May 3, 2010 at 11:00 AM, Berend Hasselman wrote: > > > I just now also did (Mac OS X 10.6.3) > > otool -L /usr/X11/lib/libpng12.0.dylib > > with result: > > /usr/X11/lib/libpng12.0.dylib: >/usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0, current > version 42.0.0) >/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version > 1.2.3) >/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 125.0.1) > > so things seem to be ok. > Something is indeed wrong with your X or something else. > > Berend > > On 03-05-2010, at 19:23, Berend Hasselman wrote: > > > > > I am running Mac OS X 10.6.3 and R 2.10.1 patched. > > > >> sessionInfo() > > R version 2.10.1 Patched (2010-04-07 r51689) > > x86_64-apple-darwin9.8.0 > > > > Result of otool -L > > /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so > > on my machine is: > > ... > > /usr/X11/lib/libpng12.0.dylib (compatibility version 36.0.0, current > > version 36.0.0) > > > > which I assume will mean that running R2.11.0 will give error messages > > similar to those of the OP. > > I have Apple's Xquartz 2.3.5 (xorg-server 1.4.2-apple53)(the latest from > > Apple for Snow Leopard, I think) > > And I have not fiddled with X at all. > > > > Berend > > > > On 03-05-2010, at 07:19, Prof Brian Ripley wrote: > > > >> Something is wrong with your system software. On my Leopard box: > >> > >> tystie% otool -L > >> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so > >> ... > >> /usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0, current > >> version 42.0.0) > >> > >> So your /usr/X11/lib/libpng12.0.dylib is different from mine (and from the > >> CRAN build machine's). > >> > >> Your choices are > >> > >> - to resolve this (and it is not an R issue). I'd start by running the > >> software updater > >> > >> - to build R from the sources against the software on your machine. > >> > >> On Sun, 2 May 2010, steven mosher wrote: > >> > >>> I had the same Issue with 2.10.1. never got it resolved. I was hoping that > >>> 2.11 would fix it...alas > >>> > >>> On Thu, Apr 29, 2010 at 2:59 PM, Seth Schommer > >>> wrote: > >>> > >>>> I installed R 2.11.0 today and immediately came across an issue I did > >>>> not experience using version 2.10.1. For some reason, I can not use > >>>> X11 in R. Here's a simple example: > >>>> > >>>> > >>>>> X11() > >>>> Error in X11() : X11 module cannot be loaded > >>>> In addition: Warning message: > >>>> In X11() : > >>>> unable to load shared library > >>>> '/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so': > >>>> dlopen(/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so, > >>>> 6): Library not loaded: /usr/X11/lib/libpng12.0.dylib > >>>> Referenced from: > >>>> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so > >>>> Reason: Incompatible library version: R_X11.so requires version > >>>> 42.0.0 or later, but libpng12.0.dylib provides version 36.0.0 > >>>>> sessionInfo() > >>>> R version 2.11.0 (2010-04-22) > >>>> i386-apple-darwin9.8.0 > >>>> > >>>> locale: > >>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > >>>> > >>>> attached base packages: > >>>> [1] stats graphics grDevices utils datasets methods base > >>>> > >>>> > >>>> I'm running Mac OS X 10.5.8. This error occurs when running R.app and > >>>> while running R from the terminal. After experience this I
Re: [R-SIG-Mac] problems with X11 in R 2.11.0
I just now also did (Mac OS X 10.6.3) otool -L /usr/X11/lib/libpng12.0.dylib with result: /usr/X11/lib/libpng12.0.dylib: /usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0, current version 42.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.0.1) so things seem to be ok. Something is indeed wrong with your X or something else. Berend On 03-05-2010, at 19:23, Berend Hasselman wrote: > > I am running Mac OS X 10.6.3 and R 2.10.1 patched. > >> sessionInfo() > R version 2.10.1 Patched (2010-04-07 r51689) > x86_64-apple-darwin9.8.0 > > Result of otool -L > /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so > on my machine is: > ... > /usr/X11/lib/libpng12.0.dylib (compatibility version 36.0.0, current > version 36.0.0) > > which I assume will mean that running R2.11.0 will give error messages > similar to those of the OP. > I have Apple's Xquartz 2.3.5 (xorg-server 1.4.2-apple53)(the latest from > Apple for Snow Leopard, I think) > And I have not fiddled with X at all. > > Berend > > On 03-05-2010, at 07:19, Prof Brian Ripley wrote: > >> Something is wrong with your system software. On my Leopard box: >> >> tystie% otool -L >> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so >> ... >> /usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0, current >> version 42.0.0) >> >> So your /usr/X11/lib/libpng12.0.dylib is different from mine (and from the >> CRAN build machine's). >> >> Your choices are >> >> - to resolve this (and it is not an R issue). I'd start by running the >> software updater >> >> - to build R from the sources against the software on your machine. >> >> On Sun, 2 May 2010, steven mosher wrote: >> >>> I had the same Issue with 2.10.1. never got it resolved. I was hoping that >>> 2.11 would fix it...alas >>> >>> On Thu, Apr 29, 2010 at 2:59 PM, Seth Schommer wrote: >>> >>>> I installed R 2.11.0 today and immediately came across an issue I did >>>> not experience using version 2.10.1. For some reason, I can not use >>>> X11 in R. Here's a simple example: >>>> >>>> >>>>> X11() >>>> Error in X11() : X11 module cannot be loaded >>>> In addition: Warning message: >>>> In X11() : >>>> unable to load shared library >>>> '/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so': >>>> dlopen(/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so, >>>> 6): Library not loaded: /usr/X11/lib/libpng12.0.dylib >>>> Referenced from: >>>> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so >>>> Reason: Incompatible library version: R_X11.so requires version >>>> 42.0.0 or later, but libpng12.0.dylib provides version 36.0.0 >>>>> sessionInfo() >>>> R version 2.11.0 (2010-04-22) >>>> i386-apple-darwin9.8.0 >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> I'm running Mac OS X 10.5.8. This error occurs when running R.app and >>>> while running R from the terminal. After experience this I >>>> reinstalled 2.10.1 and tried the same command and had no problems. >>>> Just to make sure, I installed 2.11.0 again, and sure enough, I got >>>> the same error. Is this a bug, or have I done something wrong? >>>> >>>> Thanks, >>>> >>>> Seth >>>> >>>> ___ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> -- >> 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-SIG-Mac mailing list >> R-SIG-Mac@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] problems with X11 in R 2.11.0
I am running Mac OS X 10.6.3 and R 2.10.1 patched. > sessionInfo() R version 2.10.1 Patched (2010-04-07 r51689) x86_64-apple-darwin9.8.0 Result of otool -L /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so on my machine is: ... /usr/X11/lib/libpng12.0.dylib (compatibility version 36.0.0, current version 36.0.0) which I assume will mean that running R2.11.0 will give error messages similar to those of the OP. I have Apple's Xquartz 2.3.5 (xorg-server 1.4.2-apple53)(the latest from Apple for Snow Leopard, I think) And I have not fiddled with X at all. Berend On 03-05-2010, at 07:19, Prof Brian Ripley wrote: > Something is wrong with your system software. On my Leopard box: > > tystie% otool -L > /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so > ... > /usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0, current > version 42.0.0) > > So your /usr/X11/lib/libpng12.0.dylib is different from mine (and from the > CRAN build machine's). > > Your choices are > > - to resolve this (and it is not an R issue). I'd start by running the > software updater > > - to build R from the sources against the software on your machine. > > On Sun, 2 May 2010, steven mosher wrote: > >> I had the same Issue with 2.10.1. never got it resolved. I was hoping that >> 2.11 would fix it...alas >> >> On Thu, Apr 29, 2010 at 2:59 PM, Seth Schommer wrote: >> >>> I installed R 2.11.0 today and immediately came across an issue I did >>> not experience using version 2.10.1. For some reason, I can not use >>> X11 in R. Here's a simple example: >>> >>> X11() >>> Error in X11() : X11 module cannot be loaded >>> In addition: Warning message: >>> In X11() : >>> unable to load shared library >>> '/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so': >>> dlopen(/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so, >>> 6): Library not loaded: /usr/X11/lib/libpng12.0.dylib >>> Referenced from: >>> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so >>> Reason: Incompatible library version: R_X11.so requires version >>> 42.0.0 or later, but libpng12.0.dylib provides version 36.0.0 sessionInfo() >>> R version 2.11.0 (2010-04-22) >>> i386-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> I'm running Mac OS X 10.5.8. This error occurs when running R.app and >>> while running R from the terminal. After experience this I >>> reinstalled 2.10.1 and tried the same command and had no problems. >>> Just to make sure, I installed 2.11.0 again, and sure enough, I got >>> the same error. Is this a bug, or have I done something wrong? >>> >>> Thanks, >>> >>> Seth >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> [[alternative HTML version deleted]] >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > -- > 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-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] gfortran bug?
On 27-04-2010, at 20:28, Andreas Noack Jensen wrote:
> Thank you so much for looking at it. Initially my code was in the "free"
> F95 format but partly because of the error and partly because of portability
> concerns I chose to translate it to strict F77 even thought it is ugly and
> annoying with the line width limit.
>
> Indeed I think something is going wrong with the initial values but I cannot
> figure out why. Maybe because of missing Fortran skills but I am puzzled
> because the code works fine on Windows and Linux.
>
Indeed, that is what I have found. See below.
> I think the "-mtune=core2" problem has disappeared in the latest 4.2.3
> gfortran at r.research because I had the error in the beginning but after
> reinstall of gfortran it was gone (right now, however, I am on gfortran
> 4.2.4 aka gcc 4.2.1).
>
> Thank you once again and hope some new ideas to isolate the problem will
> appear.
The error is in the fortran line
double precision, intent(in) :: coef(ndim(1),ndim(2),ndim(3)),
init(ndim(3),ndim(nl(2)))
The dimensions of init are wrong.
The line should read:
double precision, intent(in) :: coef(ndim(1),ndim(2),ndim(3)),
init(ndim(3),nl(2))
I have attached the corrected rmfilter.f90, a slightly modified rmfilter.R that
I used to print various stuff
the test1.R and the output.
In the test case your code declares init(2,2)
In the corrected code it is declared as init(2,3)
The actual dimension is init(2,3)
Berend
rmfilter.f90
Description: Binary data
test1.R
Description: Binary data
rmfilter.R
Description: Binary data
>
> dyn.load('rmfilter.so')
> source("rmfilter.R")
>
> set.seed(407)
>
> eps <- matrix(rnorm(30), ncol = 3)
> eps
[,1] [,2] [,3]
[1,] 0.841081288 1.7100891 0.9161884
[2,] 1.072881139 1.1351244 -0.4314795
[3,] -0.543593265 -1.0828613 -0.6333517
[4,] 0.441951763 -1.0539372 -1.8468529
[5,] 0.004920633 -0.9635668 0.6060301
[6,] -0.731256023 0.4951620 -1.9168646
[7,] -1.216400546 -1.5097126 1.1407077
[8,] -0.210674189 -1.1110270 -0.3563495
[9,] -0.378021236 -1.5624664 -2.5094364
[10,] -0.939183015 -0.2886860 2.1596868
>
> z <- rmfilter(eps, array(diag(3)*0.5, c(3,3,2)))
[1] 10 3
[1] 3 3 2
[1] 2 3
[,1] [,2] [,3]
[1,]000
[2,]000
[1] 2
[1] 2
> z
[,1] [,2][,3]
[1,] 0.8410813 1.7100891 0.91618843
[2,] 1.4934218 1.9901689 0.02661472
[3,] 0.6236583 0.7672677 -0.16195012
[4,] 1.5004918 0.3247811 -1.91452060
[5,] 1.0669957 -0.4175424 -0.43220526
[6,] 0.5524877 0.4487814 -3.09022752
[7,] -0.4066589 -1.4940931 -0.62050867
[8,] -0.1377598 -1.6336829 -2.21171758
[9,] -0.6502306 -3.1263543 -3.92554948
[10,] -1.3331782 -2.6687046 -0.90894674
attr(,"tsp")
[1] 1 10 1
>
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Re: [R-SIG-Mac] gfortran bug?
On 25-04-2010, at 22:22, Andreas Noack Jensen wrote:
...
> On Mac I quite randomly get very weird results from the subroutine. It is
> like the initial values explodes to fx 2e+290 even for identical calls
> without random number generation. Most results are identical to results I
> get from a pure R code but at some calls they explode in a non systematic
> fashion.
...
I have experimented with your stuff.
Find attached the R files needed to run my test.
Below is what I have done together with the R output.
As you can see the third column of the result matrix is weird.
This result is independent from setting the seed.
Some sort of initialisation issue?
Since I haven't got a clue what rmfilter does and my memory needs some
refreshing wrt dgemm,
I can't pinpoint the problem.
Berend
I am (still) using the gfortran from gfortran-4.2.3.dmg
--
I made the rmfilter.so with
MAKEFLAGS="FCFLAGS=-O2" R CMD SHLIB rmfilter.f90
NB. had to do it since this gfortran doesn't accept the -mtune=core2 option!!
--
sessionInfo()
R version 2.10.1 Patched (2010-04-07 r51689)
x86_64-apple-darwin9.8.0
locale:
[1] en_GB/en_GB/C/C/en_GB/en_GB
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Mac OS X 10.6.3 Intel
--
I ran this test job
dyn.load('rmfilter.so')
source("rmfilter.R")
set.seed(407)
eps <- matrix(rnorm(30), ncol = 3)
eps
z <- rmfilter(eps, array(diag(3)*0.5, c(3,3,2)))
z
with this as output
>
> dyn.load('rmfilter.so')
> source("rmfilter.R")
>
> set.seed(407)
>
> eps <- matrix(rnorm(30), ncol = 3)
> eps
[,1] [,2] [,3]
[1,] 0.841081288 1.7100891 0.9161884
[2,] 1.072881139 1.1351244 -0.4314795
[3,] -0.543593265 -1.0828613 -0.6333517
[4,] 0.441951763 -1.0539372 -1.8468529
[5,] 0.004920633 -0.9635668 0.6060301
[6,] -0.731256023 0.4951620 -1.9168646
[7,] -1.216400546 -1.5097126 1.1407077
[8,] -0.210674189 -1.1110270 -0.3563495
[9,] -0.378021236 -1.5624664 -2.5094364
[10,] -0.939183015 -0.2886860 2.1596868
>
> z <- rmfilter(eps, array(diag(3)*0.5, c(3,3,2)))
> z
[,1] [,2] [,3]
[1,] 0.8410813 1.7100891 1.018209e+277
[2,] 1.4934218 1.9901689 1.018209e+277
[3,] 0.6236583 0.7672677 1.018209e+277
[4,] 1.5004918 0.3247811 1.018209e+277
[5,] 1.0669957 -0.4175424 1.018209e+277
[6,] 0.5524877 0.4487814 1.018209e+277
[7,] -0.4066589 -1.4940931 1.018209e+277
[8,] -0.1377598 -1.6336829 1.018209e+277
[9,] -0.6502306 -3.1263543 1.018209e+277
[10,] -1.3331782 -2.6687046 1.018209e+277
attr(,"tsp")
[1] 1 10 1
rmfilter.R
Description: Binary data
test1.R
Description: Binary data
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Re: [R-SIG-Mac] gfortran bug?
On 25-04-2010, at 22:22, Andreas Noack Jensen wrote:
> Dear list members
>
> I have organised some code in a package including a Fortran subroutine for a
> multivariate recursive filter to simulate VAR-porcesses. I have worked with
> R for some time, but I am new to writing packages and coding Fortran so
> first I thought I had made some mistakes in the Fortran code but I have now
> tested the package on Ubuntu 10.4 and Windows XP and the problem is only
> present on Mac.
>
> On Mac I quite randomly get very weird results from the subroutine. It is
> like the initial values explodes to fx 2e+290 even for identical calls
> without random number generation. Most results are identical to results I
> get from a pure R code but at some calls they explode in a non systematic
> fashion.
>
> I would have tried to use the gfortran 4.2.4 from r.research.att.com, to
> isolate the error (right now I use their 4.2.3), but it seems like it
> installs 4.2.1 instead and I get the same error still. I have tried to build
> gfortran myself but was unsuccessful in doing so.
As far as I can tell, your fortran code is in fixed format which is not
immediately obvious.
I have put the code in free format and have reformatted the code with more
indentation (1 space of indent is really not enough).
See below after my signature.
It now compiles with no errors.
I don't see anything immediately wrong.
It would be nice to have a small test program in fortran to check the code.
Berend
subroutine rmfilter(x, nl, coef, ndim, init)
implicit none
integer, intent(in) :: nl(2), ndim(3)
double precision, intent(inout) :: x(nl(1),nl(2))
double precision, intent(in) :: coef(ndim(1),ndim(2),ndim(3)),
init(ndim(3),ndim(nl(2)))
double precision :: y(nl(1),nl(2))
integer :: i, j
y = 0.0d+0
do i = 1, nl(1), 1
do j = 1, ndim(3), 1
if ( i <= j ) then
call dgemm('N', 'T', 1, ndim(1), nl(2), 1.0d+0,&
init(ndim(3)-j+1,:), 1, coef(:,:,j), ndim(1), 1.0d+0,
y(i,:), 1)
else
call dgemm('N', 'T', 1, ndim(1), nl(2), 1.0d+0,&
y(i-j,:), 1, coef(:,:,j), ndim(1), 1.0d+0, y(i,:), 1)
end if
end do
y(i,:) = y(i,:) + x(i,:)
end do
x = y
return
end subroutine rmfilter
BTW. in do i = 1, nl(1), 1 anddo j = 1, ndim(3), 1
the steps 1 are not necessary: 1 is the default
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Re: [R-SIG-Mac] Permanently change default console font
On 24-04-2010, at 03:59, Mike Lawrence wrote: > I tried poking at the source code again and I guess I didn't try hard > enough the first time because this time I found that changing the > default font is trivial: > > In files "RConsoleController.m" & "RController.m", change all instances of > NSFont userFixedPitchFontOfSize:currentFontSize > to > NSFont fontWithName:@"Menlo-Regular" size:currentFontSize You could also have a look at the free TinkerTool, which lets you set several fonts for the system. Amongst others the fixed width font. You can find it here: www.bresink.com (goto Products, TinkerTool (not the system variation). Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Help links in R Package Manager window inoperative
1. Open a Package Manager window in the R.app GUI (menu Packages & Data, Package Manager) 2. Click on any package listed in the top half of the window to get the documentation overview in the bottom half of the window. 3. Clicking on any item in the Help Pages list does not take you to the requested page. (Note. if there is an "overview" link, clicking on the link works. Clicking on a browse "directory" link also doesn't do anything). (This has been the case since R 2.10.0) Berend Using R 2.10.0 GUI 1.30 (5521 Leopard build 32-bit) > R.Version() $platform [1] "i386-apple-darwin9.8.0" $arch [1] "i386" $os [1] "darwin9.8.0" $system [1] "i386, darwin9.8.0" $status [1] "Patched" $major [1] "2" $minor [1] "10.0" $year [1] "2009" $month [1] "11" $day [1] "18" $`svn rev` [1] "50482" $language [1] "R" $version.string [1] "R version 2.10.0 Patched (2009-11-18 r50482)" ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Getting to the Rgui Configuration Editor on a MAC
I keep forgetting to do a reply to all with R-Sig Mac. Sorry. On 06/11/2009, at 23:26, Steven Lewis wrote: I teach a class in R and have instructed my students to change their GUI preferences to match mine by going to the Rgui Configuration Editor under the Edit menu. I want them to select MDI and MDI toolbar. Why? This works fine for those who have a Windows-based PC. What do I tell my students who have a MAC? How and where can they go to accomplish this same task? They can't. R.app does not have an MDI interface. Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] BBEdit Language Module Enhancements
On 30/10/2009, at 21:36, Steve Lianoglou wrote: Hi, On Oct 30, 2009, at 4:17 PM, Berend Hasselman wrote: Could be a difference between BBEdit 8.5 and TextWrangler 3.0, which is related to BBEdit 9.2 BTW. I use TextMate for R. Brilliant. OOC, have you made any mods to the R.tmbundle? No, I haven't. Perfectly satisfied with the bundle out of the box. I'd like to get it to recognize s4 function defs. It's not a huge thing for me, so haven't spent the time to figure out the lang definitions, but was thinking if lazyness could prevail and see if anyone else has done so :-) Sorry can't help you. You'll just have to start being not lazy:-) Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] BBEdit Language Module Enhancements
On 30/10/2009, at 21:12, Jonathan Marc Bearak wrote: Hi, Thanks for noticing the missing 0. I wonder why the function pattern works in BBEdit but not in TextWrangler, but since your revision seems to work in both, I swapped it in. Could be a difference between BBEdit 8.5 and TextWrangler 3.0, which is related to BBEdit 9.2 BTW. I use TextMate for R. Brilliant. Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] BBEdit Language Module Enhancements
On 30/10/2009, at 20:10, Jonathan Marc Bearak wrote: Hi, I made a couple of enhancements to the BBEdit Language Module found in this thread: https://stat.ethz.ch/pipermail/r-sig-mac/2005-December/002520.html I have uploaded the language module here: http://homepages.nyu.edu/~jmb736/code/R_language_module_for_BBEdit/R.plist This language module, as revised, will detect R functions, so you can browse functions in the symbols menu. I have not yet figured out how to match the function body. As such, when the cursor is placed, not in the function name, but in the function body, the symbols menu will display "(no symbols selected)". I am not sure when I will next have time to look at this, but in any case, simply being able to browse function names is the really important thing (for me, anyway) so I do not have to scroll down a file or use the find dialog just to find a function. I tried your R.plist in TextWrangler 3 and it failed to recognise functions. I changed the function pattern to this Function Pattern (?P[a-z0-9_A-Z.]+)\s*<-\s*functionstring> and then TextWrangler does recognise R functions with function names appearing in the symbols popup menu. The string for Identifier and Keyword Characters should also contain a 0 (zero digit). Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 2.10.0 beta -- please test!
On 23/10/2009, at 00:26, Rob Goedman wrote: Berend, Are you running SnowLeopard? Yes. Berend Running the 32 bit R.app GUI. I start out with my Home directory as working directory. I do a Change Working Directory to: /Users/berendhasselman/ Documents/Programming/R/NonLinearEq.Test/nleq.test/nslv Then do an Open Document... (Cmd+O) or a Source File... (Shift+Cmd +O). The open file dialog doesn't start in the current working directory but in /Users/berendhasselman/Documents/Programming/R/NonLinearEq.Test. After navigating to the working directory and opening a file, and then doing another open file the open dialog hasn't remembered the previous directory. I have to navigate to the desired directory all over again. I can't remember if this also happened with R2.9.2. Sorry about that. Berend --- sessionInfo() gives R version 2.10.0 RC (2009-10-20 r50178) i386-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 2.10.0 beta -- please test!
On 19/10/2009, at 14:46, Simon Urbanek wrote: Dear Mac users, please consider testing R 2.10.0 beta *before* the release. First, we have now an automated installer generator system for Leopard and Snow Leopard (incl. 64-bit R), so it will be useful to test that it works as desired and second there was one very fundamental change in the GUI (not necessarily visible for the user but it makes sure any new debugging/browser support in R is passed into the GUI) so we want to make sure *before* the release that any issues are ironed out -- but we can only do that with your feedback. Running the 32 bit R.app GUI. I start out with my Home directory as working directory. I do a Change Working Directory to: /Users/berendhasselman/Documents/ Programming/R/NonLinearEq.Test/nleq.test/nslv Then do an Open Document... (Cmd+O) or a Source File... (Shift+Cmd+O). The open file dialog doesn't start in the current working directory but in /Users/berendhasselman/Documents/Programming/R/NonLinearEq.Test. After navigating to the working directory and opening a file, and then doing another open file the open dialog hasn't remembered the previous directory. I have to navigate to the desired directory all over again. I can't remember if this also happened with R2.9.2. Sorry about that. Berend --- sessionInfo() gives R version 2.10.0 RC (2009-10-20 r50178) i386-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 2.10.0 beta -- please test!
On 22/10/2009, at 19:58, Peter Cowan wrote: Thanks, I can confirm that these are fixed in the latest nightly. However, I think I've uncovered one more issue w/ the help system. In the Package Manager window selecting a package displays the help index. *I think*, in previous versions, clicking on a function name would take you to it's help page. In the nightly version, nothing happens. I hope I've described it clearly enough to reproduce. R version 2.10.0 RC (2009-10-20 r50178) [R.app GUI 1.30 (5510) x86_64-apple-darwin9.8.0] Same thing for me. Berend - Gui: R.app GUI 1.30-devel (5510 Leopard build 64-bit), Session info: R version 2.10.0 RC (2009-10-20 r50178) x86_64-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] nleqslv_1.5 ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] tcltk
On 14-07-2009, at 17:52, David Winsemius wrote: Thanks Berend. I was not having difficulties using Terminal sessions for navigating the folder tree of hidden folders, but I think this will benefit those not raised on CLI systems in the pre-GUI years, so I am taking the liberty of copying to the list. O dear. I've done it again. Reply without looking. So it isn't sent to the list. Maybe a Reply-To field could be added to the mail header as other mailing lists seem to do? Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with R CMD check, pdflatex
On 17-05-2009, at 14:52, Michael Höhle wrote: however, my pdflatex is located in e.g. $ which pdflatex /usr/local/teTeX/bin/i386-apple-darwin-current/pdflatex That would be quite an old TeX installation? The teTeX distribution is no longer maintained. You should consider switching to MacTeX ( http://www.tug.org/mactex/ ) It has everything you need. It's excellent. Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] uninstall R and update
On 7 Nov 2007, at 18:32, Roland Kaiser wrote: > Hi all! > > I get confused wenn uninstalling R > and reinstalling it using the installer. > > I removed > /Applications/R.app > /Library/Frameworks/R.framework > ~/Library/R/ > > Wenn I start the Installer R-2.6.0.dmg > it wants to update my previous installation. > > What is the cause of this behaviour? > Do I have to delete other files or directories? Try deleting ~/Library/Preferences/org.R-project.R.plist I had a look at what AppZapper suggested deleting if one were to delete R.app. It seems to want to delete files which are totally unrelated to R. The org.R-project.R.plist file was in the list. Beware of AppZapper for deleting R. Berend (using Mac OS X Leopard) ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
