Re: [R-SIG-Mac] R2.12 for Mac
Hi, On Mon, Nov 15, 2010 at 5:24 AM, Ivan Calandra ivan.calan...@uni-hamburg.de 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. I've been using R-2.12 since day 0 and don't have any issues to report. I've also stopped using R from the GUI for a long time now (I only run it via the terminal, or through emacs/terminal), so if there are problems with using that for an extended period of time, I wouldn't know (I'm guessing there aren't, though). 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)? Keep in mind that you can keep R-2.11 on your machine *and* install R-2.12. If for some reason you think R-2.12 isn't stable enough for you, you can switch back to R-2.11 with Rswitch, which you can find here: http://r.research.att.com/#other -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ 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 Mon, 15 Nov 2010, Steve Lianoglou wrote: Hi, On Mon, Nov 15, 2010 at 5:24 AM, Ivan Calandra ivan.calan...@uni-hamburg.de 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. I've been using R-2.12 since day 0 and don't have any issues to report. I've also stopped using R from the GUI for a long time now (I only run it via the terminal, or through emacs/terminal), so if there are problems with using that for an extended period of time, I wouldn't know (I'm guessing there aren't, though). I second that (and since I do quite a lot of development on my MacBook Air, I was using pre-2.12.0 from ca day -30). 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)? Keep in mind that you can keep R-2.11 on your machine *and* install R-2.12. If for some reason you think R-2.12 isn't stable enough for you, you can switch back to R-2.11 with Rswitch, which you can find here: http://r.research.att.com/#other -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ 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
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
IF you are using a CRAN binary version of R, it is strange how fink is involved at all. You must have a messed up system My best guess is that DYLD_LIBRARY_PATH or LD_LIBRARY_PATH has been set (you can do echo $LD_LIBRARY_PATH in the terminal). Unset those variables, and proceed. Kasper On Mon, Nov 15, 2010 at 3:20 PM, Berend Hasselman b...@xs4all.nl wrote: 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 $PATH show? etc.,... I did an otool -L on /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib l and got this libR.dylib: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib (compatibility version 2.12.0, current version 2.12.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib (compatibility version 3.0.0, current version 3.0.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 476.19.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib (compatibility version 5.0.0, current version 5.2.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 36.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.5) /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) Berend ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R2.12 for Mac
Thanks, Steve Pointed out that it was probably a fink thing I also had issues getting Rcurl to point at the latest version of libcurl which was another fink think I fink I have problems. hehe.. gallows humour. So, I'm figuring my .profile or bash is busted. CURL_CONFIG=/sw/bin/curl-config DIRSTACK=() DISPLAY=/tmp/launch-NfpUEf/org.x:0 DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: EUID=501 GROUPS=() HISTFILE=/Users/mosher/.bash_history HISTFILESIZE=500 HISTSIZE=500 HOME=/Users/mosher HOSTNAME=mosher.local HOSTTYPE=i386 IFS=$' \t\n' LINES=24 LOGNAME=mosher MACHTYPE=i386-apple-darwin9.0 MAILCHECK=60 MANPATH=/usr/share/man:/usr/local/share/man:/usr/X11/share/man:/usr/X11/man OPTERR=1 OPTIND=1 OSTYPE=darwin9.0 PATH=/opt/subversion/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11/bin:/sw/bin:sw/sbin:/usr/local/bin:usr/local/sbin:/usr/bin:usr/sbin:bin:sbin PIPESTATUS=([0]=0) PPID=2922 PS1='\s-\v\$ ' PS2=' ' PS4='+ ' PWD=/Users/mosher SECURITYSESSIONID=a9cb40 SHELL=/bin/bash SHELLOPTS=braceexpand:emacs:hashall:histexpand:history:interactive-comments:monitor SHLVL=2 SSH_AUTH_SOCK=/tmp/launch-plLI4O/Listeners TERM=xterm TMPDIR=/var/folders/ea/eaXeR9KIEZSbgaDPdoLSwU+++TI/-Tmp-/ UID=501 USER=mosher WINDOWID=8388621 X11_PREFS_DOMAIN=org.x.X11 XTERM_LOCALE=C XTERM_SHELL=/bin/bash XTERM_VERSION='XTerm(261)' _=CURL_CONFIG __CF_USER_TEXT_ENCODING=0x1F5:0:0 The ECHO PATH yields the following. ECHO $PATH /opt/subversion/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11/bin:/sw/bin:sw/sbin:/usr/local/bin:usr/local/sbin:/usr/bin:usr/sbin:bin:sbin bash-3.2$ bash-3.2$ otool -L Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib Library/Frameworks/R.framework/Versions/2.12/Resources/lib/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) On Mon, Nov 15, 2010 at 12:20 PM, Berend Hasselman b...@xs4all.nl wrote: 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 $PATH show? etc.,... I did an otool -L on /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib l and got this libR.dylib: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib (compatibility version 2.12.0, current version 2.12.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib (compatibility version 3.0.0, current version 3.0.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 476.19.0) /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib (compatibility version 5.0.0, current version 5.2.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 36.0.0)
Re: [R-SIG-Mac] R2.12 for Mac
I found the offending file. .bashrc export PATH=$PATH:/sw/bin:sw/sbin:/usr/local/bin:usr/local/sbin:/usr/bin:usr/sbin:bin:sbin export DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: export CURL_CONFIG=/sw/bin/curl-config When I was trying to get RCurl working this was suggested as the way to do it. So I assume i should not do: export DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: On Mon, Nov 15, 2010 at 3:38 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Nov 15, 2010 at 5:13 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: Your DYLD_LIBRARY_PATH is, in fact, hosing you. Comment out that line. This line screws up your entire system. You sometimes see people on various email lists recommend doing stuff like this, but this is a specific place where OS X is very different from Linux. In principle, this could also mess with your other applications. However, you also need to figure out how that got set in your GUI (check by doing Sys.getenv(DYLD_LIBRARY_PATH) ) and you will need to fix that as well in case fixing .profile does not fix the GUI. Kasper [[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
Re: [R-SIG-Mac] R2.12 for Mac
Yeah remove that But I don't even get why you are doing this. On a mac (at least with a newer version of the OS like Tiger or newer) RCurl works out of the box. So what you do it remove offending line in bashrc do a grep in you home folder to check you don't have other offending lines including either LD_LIBRARY_PATH or DYLD_LIBRARYPATH cd /etc and do a recursive grep for LD_LIBRARY_PATH, and see if it hits anything. restart Terminal start R and verify it works Now, after this you start the _GUI_ and do the Sys.getenv thing. The GUI works differently from terminal R in this case. If the offending value is still there, you might want to have a look in .MacOS/environment.plist There might be a similar line somewhere Finally, write 100 times I will not do random things to my system I read on random websites. Ok, that is a little tough, but you do realize this is all your own doing, right. Kasper On Mon, Nov 15, 2010 at 7:11 PM, steven mosher mosherste...@gmail.com wrote: I found the offending file. .bashrc export PATH=$PATH:/sw/bin:sw/sbin:/usr/local/bin:usr/local/sbin:/usr/bin:usr/sbin:bin:sbin export DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: export CURL_CONFIG=/sw/bin/curl-config When I was trying to get RCurl working this was suggested as the way to do it. So I assume i should not do: export DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: On Mon, Nov 15, 2010 at 3:38 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Nov 15, 2010 at 5:13 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: Your DYLD_LIBRARY_PATH is, in fact, hosing you. Comment out that line. This line screws up your entire system. You sometimes see people on various email lists recommend doing stuff like this, but this is a specific place where OS X is very different from Linux. In principle, this could also mess with your other applications. However, you also need to figure out how that got set in your GUI (check by doing Sys.getenv(DYLD_LIBRARY_PATH) ) and you will need to fix that as well in case fixing .profile does not fix the GUI. Kasper ___ 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
See inlined. On Mon, Nov 15, 2010 at 4:24 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Yeah remove that But I don't even get why you are doing this. On a mac (at least with a newer version of the OS like Tiger or newer) RCurl works out of the box. Rcurl is the R package. So what you do it remove offending line in bashrc do a grep in you home folder to check you don't have other offending lines including either LD_LIBRARY_PATH or DYLD_LIBRARYPATH cd /etc and do a recursive grep for LD_LIBRARY_PATH, and see if it hits anything. restart Terminal start R and verify it works Ok. Thanks for the advice will do. Now, after this you start the _GUI_ and do the Sys.getenv thing. The GUI works differently from terminal R in this case. If the offending value is still there, you might want to have a look in .MacOS/environment.plist There might be a similar line somewhere Sys.getenv(DYLD_LIBRARY_PATH) DYLD_LIBRARY_PATH /Library/Frameworks/R.framework/Resources/lib/i386 However, if I start using the GUI Sys.getenv(DYLD_LIBRARY_PATH) DYLD_LIBRARY_PATH Finally, write 100 times I will not do random things to my system I read on random websites. Ok, that is a little tough, but you do realize this is all your own doing, right. Actually, it was advice I got here, But Ya. I'm suitably chastised Kasper On Mon, Nov 15, 2010 at 7:11 PM, steven mosher mosherste...@gmail.com wrote: I found the offending file. .bashrc export PATH=$PATH:/sw/bin:sw/sbin:/usr/local/bin:usr/local/sbin:/usr/bin:usr/sbin:bin:sbin export DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: export CURL_CONFIG=/sw/bin/curl-config When I was trying to get RCurl working this was suggested as the way to do it. So I assume i should not do: export DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: On Mon, Nov 15, 2010 at 3:38 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Nov 15, 2010 at 5:13 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: Your DYLD_LIBRARY_PATH is, in fact, hosing you. Comment out that line. This line screws up your entire system. You sometimes see people on various email lists recommend doing stuff like this, but this is a specific place where OS X is very different from Linux. In principle, this could also mess with your other applications. However, you also need to figure out how that got set in your GUI (check by doing Sys.getenv(DYLD_LIBRARY_PATH) ) and you will need to fix that as well in case fixing .profile does not fix the GUI. Kasper [[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
