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 a newer version of the OS like Tiger or newer) RCurl works out of the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
> 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
> > wrote:
> >>
> >> On Mon, Nov 15, 2010 at 5:13 PM, Steve Lianoglou
> >> 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
> >
> >
>
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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 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
> wrote:
>>
>> On Mon, Nov 15, 2010 at 5:13 PM, Steve Lianoglou
>> 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
>
>
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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
> 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
>
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Re: [R-SIG-Mac] R2.12 for Mac
from R:
Sys.getenv("DYLD_LIBRARY_PATH")
DYLD_LIBRARY_PATH
""
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
> 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
>
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Re: [R-SIG-Mac] R2.12 for Mac
On Mon, Nov 15, 2010 at 5:13 PM, Steve Lianoglou
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
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Re: [R-SIG-Mac] R2.12 for Mac
Hi, On Mon, Nov 15, 2010 at 4:51 PM, steven mosher wrote: > bash3.2$ ECHO $LD_LIBRARY_PATH > > Nothing. `echo` in lowercase, not capitals. But anyway, we already see the problem from your previous email. I guess this was what was in your ~/.profile file, or something? > CURL_CONFIG=/sw/bin/curl-config > DIRSTACK=() > DISPLAY=/tmp/launch-NfpUEf/org.x:0 > DYLD_LIBRARY_PATH=/sw/lib:/usr/local/lib: Your DYLD_LIBRARY_PATH is, in fact, hosing you. Comment out that line. Or, you can temporary move /sw to /sw2 to get fink out of the way for now, and see what is the what. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R2.12 for Mac
bash3.2$ ECHO $LD_LIBRARY_PATH Nothing. On Mon, Nov 15, 2010 at 1:03 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > 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 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 > > > [[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
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 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) >/u
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 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
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
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 This was crazy. I had R working from the terminal. I removed it and re installed and ended up with a version that doesnt work from terminal. Not sure exactly what is going on, But I've been dead in the water for 2-3 days. On Mon, Nov 15, 2010 at 2:24 AM, 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)? > > Thanks for the advice! > Ivan > > -- > Ivan CALANDRA > PhD Student > University of Hamburg > Biozentrum Grindel und Zoologisches Museum > Abt. Säugetiere > Martin-Luther-King-Platz 3 > D-20146 Hamburg, GERMANY > +49(0)40 42838 6231 > ivan.calan...@uni-hamburg.de > > ** > http://www.for771.uni-bonn.de > http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php > > ___ > 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
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] R2.12 for Mac
On Mon, 15 Nov 2010, Steve Lianoglou wrote: Hi, On Mon, Nov 15, 2010 at 5:24 AM, 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. 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
Hi, On Mon, Nov 15, 2010 at 5:24 AM, 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. 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
David, thank you for your answer. If I understand you right, it looks like one should be patient during the installation process! When I installed packages for R2.10, I ended up installing the dependencies manually one by one or else it was always installing many unnecessary packages (I guess they are unnecessary because I've never installed all of them on Windows), making the process last for ages. Looks like it still persists with R2.12 Regarding the packages, I thought that this website http://cran.r-project.org/web/checks/check_summary.html provided an up-to-date check of the packages, but I'm not sure it does. The packages were only tested with the pre-release for MacOSX and some packages (even the basics like plyr and reshape) show errors (which I don't really understand). Maybe I should just try out or contact the maintainer of the packages I need. And since you've upgraded, you don't have any speed problem, as reported I think twice on the list? Regards, Ivan Le 11/15/2010 15:35, David Winsemius a écrit : On Nov 15, 2010, at 5:24 AM, 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)? Thanks for the advice! I installed it yesterday and had three "moments" when I thought things had gone wrong, none of which proved to be enduring problems. During the install process using the downloaded bundle from the ATT site I noticed that the progress bar had stopped for what seemed to be an unreasonable period and realized that I had a running instance of R. Quit()-ting appeared to allow progress to resume. (So my first bit of potentially glaringly obvious advice would be to shutdown all instances of R before the install. I couldn't find this bit of advice on the Install directions but it is certainly possible that the authors thought to too obvious to mention.) The next puzzle was when I checked the installation of the R.app and R64.app GUI's. I assumed (wrongly as I eventually figured out) that they would have a more recent date than 2009 when viewed in the Applications folder. It turned out that they should (still) be version 1.35 and that the new ones looked just like my old ones and work just fine. The third "moment(s)" was when reinstalling package rms and dependent packages. I first tried installing the binary versions from my CRAN mirror and nothing seemed to be happening in hte time frame to which I have been accustomed. I "Force quit". I then restarted and installed from source. There was a very long period of no console activity, but I couldn't see any burning need to "Force quit" and I went away and came back 10 minutes later, to find the compliation process begun and then watch it run throught o completion and notice of success. Looking up at the intial portion of the console massages I discovered that about 20 packages were installed, so my initial impatience cause me to prematurely interupt what was probably a normal pause for the packages to be downloaded. Normal behavior seems to have been restored after a few temporary moments of cluelessness on my part. -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php ___ 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 Nov 15, 2010, at 5:24 AM, 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)? Thanks for the advice! I installed it yesterday and had three "moments" when I thought things had gone wrong, none of which proved to be enduring problems. During the install process using the downloaded bundle from the ATT site I noticed that the progress bar had stopped for what seemed to be an unreasonable period and realized that I had a running instance of R. Quit()-ting appeared to allow progress to resume. (So my first bit of potentially glaringly obvious advice would be to shutdown all instances of R before the install. I couldn't find this bit of advice on the Install directions but it is certainly possible that the authors thought to too obvious to mention.) The next puzzle was when I checked the installation of the R.app and R64.app GUI's. I assumed (wrongly as I eventually figured out) that they would have a more recent date than 2009 when viewed in the Applications folder. It turned out that they should (still) be version 1.35 and that the new ones looked just like my old ones and work just fine. The third "moment(s)" was when reinstalling package rms and dependent packages. I first tried installing the binary versions from my CRAN mirror and nothing seemed to be happening in hte time frame to which I have been accustomed. I "Force quit". I then restarted and installed from source. There was a very long period of no console activity, but I couldn't see any burning need to "Force quit" and I went away and came back 10 minutes later, to find the compliation process begun and then watch it run throught o completion and notice of success. Looking up at the intial portion of the console massages I discovered that about 20 packages were installed, so my initial impatience cause me to prematurely interupt what was probably a normal pause for the packages to be downloaded. Normal behavior seems to have been restored after a few temporary moments of cluelessness on my part. -- David. Ivan -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius, MD West Hartford, CT ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] R2.12 for Mac
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)? Thanks for the advice! Ivan -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
