Re: [R] installing problems
INSTALL says The main source of information on installation is the `R Installation and Administration Manual', an HTML copy of which is available as file `doc/html/R-admin.html'. Please read that before installing R. But if you are impatient, read on but please refer to the manual to resolve any problems. The 'problem' is discussed in detail in that manual. On Thu, 31 May 2007, dohyedan wrote: > > Would like to share that I am having the exact same problem running on Ubuntu > 7.04 trying to install the R-2.5.0.tar.gz file > > After trying './configure' I also get the same error message: > configure: error: --with-readline=yes (default) and headers/libs are > not available > > Hope some one can help us out on this one > Cheers, > Daniel > > > Xyoby Chavez wrote: >> >> hi every body. >> >> Im new in this program. Im traying to install R in linux suse10.0 in >> two following form: >> >> a) with the file R-2.5.0.tar.gz >> >> b) and the rpm file : R-base-2.5.0-2.1.i586.rpm >> >> ** In the first case a) when i uncompressed and type: >> >> linux:/opt/R/R-2.5.0 # ./configure >> >> the followind message is showed >> >> >> linux:/opt/R/R-2.5.0 # ./configure >> checking build system type... i686-pc-linux-gnu >> checking host system type... i686-pc-linux-gnu >> loading site script './config.site' >> loading build specific script './config.site' >> checking for pwd... /bin/pwd >> checking whether builddir is srcdir... yes >> . >> . >> . >> checking for dlopen in -ldl... yes >> checking readline/history.h usability... no >> checking readline/history.h presence... no >> checking for readline/history.h... no >> checking readline/readline.h usability... no >> checking readline/readline.h presence... no >> checking for readline/readline.h... no >> checking for rl_callback_read_char in -lreadline... no >> checking for main in -lncurses... yes >> checking for rl_callback_read_char in -lreadline... no >> checking for history_truncate_file... no >> configure: error: --with-readline=yes (default) and headers/libs are >> not available >> linux:/opt/R/R-2.5.0 # >> >> after that i try to do : >> >> linux:/opt/R/R-2.5.0 # make >> make: *** No targets specified and no makefile found. Stop. >> >> i installed : xorg-x11-devel and libpng-devel ,suggested by >> somebody >> and nothing. >> >> **Affter with b) tray to install with the YAST. It installed >> without errors, but when i try to run R the following message is >> showed: >> >> /usr/lib/R/bin/exec/R: error while loading shared libraries: >> libgfortran.so.0: cannot open shared object file: No such file or >> directory >> >> then i do >> >> linux:/usr/lib # ln /opt/gnat/lib/libgfortran.so libgfortran.so.0 >> >> it also doesnt work. >> >> Thanks for yor help >> >> Xyoby Chavez P >> Lima Peru >> >> __ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing problems
Would like to share that I am having the exact same problem running on Ubuntu 7.04 trying to install the R-2.5.0.tar.gz file After trying './configure' I also get the same error message: configure: error: --with-readline=yes (default) and headers/libs are not available Hope some one can help us out on this one Cheers, Daniel Xyoby Chavez wrote: > > hi every body. > > Im new in this program. Im traying to install R in linux suse10.0 in > two following form: > > a) with the file R-2.5.0.tar.gz > > b) and the rpm file : R-base-2.5.0-2.1.i586.rpm > > ** In the first case a) when i uncompressed and type: > > linux:/opt/R/R-2.5.0 # ./configure > > the followind message is showed > > > linux:/opt/R/R-2.5.0 # ./configure > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > loading site script './config.site' > loading build specific script './config.site' > checking for pwd... /bin/pwd > checking whether builddir is srcdir... yes > . > . > . > checking for dlopen in -ldl... yes > checking readline/history.h usability... no > checking readline/history.h presence... no > checking for readline/history.h... no > checking readline/readline.h usability... no > checking readline/readline.h presence... no > checking for readline/readline.h... no > checking for rl_callback_read_char in -lreadline... no > checking for main in -lncurses... yes > checking for rl_callback_read_char in -lreadline... no > checking for history_truncate_file... no > configure: error: --with-readline=yes (default) and headers/libs are > not available > linux:/opt/R/R-2.5.0 # > > after that i try to do : > > linux:/opt/R/R-2.5.0 # make > make: *** No targets specified and no makefile found. Stop. > > i installed : xorg-x11-devel and libpng-devel ,suggested by > somebody > and nothing. > > **Affter with b) tray to install with the YAST. It installed > without errors, but when i try to run R the following message is > showed: > > /usr/lib/R/bin/exec/R: error while loading shared libraries: > libgfortran.so.0: cannot open shared object file: No such file or > directory > > then i do > > linux:/usr/lib # ln /opt/gnat/lib/libgfortran.so libgfortran.so.0 > > it also doesnt work. > > Thanks for yor help > > Xyoby Chavez P > Lima Peru > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/installing-problems-tf3806626.html#a10892609 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing problems
Xyoby Chavez wrote: > hi every body. > > Im new in this program. Im traying to install R in linux suse10.0 in > two following form: > > a) with the file R-2.5.0.tar.gz > > b) and the rpm file : R-base-2.5.0-2.1.i586.rpm > > ** In the first case a) when i uncompressed and type: > > linux:/opt/R/R-2.5.0 # ./configure > > the followind message is showed > > > linux:/opt/R/R-2.5.0 # ./configure > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > loading site script './config.site' > loading build specific script './config.site' > checking for pwd... /bin/pwd > checking whether builddir is srcdir... yes > . > . > . > checking for dlopen in -ldl... yes > checking readline/history.h usability... no > checking readline/history.h presence... no > checking for readline/history.h... no > checking readline/readline.h usability... no > checking readline/readline.h presence... no > checking for readline/readline.h... no > checking for rl_callback_read_char in -lreadline... no > checking for main in -lncurses... yes > checking for rl_callback_read_char in -lreadline... no > checking for history_truncate_file... no > configure: error: --with-readline=yes (default) and headers/libs are > not available As the message tells you: You need to install readline headers and libs. Uwe Ligges > linux:/opt/R/R-2.5.0 # > > after that i try to do : > > linux:/opt/R/R-2.5.0 # make > make: *** No targets specified and no makefile found. Stop. > > i installed : xorg-x11-devel and libpng-devel ,suggested by somebody > and nothing. > > **Affter with b) tray to install with the YAST. It installed > without errors, but when i try to run R the following message is > showed: > > /usr/lib/R/bin/exec/R: error while loading shared libraries: > libgfortran.so.0: cannot open shared object file: No such file or > directory > > then i do > > linux:/usr/lib # ln /opt/gnat/lib/libgfortran.so libgfortran.so.0 > > it also doesnt work. > > Thanks for yor help > > Xyoby Chavez P > Lima Peru > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing problems
hi every body. Im new in this program. Im traying to install R in linux suse10.0 in two following form: a) with the file R-2.5.0.tar.gz b) and the rpm file : R-base-2.5.0-2.1.i586.rpm ** In the first case a) when i uncompressed and type: linux:/opt/R/R-2.5.0 # ./configure the followind message is showed linux:/opt/R/R-2.5.0 # ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu loading site script './config.site' loading build specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes . . . checking for dlopen in -ldl... yes checking readline/history.h usability... no checking readline/history.h presence... no checking for readline/history.h... no checking readline/readline.h usability... no checking readline/readline.h presence... no checking for readline/readline.h... no checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... yes checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available linux:/opt/R/R-2.5.0 # after that i try to do : linux:/opt/R/R-2.5.0 # make make: *** No targets specified and no makefile found. Stop. i installed : xorg-x11-devel and libpng-devel ,suggested by somebody and nothing. **Affter with b) tray to install with the YAST. It installed without errors, but when i try to run R the following message is showed: /usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.0: cannot open shared object file: No such file or directory then i do linux:/usr/lib # ln /opt/gnat/lib/libgfortran.so libgfortran.so.0 it also doesnt work. Thanks for yor help Xyoby Chavez P Lima Peru __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing problems about randomForest
Liaw, Andy wrote:
>Thanks for catching that! It must have slipped when I was going back and
>forth between C and Fortran...
>
>Update should appear on CRAN this week, I hope.
>
>Best,
>Andy
>
>
Thanks for your quick replay.
I just want you to know that I have tried R 2.1.0 on my pc running
Debian etch. I used 'apt-get r-base' to install R, and
'install("randomForest",
dependencies = TRUE)' from within R to install randomForest, but it failed
again.
Regards,
Xiao Jianfeng
__
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Re: [R] installing problems about randomForest
> From: Prof Brian Ripley
>
> On Mon, 8 Aug 2005, Uwe Ligges wrote:
>
> > Xiao Jianfeng wrote:
> >
> >> Hi all,
> >>
> >> When I tried to install package randomForest, it gave out
> the following
> >> error message:
> >> "
> >> > install.packages("randomForest", dependencies = TRUE)
> >> trying URL
> >>
> 'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-
> 12.tar.gz'
> >> Content type 'application/x-gzip' length 82217 bytes
> >> opened URL
> >> ==
> >> downloaded 80Kb
> >>
> >> Cannot create directory "": No such file or directory
>
> I have no idea what that is about.
>
> >> * Installing *source* package 'randomForest' ...
> >> ** libs
> >> gcc -I/user_data2/jfxiao/local/lib/R/include
> >> -I/usr/freeware/include -g -O2 -c classTree.c -o classTree.o
> >> gcc -I/user_data2/jfxiao/local/lib/R/include
> >> -I/usr/freeware/include -g -O2 -c regTree.c -o regTree.o
> >> gcc -I/user_data2/jfxiao/local/lib/R/include
> >> -I/usr/freeware/include -g -O2 -c regrf.c -o regrf.o
> >> gcc -I/user_data2/jfxiao/local/lib/R/include
> >> -I/usr/freeware/include -g -O2 -c rf.c -o rf.o
> >> f77 -OPT:IEEE_NaN_inf=ON-O2 -c rfsub.f -o rfsub.o
> >> "rfsub.f", line 90: error(2346): expression must have
> logical or integer
> >> type
> >> if (decsplit < 0.0) decsplit = 0.0
> >> ^
> >>
> >> "rfsub.f", line 90: error(2051): expected a ")"
> >> if (decsplit < 0.0) decsplit = 0.0
> >> ^
> >>
> >> 2 errors detected in the compilation of "rfsub.f".
> >> gmake: *** [rfsub.o] Error 2
> >> ERROR: compilation failed for package 'randomForest'
> >> "
> >> Can somebody help me ?
> >
> >
> > Which OS/platform and compiler are we talking about?
>
> >From his multitudinous recent postings, a peculiar IRIX setup.
>
> However, that line is not valid Fortran: replace < by .LT.
> Please note the posting guide asks you to discuss problems in
> packages
> with the maintainer (and to state your platform and R version).
Thanks for catching that! It must have slipped when I was going back and
forth between C and Fortran...
Update should appear on CRAN this week, I hope.
Best,
Andy
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
>
>
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installing problems about randomForest
Prof Brian Ripley wrote:
>On Mon, 8 Aug 2005, Uwe Ligges wrote:
>
>
>
>>Xiao Jianfeng wrote:
>>
>>
>>
>>>Hi all,
>>>
>>>When I tried to install package randomForest, it gave out the following
>>>error message:
>>>"
>>>
>>>
install.packages("randomForest", dependencies = TRUE)
>>>trying URL
>>>'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-12.tar.gz'
>>>Content type 'application/x-gzip' length 82217 bytes
>>>opened URL
>>>==
>>>downloaded 80Kb
>>>
>>>Cannot create directory "": No such file or directory
>>>
>>>
>
>I have no idea what that is about.
>
>
In my .cshrc, I set "R_LIBS" like this:
' setenv R_LIBS="$HOME/local/lib/R/library" ', is it OK?
>
>
>>>* Installing *source* package 'randomForest' ...
>>>** libs
>>>gcc -I/user_data2/jfxiao/local/lib/R/include
>>>-I/usr/freeware/include -g -O2 -c classTree.c -o classTree.o
>>>gcc -I/user_data2/jfxiao/local/lib/R/include
>>>-I/usr/freeware/include -g -O2 -c regTree.c -o regTree.o
>>>gcc -I/user_data2/jfxiao/local/lib/R/include
>>>-I/usr/freeware/include -g -O2 -c regrf.c -o regrf.o
>>>gcc -I/user_data2/jfxiao/local/lib/R/include
>>>-I/usr/freeware/include -g -O2 -c rf.c -o rf.o
>>>f77 -OPT:IEEE_NaN_inf=ON-O2 -c rfsub.f -o rfsub.o
>>>"rfsub.f", line 90: error(2346): expression must have logical or integer
>>>type
>>> if (decsplit < 0.0) decsplit = 0.0
>>> ^
>>>
>>>"rfsub.f", line 90: error(2051): expected a ")"
>>> if (decsplit < 0.0) decsplit = 0.0
>>> ^
>>>
>>>2 errors detected in the compilation of "rfsub.f".
>>>gmake: *** [rfsub.o] Error 2
>>>ERROR: compilation failed for package 'randomForest'
>>>"
>>>Can somebody help me ?
>>>
>>>
>>Which OS/platform and compiler are we talking about?
>>
>>
SGI IRIX 6.5, gcc 3.3, and f77 shiped with IRIX
>
>>From his multitudinous recent postings, a peculiar IRIX setup.
>
>However, that line is not valid Fortran: replace < by .LT.
>Please note the posting guide asks you to discuss problems in packages
>with the maintainer (and to state your platform and R version).
>
>
Thanks, I will try to contact the maintainer.
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installing problems about randomForest
On Mon, 8 Aug 2005, Uwe Ligges wrote:
> Xiao Jianfeng wrote:
>
>> Hi all,
>>
>> When I tried to install package randomForest, it gave out the following
>> error message:
>> "
>> > install.packages("randomForest", dependencies = TRUE)
>> trying URL
>> 'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-12.tar.gz'
>> Content type 'application/x-gzip' length 82217 bytes
>> opened URL
>> ==
>> downloaded 80Kb
>>
>> Cannot create directory "": No such file or directory
I have no idea what that is about.
>> * Installing *source* package 'randomForest' ...
>> ** libs
>> gcc -I/user_data2/jfxiao/local/lib/R/include
>> -I/usr/freeware/include -g -O2 -c classTree.c -o classTree.o
>> gcc -I/user_data2/jfxiao/local/lib/R/include
>> -I/usr/freeware/include -g -O2 -c regTree.c -o regTree.o
>> gcc -I/user_data2/jfxiao/local/lib/R/include
>> -I/usr/freeware/include -g -O2 -c regrf.c -o regrf.o
>> gcc -I/user_data2/jfxiao/local/lib/R/include
>> -I/usr/freeware/include -g -O2 -c rf.c -o rf.o
>> f77 -OPT:IEEE_NaN_inf=ON-O2 -c rfsub.f -o rfsub.o
>> "rfsub.f", line 90: error(2346): expression must have logical or integer
>> type
>> if (decsplit < 0.0) decsplit = 0.0
>> ^
>>
>> "rfsub.f", line 90: error(2051): expected a ")"
>> if (decsplit < 0.0) decsplit = 0.0
>> ^
>>
>> 2 errors detected in the compilation of "rfsub.f".
>> gmake: *** [rfsub.o] Error 2
>> ERROR: compilation failed for package 'randomForest'
>> "
>> Can somebody help me ?
>
>
> Which OS/platform and compiler are we talking about?
>From his multitudinous recent postings, a peculiar IRIX setup.
However, that line is not valid Fortran: replace < by .LT.
Please note the posting guide asks you to discuss problems in packages
with the maintainer (and to state your platform and R version).
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installing problems about randomForest
Xiao Jianfeng wrote:
> Hi all,
>
> When I tried to install package randomForest, it gave out the following
> error message:
> "
> > install.packages("randomForest", dependencies = TRUE)
> trying URL
> 'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-12.tar.gz'
> Content type 'application/x-gzip' length 82217 bytes
> opened URL
> ==
> downloaded 80Kb
>
> Cannot create directory "": No such file or directory
> * Installing *source* package 'randomForest' ...
> ** libs
> gcc -I/user_data2/jfxiao/local/lib/R/include
> -I/usr/freeware/include -g -O2 -c classTree.c -o classTree.o
> gcc -I/user_data2/jfxiao/local/lib/R/include
> -I/usr/freeware/include -g -O2 -c regTree.c -o regTree.o
> gcc -I/user_data2/jfxiao/local/lib/R/include
> -I/usr/freeware/include -g -O2 -c regrf.c -o regrf.o
> gcc -I/user_data2/jfxiao/local/lib/R/include
> -I/usr/freeware/include -g -O2 -c rf.c -o rf.o
> f77 -OPT:IEEE_NaN_inf=ON-O2 -c rfsub.f -o rfsub.o
> "rfsub.f", line 90: error(2346): expression must have logical or integer
> type
> if (decsplit < 0.0) decsplit = 0.0
> ^
>
> "rfsub.f", line 90: error(2051): expected a ")"
> if (decsplit < 0.0) decsplit = 0.0
> ^
>
> 2 errors detected in the compilation of "rfsub.f".
> gmake: *** [rfsub.o] Error 2
> ERROR: compilation failed for package 'randomForest'
> "
> Can somebody help me ?
Which OS/platform and compiler are we talking about?
Uwe Ligges
> Thanks in advance.
>
> Xiao Jianfeng
>
>
>
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] installing problems about randomForest
Hi all,
When I tried to install package randomForest, it gave out the following
error message:
"
> install.packages("randomForest", dependencies = TRUE)
trying URL
'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-12.tar.gz'
Content type 'application/x-gzip' length 82217 bytes
opened URL
==
downloaded 80Kb
Cannot create directory "": No such file or directory
* Installing *source* package 'randomForest' ...
** libs
gcc -I/user_data2/jfxiao/local/lib/R/include
-I/usr/freeware/include -g -O2 -c classTree.c -o classTree.o
gcc -I/user_data2/jfxiao/local/lib/R/include
-I/usr/freeware/include -g -O2 -c regTree.c -o regTree.o
gcc -I/user_data2/jfxiao/local/lib/R/include
-I/usr/freeware/include -g -O2 -c regrf.c -o regrf.o
gcc -I/user_data2/jfxiao/local/lib/R/include
-I/usr/freeware/include -g -O2 -c rf.c -o rf.o
f77 -OPT:IEEE_NaN_inf=ON-O2 -c rfsub.f -o rfsub.o
"rfsub.f", line 90: error(2346): expression must have logical or integer
type
if (decsplit < 0.0) decsplit = 0.0
^
"rfsub.f", line 90: error(2051): expected a ")"
if (decsplit < 0.0) decsplit = 0.0
^
2 errors detected in the compilation of "rfsub.f".
gmake: *** [rfsub.o] Error 2
ERROR: compilation failed for package 'randomForest'
"
Can somebody help me ?
Thanks in advance.
Xiao Jianfeng
__
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Re: [R] Installing Problems
Hi Ashok, On Thu, Jan 27, 2005 at 11:48:08AM -0500, Ashok Veeraraghavan wrote: > I tried installing R on my MAC OS 10.3. After R installation I tried > installing BioConductor which requires R. I ran into some problems > with Bioconductor. Right now I want to remove (uninstall) all R and > Bioconductor components from my machine and start afresh. Can somebody > tell me how i can remove(uninstall) all R and Bioconductor components. It is a little hard to answer that because you didn't tell us exactly how you went about installing R and Bioconductor. To remove the binary OS X installed R (and Bioconductor) I think it suffices to delete the R application from /Applications and remove the R framework from /Library/Frameworks. For questions regarding Bioconductor, you may find the Bioconductor mail list more receptive: https://stat.ethz.ch/mailman/listinfo/bioconductor + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing Problems
Hi, I tried installing R on my MAC OS 10.3. After R installation I tried installing BioConductor which requires R. I ran into some problems with Bioconductor. Right now I want to remove (uninstall) all R and Bioconductor components from my machine and start afresh. Can somebody tell me how i can remove(uninstall) all R and Bioconductor components. Thanks Regards Ashok __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] installing problems repeated.tgz linux
I echo Andy's experience on FC2. I was able to install the package here and got the same warning messages. Despite trying to use some web sites to translate the german text, I am unsure of the 'true' meaning. I think it is something pertaining to target patterns not being found, which leads me to think that this might be a locale/character encoding issue in the package. Anyone? Marc On Mon, 2004-07-26 at 14:16, Liaw, Andy wrote: > I downloaded repeated.tgz and tried it myself on one of our AMD Opterons > running SLES8, and it worked (R-1.9.1 compiled as 64-bit). Notice that I do > get a couple of warnings from gcc about labels, and from g77 about the use > of `sum' function. > > Andy SNIPPED > > From: Liaw, Andy > > > > Sorry, Christian. I have no idea what those error messages > > in German say. > > > > Andy > > > > > From: [EMAIL PROTECTED] > > > > > > Hello, > > > > > > thanks for your and Marc's hint, but it seems not the probleme!? > > > Is there any probleme with my make? > > > > > > many thanks and regards, > > > christian > > > > > > > > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > > > -l /usr/lib/R/library /space/downs/repeated.tgz > > > * Installing *source* package 'repeated' ... > > > ** libs > > > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthÃlt > > > kein Â%Â. > > > Schluss. > > > ERROR: compilation failed for package 'repeated' > > > ** Removing '/usr/lib/R/library/repeated' > > > > > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > > > -l /usr/lib/R/library /space/downs/repeated > > > * Installing *source* package 'repeated' ... > > > ** libs > > > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthÃlt > > > kein Â%Â. > > > Schluss. > > > ERROR: compilation failed for package 'repeated' > > > ** Removing '/usr/lib/R/library/repeated' SNIPPED __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] installing problems repeated.tgz linux
I downloaded repeated.tgz and tried it myself on one of our AMD Opterons running SLES8, and it worked (R-1.9.1 compiled as 64-bit). Notice that I do get a couple of warnings from gcc about labels, and from g77 about the use of `sum' function. Andy [EMAIL PROTECTED]:lindsey]% R CMD INSTALL -l ~/rlibs repeated * Installing *source* package 'repeated' ... ** libs g77 -fPIC -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c chidden.f -o chidden.o g77 -fPIC -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c cphidden.f -o cphidden.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c cutil.c -o cutil.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c dist.c -o dist.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c gar.c -o gar.o g77 -fPIC -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c hidden.f -o hidden.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c kcountb.c -o kcountb.o kcountb.c: In function `kcountb': kcountb.c:263: warning: deprecated use of label at end of compound statement kcountb.c:270: warning: deprecated use of label at end of compound statement gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c kserieb.c -o kserieb.o g77 -fPIC -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c logitord.f -o logitord.o g77 -fPIC -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c binnest.f -o binnest.o binnest.f: In subroutine `calcbn': binnest.f:537: warning: J_Prod = J_Prod * Sum(H2,uph2) ! Calculate the product of J ^ Reference to unimplemented intrinsic `SUM' at (^) (assumed EXTERNAL) binnest.f: In subroutine `calcbn2': binnest.f:1255: warning: J_Prod = J_Prod * Sum(H2,uph2) ! Calculate the product of J ^ Reference to unimplemented intrinsic `SUM' at (^) (assumed EXTERNAL) g77 -fPIC -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c gausscop.f -o gausscop.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c gaps.c -o gaps.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c calcs.c -o calcs.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c calcs1.c -o calcs1.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c calcs2.c -o calcs2.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c calcs3.c -o calcs3.o gcc -I/usr/local/lib/R/include -I/usr/local/include -fPIC -O7 -m64 -msse2 -march=k8 -mcpu=k8 -g -c calcs4.c -o calcs4.o gcc -shared -o repeated.so chidden.o cphidden.o cutil.o dist.o gar.o hidden.o kcountb.o kserieb.o logitord.o binnest.o gausscop.o gaps.o calcs.o calcs1.o calcs2.o calcs3.o calcs4.o -L/usr/local/lib -L/opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3 -L/opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3/../../../../lib64 -L/opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s ** R ** help >>> Building/Updating help pages for package 'repeated' Formats: text html latex example [snipped. I think you get the idea...] > From: Liaw, Andy > > Sorry, Christian. I have no idea what those error messages > in German say. > > Andy > > > From: [EMAIL PROTECTED] > > > > Hello, > > > > thanks for your and Marc's hint, but it seems not the probleme!? > > Is there any probleme with my make? > > > > many thanks and regards, > > christian > > > > > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > > -l /usr/lib/R/library /space/downs/repeated.tgz > > * Installing *source* package 'repeated' ... > > ** libs > > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält > > kein »%«. > > Schluss. > > ERROR: compilation failed for package 'repeated' > > ** Removing '/usr/lib/R/library/repeated' > > > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > > -l /usr/lib/R/library /space/downs/repeated > > * Installing *source* package 'repeated' ... > > ** libs > > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält > > kein »%«. > > Schluss. > > ERROR: compilation failed for package 'repeated' > > ** Removing '/usr/lib/R/library/repeated' > > > > ...with your great RandomForest and other packages > > it works! > > > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > > -l /usr/lib/R/library /space/downs/randomForest*.tar.gz > > * Installing *source* package 'randomForest' ... > > ** libs > > gcc -I/usr/lib/R/include -I/usr/local/include -I/opt/gnome/include > > -D__NO_MATH_INLINES -mieee-fp -fPIC -c regrf.c -o regrf.o > > g77 -mieee-fp -fPIC -c regrfsub.f -o regrfsub.o > > gcc -I/usr/lib/R/include -I/usr/local/incl
RE: [R] installing problems repeated.tgz linux
Sorry, Christian. I have no idea what those error messages in German say. Andy > From: [EMAIL PROTECTED] > > Hello, > > thanks for your and Marc's hint, but it seems not the probleme!? > Is there any probleme with my make? > > many thanks and regards, > christian > > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > -l /usr/lib/R/library /space/downs/repeated.tgz > * Installing *source* package 'repeated' ... > ** libs > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält > kein »%«. > Schluss. > ERROR: compilation failed for package 'repeated' > ** Removing '/usr/lib/R/library/repeated' > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > -l /usr/lib/R/library /space/downs/repeated > * Installing *source* package 'repeated' ... > ** libs > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält > kein »%«. > Schluss. > ERROR: compilation failed for package 'repeated' > ** Removing '/usr/lib/R/library/repeated' > > ...with your great RandomForest and other packages > it works! > > [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL > -l /usr/lib/R/library /space/downs/randomForest*.tar.gz > * Installing *source* package 'randomForest' ... > ** libs > gcc -I/usr/lib/R/include -I/usr/local/include -I/opt/gnome/include > -D__NO_MATH_INLINES -mieee-fp -fPIC -c regrf.c -o regrf.o > g77 -mieee-fp -fPIC -c regrfsub.f -o regrfsub.o > gcc -I/usr/lib/R/include -I/usr/local/include -I/opt/gnome/include > -D__NO_MATH_INLINES -mieee-fp -fPIC -c rf.c -o rf.o > g77 -mieee-fp -fPIC -c rfsub.f -o rfsub.o > gcc -shared -L/usr/local/lib -L/opt/gnome/lib -o > randomForest.so regrf.o > regrfsub.o rf.o rfsub.o -L/usr/local/lib -L/opt/gnome/lib > -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1 > -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1/../../../../i586-suse > -linux/lib > -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1/../../.. -lfrtbegin > -lg2c -lm > -lgcc_s -L/usr/lib/R/bin -lR > ** R > ** inst > ** help > >>> Building/Updating help pages for package 'randomForest' > Formats: text html latex example > MDSplot texthtmllatex example > combine texthtmllatex example > getTree texthtmllatex example > grow texthtmllatex example > importancetexthtmllatex > margintexthtmllatex example > na.roughfix texthtmllatex example > partialPlot texthtmllatex example > plot.randomForest texthtmllatex example > predict.randomForest texthtmllatex example > randomForest texthtmllatex example > rfImpute texthtmllatex example > treesize texthtmllatex example > tuneRFtexthtmllatex example > varImpPlottexthtmllatex example > varUsed texthtmllatex example > * DONE (randomForest) > > > > > > > Am Montag, 26. Juli 2004 18:56 schrieb Liaw, Andy: > > > From: Christian Schulz > > > > > > Hi, > > > > > > i try several possibilities adn looking in the archive, > > > but didn't getting success to install j.lindsey's > usefuel "library > > > repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) > > > > > > P.S. Windows, works fine > > > > > > Many thanks for help > > > Christian > > > > > > > R CMD INSTALL - l /usr/lib/R/library repeated > > > >^ > > Try again without that space. > > > > Andy > > > > > > > > > -- > - > >--- Notice: This e-mail message, together with any > attachments, contains > > information of Merck & Co., Inc. (One Merck Drive, > Whitehouse Station, New > > Jersey, USA 08889), and/or its affiliates (which may be > known outside the > > United States as Merck Frosst, Merck Sharp & Dohme or MSD > and in Japan, as > > Banyu) that may be confidential, proprietary copyrighted > and/or legally > > privileged. It is intended solely for the use of the > individual or entity > > named on this message. If you are not the intended > recipient, and have > > received this message in error, please notify us > immediately by reply > > e-mail and then delete it from your system. > > > -- > - > >--- > > __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installing problems repeated.tgz linux
On Mon, 2004-07-26 at 09:34, Christian Schulz wrote:
> Hi,
>
> i try several possibilities adn looking in the archive,
> but didn't getting success to install j.lindsey's usefuel "library
> repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1)
>
> P.S. Windows, works fine
>
> Many thanks for help
> Christian
>
>
> [EMAIL PROTECTED]:/space/downs> R CMD INSTALL - l /usr/lib/R/library repeated
> WARNING: invalid package '-'
> WARNING: invalid package 'l'
> WARNING: invalid package '/usr/lib/R/library'
> * Installing *source* package 'repeated' ...
> ** libs
> /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthÃlt kein Â%Â.
> Schluss.
> ERROR: compilation failed for package 'repeated'
> ** Removing '/usr/lib/R/library/repeated'
Christian,
There is a space (' ') between the '-' and the 'l', which will be parsed
as two separate arguments. Hence the initial WARNING messages.
You need to use:
R CMD INSTALL -l /usr/lib/R/library repeated
Also note that you need to have 'root' privileges in order to install
the packages into the /usr/lib/R tree. Thus, you should 'su' to root
before running the command.
You should verify that your R tree is in /usr/lib, as the default is
/usr/local/lib, for which you would not require the '-l
/usr/lib/R/library' argument.
Presumably Windows worked fine because you typically do not require
administrator privileges to install the package locally on Windows or
your account has administrative privileges, which is typical (and bad)
on Windows NT/XP.
HTH,
Marc Schwartz
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] installing problems repeated.tgz linux
> From: Christian Schulz > > Hi, > > i try several possibilities adn looking in the archive, > but didn't getting success to install j.lindsey's usefuel "library > repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) > > P.S. Windows, works fine > > Many thanks for help > Christian > > > > R CMD INSTALL - l /usr/lib/R/library repeated ^ Try again without that space. Andy __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installing problems repeated.tgz linux
Hello, thanks for your and Marc's hint, but it seems not the probleme!? Is there any probleme with my make? many thanks and regards, christian [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL -l /usr/lib/R/library /space/downs/repeated.tgz * Installing *source* package 'repeated' ... ** libs /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält kein »%«. Schluss. ERROR: compilation failed for package 'repeated' ** Removing '/usr/lib/R/library/repeated' [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL -l /usr/lib/R/library /space/downs/repeated * Installing *source* package 'repeated' ... ** libs /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält kein »%«. Schluss. ERROR: compilation failed for package 'repeated' ** Removing '/usr/lib/R/library/repeated' ...with your great RandomForest and other packages it works! [EMAIL PROTECTED]:/usr/lib/R> R CMD INSTALL -l /usr/lib/R/library /space/downs/randomForest*.tar.gz * Installing *source* package 'randomForest' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c regrf.c -o regrf.o g77 -mieee-fp -fPIC -c regrfsub.f -o regrfsub.o gcc -I/usr/lib/R/include -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c rf.c -o rf.o g77 -mieee-fp -fPIC -c rfsub.f -o rfsub.o gcc -shared -L/usr/local/lib -L/opt/gnome/lib -o randomForest.so regrf.o regrfsub.o rf.o rfsub.o -L/usr/local/lib -L/opt/gnome/lib -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1 -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1/../../../../i586-suse-linux/lib -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1/../../.. -lfrtbegin -lg2c -lm -lgcc_s -L/usr/lib/R/bin -lR ** R ** inst ** help >>> Building/Updating help pages for package 'randomForest' Formats: text html latex example MDSplot texthtmllatex example combine texthtmllatex example getTree texthtmllatex example grow texthtmllatex example importancetexthtmllatex margintexthtmllatex example na.roughfix texthtmllatex example partialPlot texthtmllatex example plot.randomForest texthtmllatex example predict.randomForest texthtmllatex example randomForest texthtmllatex example rfImpute texthtmllatex example treesize texthtmllatex example tuneRFtexthtmllatex example varImpPlottexthtmllatex example varUsed texthtmllatex example * DONE (randomForest) Am Montag, 26. Juli 2004 18:56 schrieb Liaw, Andy: > > From: Christian Schulz > > > > Hi, > > > > i try several possibilities adn looking in the archive, > > but didn't getting success to install j.lindsey's usefuel "library > > repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) > > > > P.S. Windows, works fine > > > > Many thanks for help > > Christian > > > > > R CMD INSTALL - l /usr/lib/R/library repeated > >^ > Try again without that space. > > Andy > > > > --- >--- Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New > Jersey, USA 08889), and/or its affiliates (which may be known outside the > United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as > Banyu) that may be confidential, proprietary copyrighted and/or legally > privileged. It is intended solely for the use of the individual or entity > named on this message. If you are not the intended recipient, and have > received this message in error, please notify us immediately by reply > e-mail and then delete it from your system. > --- >--- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] installing problems repeated.tgz linux
Hi, i try several possibilities adn looking in the archive, but didn't getting success to install j.lindsey's usefuel "library repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) P.S. Windows, works fine Many thanks for help Christian [EMAIL PROTECTED]:/space/downs> R CMD INSTALL - l /usr/lib/R/library repeated WARNING: invalid package '-' WARNING: invalid package 'l' WARNING: invalid package '/usr/lib/R/library' * Installing *source* package 'repeated' ... ** libs /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält kein »%«. Schluss. ERROR: compilation failed for package 'repeated' ** Removing '/usr/lib/R/library/repeated' __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
