Re: [R] Running R in Bash and R GUI
There are two things that occur. Firstly, I normally have to unset no_proxy: % unset no_proxy; R Secondly, if for some reason http_proxy isn't being seen in R, you can use the Sys.putenv() function within R to manipulate the environment -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: 24 May 2007 16:05 To: R-help@stat.math.ethz.ch Subject: [R] Running R in Bash and R GUI I have been trying to get the R and package update functions in the GUI version of R to work on my Mac. Initially I got error messages that suggested I needed to set up the http_proxy for GUI R to use, but how can this be done? I eventually got to the point of writing a .bash_profile file in the Bash terminal and setting the proxy addresses there. I can now use my Bash terminal, invoke R, and run the update / install commands and they work! The problem that still remains is that in the R console of the GUI R, the http_proxy is not seen and thus I cannot connect to CRAN or any other mirror using the GUI functions in the pull-down menus. I get update.packages () Warning: unable to access index for repository http://cran.uk.r- project.org/bin/macosx/universal/contrib/2.5 Basically it still seems unable to access port 80. Is there a way of solving this so that I can use both terminals rather than just everything through Bash? Thanks Steve Hodgkinson University of Brighton __ 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.
Re: [R] Running R function as a Batch process
d. sarthi maheshwari wrote: Hi, I am struggling with using R CMD BATCH command. Kindly suggest solution to the following problem. I have a function named CinC with accept two input parameters. This can be shown as: CinC - function(start, end) where start and end both are character strings. Please suggest me how can I run this function using command R CMD BATCH. Currently I am trying to do like this - R CMD BATCH c:/tt/CinC.r c:/tt/h.Rout -20070416 08:41 -20070416 10:33 What is wrong/incorrect with it? You should use the function commandArgs in your code to retrieve supplied arguments from the command line. Look at ?commandArgs ?Startup Your R invokation should look like this C:\ R CMD BATCH c:/tt/CinC.r c:/tt/h.Rout --args 20070416 08:41 20070416 10:33 And you should add something like this in your R code command.args-commandArgs(trailingOnly=TRUE) CinC(command.args[1],command.args[2]) -- View this message in context: http://www.nabble.com/Running-R-function-as-a-Batch-process-tf3764048.html#a10640433 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] Running R function as a Batch process
Hi,
There are many clues in the help.
First I created the file c:\sumfunction.R
x-as.numeric(commandArgs()[-1:-4] )
print(x)
addtogether-function(x,y){SUM-x+y;print(SUM)}
addtogether(x[1],x[2])
Then at the command line in Windows I enter
R --vanilla --slave --args 7 10 c:\sumfunction.R c:\logout.txt
Regards
Alex
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of d. sarthi
maheshwari
Sent: May 16, 2007 8:29 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Running R function as a Batch process
Hi,
I am struggling with using R CMD BATCH command. Kindly suggest solution
to the following problem.
I have a function named CinC with accept two input parameters. This can
be shown as:
CinC - function(start, end)
where start and end both are character strings.
Please suggest me how can I run this function using command R CMD BATCH.
Currently I am trying to do like this - R CMD BATCH c:/tt/CinC.r
c:/tt/h.Rout -20070416 08:41 -20070416 10:33
What is wrong/incorrect with it?
Your suggestions are important to me. Kindly reply.
Thanks in advance.
Regards
Divya Sarthi
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] running R without X11
On Tue, 14 Nov 2006, Laurence Darby wrote: Hello, I'm trying to run R from a webserver, which doesn't have an X server, and produce pngs to go on a webpage, is this possible? Yes, see the help page for png. I'm doing it in gnuplot with gnuplot set term png gnuplot set output With $DISPLAY unset, I get the following error from R: png() Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: unable to open connection to X11 display '' Is there anyway to remove this dependency on X11? Please read the help page. R's png device uses X11 for its fonts. You need fonts from somewhere, and vanilla Unix systems don't come with any other sets. You can use ghostscript or libgdd or other resources for other graphics devices. I normally just use an Xvfb frame buffer (but, hint, it defaults to 12bit and you want a 24bit screen). -- 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] running R without X11
Prof Brian Ripley wrote: On Tue, 14 Nov 2006, Laurence Darby wrote: Is there anyway to remove this dependency on X11? Please read the help page. R's png device uses X11 for its fonts. You need fonts from somewhere, and vanilla Unix systems don't come with any other sets. You can use ghostscript or libgdd or other resources for other graphics devices. I normally just use an Xvfb frame buffer (but, hint, it defaults to 12bit and you want a 24bit screen). Thanks for your prompt answer, although getting gs to work the way I want or setting up Xvfb, on top of learning R, is too many hoops to jump through, much more than reproducing a small R script I have in gnuplot. Laurence __ 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] running R without X11
Laurence Darby wrote: Prof Brian Ripley wrote: On Tue, 14 Nov 2006, Laurence Darby wrote: Is there anyway to remove this dependency on X11? Please read the help page. R's png device uses X11 for its fonts. You need fonts from somewhere, and vanilla Unix systems don't come with any other sets. You can use ghostscript or libgdd or other resources for other graphics devices. I normally just use an Xvfb frame buffer (but, hint, it defaults to 12bit and you want a 24bit screen). Thanks for your prompt answer, although getting gs to work the way I want or setting up Xvfb, on top of learning R, is too many hoops to jump through, much more than reproducing a small R script I have in gnuplot. You can also use Simon Urbanek's GDD or Cairo packages, located on CRAN and on www.rosuda.org/R. They both create png's without an X server. Currently, there are issues with GDD: minimal truetype font support, an inability to draw lines thicker than lwd=1, and the worst is it's dependence on the neglected libgd graphics library, but apparently there's been some active development on it. Check www.libgd.org. I'm currently adding truetype font support and some antialiasing properties to the Cairo package, for the sole purpose of creating better graphics for the web. Cairo probably has a longer future as it depends on cairo (www.cairographics.org) which is used in the Firefox browser. Jeff -- http://biostat.mc.vanderbilt.edu/JeffreyHorner __ 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] Running R on a 64 bit processor
Be careful not to use clock speed as a measure of computer performance. Pentium 4s (and the comparable Xeons) were intended to be run very fast, but never managed it. So a 2.4GHz P4 proved to be slower than a 1GHz PIII. Unless you are running Windows 64, the chip having some 64-bit instructions is irrelevant, and even if you were it is irrelevant to binary builds of R for Windows (which will actually access less memory than is possible under 32-bit Windows XP). R runs large tasks much better under Linux, and there having a 64-bit CPU and 64-bit OS pay off once you have 2Gb or more of RAM. On Fri, 28 Jul 2006, Lewis G Coggins wrote: Greetings, We recently obtained a new computer in our lab with a Pentium 4 3.86 GHz processor and 4 gb of ram running windows xp with service pack 2. After installing R on this machine, I ran a bit of code and found that the execution time was actually significantly slower than a machine running windows xp with an older Pentium chip 1.73 GHz and 1 gb of ram. After speaking with the manufacturer of the new machine, I am told that the processor in the new machine is 64 bit whereas I believe the processor in the old machine is 32 bit. I have tried to sort through the documentation on the CRAN page relative to performance of R under the 32 vs 64 bit sub architecture, however, I am no computer genius and find some of this stuff extremely confusing. Well, it is under the Unix/Linux section, and you are running Windows so it does not apply to you. In a CRAN document entitled Installation and Administration , there is reference to sub architecture... it reads: 8.1 Windows Currently the Windows build of R is a 32-bit executable. This runs happily on Windows 64 on AMD64 and EM64T, but is limited to (we are told) a 2GB address space. It will not be possible to build a native version for Windows 64 until suitable compilers are available, and currently (mid-2006) that is not in prospect. So my question is: are there any options to allow R to take advantage of the faster chip, (with 64 bit architecture), and more ram. I see in the documentation that a linux version of R may be able to take advantage of this chip... is that true what would be involved in making that work? Are there other options? As we are beginning to use R more and more around here, we may send this computer back and get a celeron 3.2 GHz chip that has 32 bit architecture... is this an intelligent choice? Thanks in advance for considering my question, Lew Coggins [[alternative HTML version deleted]] __ 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] Running R as root
[EMAIL PROTECTED] writes: Hello Using R v. 2.3.1 which I installed recently, when I start it as root, there is nothing I can do. I get Error: function xx not found even when trying to leave R using q(). R works fine when started by an ordinary user. I rechecked the root environment several times and even have set it similar to that of an ordinary user (values of PATH etc.) but nothing helps. Using the command env did not reveal anything valuable. Going to root through the identity of an ordinary user and retaining his environment by doing su user instead of su - user does not help either. This does not seem related to the particular version of R. Using: Linux RedHat AS 2.1 Any hint? File permissions? (it is possible to set them so that files can be read by anyone except the user...) How exactly did you install R, and are there any other clues upon startup? I get, BTW aa() Error: could not find function aa so I suspect you paraphrased the error message. One other thing that can cause trouble is networked directories. Files that are physically on another machine can sometimes not be accessed by root on the local machine. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Running R
Does any one have solution for R not running? I am getting the error message. Please Advice. Thanks 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar 3. changed the directory to the newly created directory R-patched 4. Typed ./configure 5. Typed make 6. Make check 7. make check-all 8. Typed make install *9. Typed R # R Fatal error: unable to open the base package __ 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] Running R
Have you checked and see if there is any error in steps 5 through 8? If you can't start R, I doubt steps 6 and 7 ran fine. Andy From: Pramod Anugu Does any one have solution for R not running? I am getting the error message. Please Advice. Thanks 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar 3. changed the directory to the newly created directory R-patched 4. Typed ./configure 5. Typed make 6. Make check 7. make check-all 8. Typed make install *9. Typed R # R Fatal error: unable to open the base package __ 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] Running R
On Fri, Jun 30, 2006 at 07:56:41AM -0500, Pramod Anugu wrote: Does any one have solution for R not running? I am getting the error message. Please Advice. Yes, you have emailing the group fairly regularly about your troubles. And you have been told just about each and every time to *check the output of the configure step*. Unless that step concludes with all relevant pieces found, *there is no point in resuming with steps 5 to 9*. As you are emailing from an educational institution, consider getting local help about configuring and compiling software. Building R is *extensively documented in a dedicated manual* but the manual may need someone with more familiarity with the process than you currently have. Good luck, and consider to stop sending the *same* email to the list every couple of days. Dirk Thanks ? ? 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar ?? 3. changed the directory to the newly created directory R-patched ?? 4. Typed ./configure ? ?5. Typed make ?? 6. Make check ?? 7. make check-all ?? 8. Typed make install ?? *9. Typed R # R Fatal error: unable to open the base package __ 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 -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ 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] Running R
Just for the record. (One of the) problem was that configure picked up ATLAS, but had problem with it at link time for whatever reason. (This is on some version of Redhat, x86_64. I should think there are people who have similar setup and got both ATLAS and readline to work.) Andy From: Pramod Anugu IT WORKS!!! Thanks you very much for your help. So the below line fixed my installation #./configure --with-blas=no --with-readline=no __ 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] Running R [Broadcast]
You have two choices (AFAIK): 1. Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). 2. Compile R without readline; i.e., configure --with-readline=no. Andy _ From: [EMAIL PROTECTED] on behalf of Pramod Anugu Sent: Wed 6/28/2006 4:18 PM To: r-help@stat.math.ethz.ch Subject: Re: [R] Running R [Broadcast] [EMAIL PROTECTED] R-2.3.0]# ./configure checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-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 working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking for working makeinfo... found checking for gawk... gawk checking for egrep... grep -E checking whether ln -s works... yes checking for ranlib... ranlib checking for bison... no checking for byacc... no checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for less... /usr/bin/less checking for perl... /usr/bin/perl checking whether perl version is at least 5.004... yes checking for dvips... /usr/bin/dvips checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeinfo... /usr/bin/makeinfo checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for firefox... /usr/bin/firefox using default browser ... /usr/bin/firefox checking for acroread... no checking for acroread4... no checking for xpdf... no checking for gv... no checking for gnome-gv... no checking for ggv... /usr/bin/ggv checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc accepts -fvisibility... yes checking whether g77 accepts -fvisibility... yes checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ranlib... (cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m
Re: [R] Running R [Broadcast]
Liaw, Andy [EMAIL PROTECTED] writes: You have two choices (AFAIK): 1. Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). 2. Compile R without readline; i.e., configure --with-readline=no. Andy But first check sequencing - I'm pretty sure that configure can find header files on RedHat if they are there. He's not too good at interpreting his output: --One suggestion was to install readline-devel. But according to the below I already have readline-devel. # find . -iname readline-devel\* find -iname readline-devel\* ./os/4.1/x86_64/RedHat/RPMS/readline-devel-4.3-13.x86_64.rpm #rpm -ivh readline*.rpm Preparing...### [100%] package readline-4.3-13 is already installed and as far as I can see, this means that readline-devel got installed and readline (NOT -devel) was there already. So readline-devel is there now, but wasn't there before. Now did he rerun configure? If so, did it fail with a different message? -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Running R
Thank you Andy for your suggestion. I used the method 2 and was able to go upto Step 8. But When I type R # R Fatal error: unable to open the base package 1. Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). 2. Compile R without readline; i.e., configure --with-readline=no. Andy 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar 3. changed the directory to the newly created directory R-patched 4. Typed ./configure 5. Typed make 6. Make check 7. make check-all 8. Typed make install *9. Typed R __ 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] Running R
1. tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make make: *** No targets specified and no makefile found. Stop. I cannot run make. Please let me know. #gcc -v Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.4/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux Thread model: posix gcc version 3.4.4 20050721 (Red Hat 3.4.4-2) *5. Make check *6. make check-all *7. Typed make install *8. Typed R [[alternative HTML version deleted]] __ 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] Running R
Pramod Anugu [EMAIL PROTECTED] writes: 1. tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure and what happened here??? Presumably an error since no Makefile was created. 4. Typed make make: *** No targets specified and no makefile found. Stop. I cannot run make. Please let me know. #gcc -v Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.4/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux Thread model: posix gcc version 3.4.4 20050721 (Red Hat 3.4.4-2) *5. Make check *6. make check-all *7. Typed make install *8. Typed R [[alternative HTML version deleted]] __ 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 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Running R
[EMAIL PROTECTED] R-2.3.0]# ./configure checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-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 working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking for working makeinfo... found checking for gawk... gawk checking for egrep... grep -E checking whether ln -s works... yes checking for ranlib... ranlib checking for bison... no checking for byacc... no checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for less... /usr/bin/less checking for perl... /usr/bin/perl checking whether perl version is at least 5.004... yes checking for dvips... /usr/bin/dvips checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeinfo... /usr/bin/makeinfo checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for firefox... /usr/bin/firefox using default browser ... /usr/bin/firefox checking for acroread... no checking for acroread4... no checking for xpdf... no checking for gv... no checking for gnome-gv... no checking for ggv... /usr/bin/ggv checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc accepts -fvisibility... yes checking whether g77 accepts -fvisibility... yes checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ranlib... (cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag F77 to libtool checking if libtool supports
Re: [R] running R in batch with stdin input
?commandArgs On Thu, 2006-06-15 at 16:05 -0700, Eric Hu wrote: Hi I have a R script that needs to run a few times for different systems. I use R --no-save r.script for one system. I am trying with no luck to use R CMD BATCH to introduce an stdin input variable for the script. I wonder if anyone can provide the correct usage to put the variable in the command like R CMD BATCH r.script name_variable. Thanks. -Eric In the r.script I have name - readline(/dev/stdin) r0 - read.table(/usr/local/surface/$name/$name_c_r) ... I want to get at the end: name - 1BRS r0 - read.table(/usr/local/surface/1BRS/1BRS_c_r) ... __ 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice [[alternative HTML version deleted]] __ 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] Running R
At step 5, don't copy the file. Instead, do: make install -- Andrew J Perrin - andrew_perrin (at) unc.edu - http://perrin.socsci.unc.edu Assistant Professor of Sociology; Book Review Editor, _Social Forces_ University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl On Wed, 31 May 2006, Pramod Anugu wrote: I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice [[alternative HTML version deleted]] __ 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R
On 05/31/06 09:25, Pramod Anugu wrote: I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R The instructions say that you should use make install unless you want to run R from the directory into which you unpacked it. Fatal error: unable to open the base package I get the error message. Please advice If you are using Fedora Core 5, the RPM works well. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ 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] Running R
Still the same problem after changing the step 5 I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Typed make install 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice -Original Message- From: Andrew Perrin [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 31, 2006 9:33 AM To: Pramod Anugu Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Running R At step 5, don't copy the file. Instead, do: make install -- Andrew J Perrin - andrew_perrin (at) unc.edu - http://perrin.socsci.unc.edu Assistant Professor of Sociology; Book Review Editor, _Social Forces_ University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl On Wed, 31 May 2006, Pramod Anugu wrote: I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice [[alternative HTML version deleted]] __ 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R
It's always a good idea to do make check or even make check-all before make install. If the build does not pass the checks, there's no point in installing. (I've run into successful builds that failed the checks several times before.) Andy From: Pramod Anugu Still the same problem after changing the step 5 I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Typed make install 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice -Original Message- From: Andrew Perrin [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 31, 2006 9:33 AM To: Pramod Anugu Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Running R At step 5, don't copy the file. Instead, do: make install -- Andrew J Perrin - andrew_perrin (at) unc.edu - http://perrin.socsci.unc.edu Assistant Professor of Sociology; Book Review Editor, _Social Forces_ University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl On Wed, 31 May 2006, Pramod Anugu wrote: I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice [[alternative HTML version deleted]] __ 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 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R
On 05/31/06 09:39, Pramod Anugu wrote: 5. Typed make install 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice Other things to try (aside from make check): 1. Make sure you are root before you say make install. 2. Check to see that the packages really got installed, after make install: ls /usr/local/lib/R/ (should have several directories) 3. Open a new terminal window before you type R. (Sometimes that matters.) 4. Look at config.log. The make may not have even worked. There are many dependencies. Sometimes you need other programs, as described in the installation and administration manual. Jon __ 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] Running R
Still the same problem after the changes
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor
1. tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
5. Make check
6. make check-all
7. Typed make install
8. Typed R
Fatal error: unable to open the base package
I get the error message.
make[4]: *** No rule to make target `../../src/library/base/all.R', needed
by `base-Ex.Rout'. Stop.
make[4]: Leaving directory `/root/downloads/R-2.3.0/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/root/downloads/R-2.3.0/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/root/downloads/R-2.3.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/root/downloads/R-2.3.0/tests'
make: *** [check] Error 2
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED]
Sent: Wednesday, May 31, 2006 10:07 AM
To: [EMAIL PROTECTED]; 'Andrew Perrin'
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] Running R
It's always a good idea to do
make check
or even
make check-all
before make install. If the build does not pass the checks, there's no
point in installing. (I've run into successful builds that failed the
checks several times before.)
Andy
From: Pramod Anugu
Still the same problem after changing the step 5
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor
1. Untar tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
5. Typed make install
6. Typed R
Fatal error: unable to open the base package
I get the error message. Please advice
-Original Message-
From: Andrew Perrin [mailto:[EMAIL PROTECTED]
Sent: Wednesday, May 31, 2006 9:33 AM
To: Pramod Anugu
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Running R
At step 5, don't copy the file. Instead, do:
make install
--
Andrew J Perrin - andrew_perrin (at) unc.edu -
http://perrin.socsci.unc.edu
Assistant Professor of Sociology; Book Review Editor, _Social Forces_
University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA
New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl
On Wed, 31 May 2006, Pramod Anugu wrote:
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor
1. Untar tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
5. Copied the Script File R from directory R-2.3.0/bin/R to
/usr/local/bin/R.
6. Typed R
Fatal error: unable to open the base package
I get the error message. Please advice
[[alternative HTML version deleted]]
__
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
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Notice: This e-mail message, together with any attachments,...{{dropped}}
__
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] Running R [Broadcast]
In the R-2.3.0 directory, what do you get if you type bin/R? Does R starts
up OK, or do you get an error? What were the last few lines of output from
running configure?
Andy
_
From: Pramod Anugu [mailto:[EMAIL PROTECTED]
Sent: Wednesday, May 31, 2006 11:23 AM
To: Liaw, Andy; 'Andrew Perrin'
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] Running R [Broadcast]
Still the same problem after the changes
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor
1. tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
5. Make check
6. make check-all
7. Typed make install
8. Typed R
Fatal error: unable to open the base package
I get the error message.
make[4]: *** No rule to make target `../../src/library/base/all.R', needed
by `base-Ex.Rout'. Stop.
make[4]: Leaving directory `/root/downloads/R-2.3.0/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/root/downloads/R-2.3.0/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/root/downloads/R-2.3.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/root/downloads/R-2.3.0/tests'
make: *** [check] Error 2
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ]
Sent: Wednesday, May 31, 2006 10:07 AM
To: [EMAIL PROTECTED]; 'Andrew Perrin'
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] Running R
It's always a good idea to do
make check
or even
make check-all
before make install. If the build does not pass the checks, there's no
point in installing. (I've run into successful builds that failed the
checks several times before.)
Andy
From: Pramod Anugu
Still the same problem after changing the step 5
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor
1. Untar tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
5. Typed make install
6. Typed R
Fatal error: unable to open the base package
I get the error message. Please advice
-Original Message-
From: Andrew Perrin [mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] ]
Sent: Wednesday, May 31, 2006 9:33 AM
To: Pramod Anugu
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Running R
At step 5, don't copy the file. Instead, do:
make install
--
Andrew J Perrin - andrew_perrin (at) unc.edu -
http://perrin.socsci.unc.edu http://perrin.socsci.unc.edu
Assistant Professor of Sociology; Book Review Editor, _Social Forces_
University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA
New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl
http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl
On Wed, 31 May 2006, Pramod Anugu wrote:
I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor
1. Untar tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
5. Copied the Script File R from directory R-2.3.0/bin/R to
/usr/local/bin/R.
6. Typed R
Fatal error: unable to open the base package
I get the error message. Please advice
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
http://www.R-project.org/posting-guide.html
--
Notice: This e-mail message, together with any attachments,...{{dropped}}
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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
Re: [R] Running R
Jonathan Baron wrote: 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R The instructions say that you should use make install unless you want to run R from the directory into which you unpacked it. Another idea is to have a symlink (here assuming your R was unpacked in /usr/local/src/R-2.3.0): ln -s /usr/local/src/R-2.3.0/bin/R /usr/local/bin/R which essentially runs R from that R-2.3.0 directory. But the 'make install' solution has the advantage that you can delete the source directory where you did the make step to clear out the source and save some disk space. Barry __ 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] Running R
Under the below seection it talks about X86_64 archetecture for Linux.
1. tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure 'r_arch=name'
4. Typed make
5. Make check
6. make check-all
7. Typed make install
8. Typed R
I still get the same error message.
Fatal error: unable to open the base package
2.5 Sub-architectures
Some platforms can support closely related builds of R which can share all
but the executables and dynamic objects. Examples include builds under
Solaris for different chips (in particular, 32- and 64-bit builds), 64- and
32- bit builds on `x86_64' Linux and different CPUs (`ppc', `ppc64' and
`i386') under MacOS 10.4.
R supports the idea of architecture-specific builds, specified by adding
`r_arch=name' to the configure line. Here name can be anything non-empty,
and is used to name subdirectories of lib, etc, include and libs. Example
names from other systems are the use of sparcv9 on Solaris and 32 by gcc on
`x86_64' Linux.
If you have two or more such builds you can install them over each other
(and one build can be done without `r_arch'). The space savings can be
considerable: on `x86_64' Linux a basic install (without debugging symbols)
took 63Mb, and adding a 32-bit build added 6Mb. If you have installed
multiple build you can select which build to run by
R --arch=name
and running `R' will run the last build that was installed.
R CMD INSTALL will detect if more that one build is installed and try to
install packages with the appropriate library objects for each. This will
not be done if the package has an executable configure script or a
src/Makefile file. In such cases you can install for extra builds by
R --arch=name CMD INSTALL --libs-only pkg(s)
-
My Server Archeitecute is X86_64
-bash-2.05b# rpm -q --qf '%{ARCH}\n' zlib
x86_64
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R on Windows 2000 Terminal Services
Barry Rowlingson wrote: Gavin Simpson wrote: Dear list, My employer uses a Windows 2000 Terminal Server-based system for its college-wide managed computer service - computers connect directly to the WTS servers for their sessions, using a Citrix ICA client. When I asked them to install R (Windows) on an older version of this service the IT guys installed it but pulled it for performance issues. I am trying to get them to try again but receiving little encouragement from them. 'performance issues'? Well, if you have 100 students running MCMC simulations on one Windows 2000 TS box then you may well have 'performance issues'! Perhaps the TS service isn't intended for people to do real computer work on, but is just for Office apps. Then you come along and want your students to do serious number crunching. At that point the MS Word writers experience what we used to call 'lag'. Does anyone on the list have experience of a similar set-up? If you do, I could use that as part of my argument to invest some time in sorting these issues out. I really want to get the Windows version of R installed for teaching because at the moment I subject my students to the rather hostile world of an archaic UNIX session to run R - for them at least. We have a couple of labs that are similar - we use Wyse Thin Client Xterminals which boot Thinstation Linux from a server and then connect to Windows 2003 TS machines using RDP or Ubuntu Linux boxes using XDMCP. We dont use Citrix ICA. 'Performance issues' will depend very much on what you are doing. As a quick benchmark, last term we had 24 users in a lab all running Windows and running Matlab, Firefox, that kind of stuff. One dual 2.6GHz Xeon Dell with 4G Ram never went above 60% CPU usage. And we had another three similar Dells sitting idle waiting for installation. Sessions with R run regularly in these labs and we've never had 'performance issues'. Back in September there was some issue with your setup, but I forget the details. Do you remember? Is it something we ended up working around, or did the 2.2 release fix it? Duncan So possibly your IT support are stalling. Do they regularly say Have you tried switching it off and on again? in response to a support query [1]? Barry [1] Catchphrase of the tech support guys in comedy series 'The IT Crowd' __ 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R on Windows 2000 Terminal Services
Gavin Simpson wrote: Dear list, My employer uses a Windows 2000 Terminal Server-based system for its college-wide managed computer service - computers connect directly to the WTS servers for their sessions, using a Citrix ICA client. When I asked them to install R (Windows) on an older version of this service the IT guys installed it but pulled it for performance issues. I am trying to get them to try again but receiving little encouragement from them. 'performance issues'? Well, if you have 100 students running MCMC simulations on one Windows 2000 TS box then you may well have 'performance issues'! Perhaps the TS service isn't intended for people to do real computer work on, but is just for Office apps. Then you come along and want your students to do serious number crunching. At that point the MS Word writers experience what we used to call 'lag'. Does anyone on the list have experience of a similar set-up? If you do, I could use that as part of my argument to invest some time in sorting these issues out. I really want to get the Windows version of R installed for teaching because at the moment I subject my students to the rather hostile world of an archaic UNIX session to run R - for them at least. We have a couple of labs that are similar - we use Wyse Thin Client Xterminals which boot Thinstation Linux from a server and then connect to Windows 2003 TS machines using RDP or Ubuntu Linux boxes using XDMCP. We dont use Citrix ICA. 'Performance issues' will depend very much on what you are doing. As a quick benchmark, last term we had 24 users in a lab all running Windows and running Matlab, Firefox, that kind of stuff. One dual 2.6GHz Xeon Dell with 4G Ram never went above 60% CPU usage. And we had another three similar Dells sitting idle waiting for installation. Sessions with R run regularly in these labs and we've never had 'performance issues'. So possibly your IT support are stalling. Do they regularly say Have you tried switching it off and on again? in response to a support query [1]? Barry [1] Catchphrase of the tech support guys in comedy series 'The IT Crowd' __ 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] Running R on Windows 2000 Terminal Services
On Tue, 2006-04-25 at 17:32 +0100, Barry Rowlingson wrote: Gavin Simpson wrote: Dear list, My employer uses a Windows 2000 Terminal Server-based system for its college-wide managed computer service - computers connect directly to the WTS servers for their sessions, using a Citrix ICA client. When I asked them to install R (Windows) on an older version of this service the IT guys installed it but pulled it for performance issues. I am trying to get them to try again but receiving little encouragement from them. 'performance issues'? Well, if you have 100 students running MCMC simulations on one Windows 2000 TS box then you may well have 'performance issues'! I think they meant more along the lines of one user running it - doing nothing with R as the guys don't know how to use R - was causing issues, rather than CPU load hitting 100% across all the 4-8 processors per server (and there are lots of servers) Perhaps the TS service isn't intended for people to do real computer work on, but is just for Office apps. Then you come along and want your students to do serious number crunching. At that point the MS Word writers experience what we used to call 'lag'. The system has SPSS, various Adobe products (Photoshop Illustrator) and tonnes of other apps I would consider more number crunching than R, so I don't think this was a problem. I was deliberately vague as I don't know what the actual problem was - we aren't allowed to know who these IT people R but I have asked to speak to one of the WTS people to see what the problem is. If I turn up anything I'll email R-Devel to see if this is an R thing or a local thing. Does anyone on the list have experience of a similar set-up? If you do, I could use that as part of my argument to invest some time in sorting these issues out. I really want to get the Windows version of R installed for teaching because at the moment I subject my students to the rather hostile world of an archaic UNIX session to run R - for them at least. We have a couple of labs that are similar - we use Wyse Thin Client Xterminals which boot Thinstation Linux from a server and then connect to Windows 2003 TS machines using RDP or Ubuntu Linux boxes using XDMCP. We dont use Citrix ICA. 'Performance issues' will depend very much on what you are doing. As a quick benchmark, last term we had 24 users in a lab all running Windows and running Matlab, Firefox, that kind of stuff. One dual 2.6GHz Xeon Dell with 4G Ram never went above 60% CPU usage. And we had another three similar Dells sitting idle waiting for installation. Sessions with R run regularly in these labs and we've never had 'performance issues'. Thanks for this Barry - so we aren't talking about an incompatibility per se with WTS. So possibly your IT support are stalling. Do they regularly say Have you tried switching it off and on again? in response to a support query [1]? Once you speak to the IT guys themselves they are incredibly helpful and knowledgeable - getting to speak to them is more difficult Barry [1] Catchphrase of the tech support guys in comedy series 'The IT Crowd' That was a funny show... Cheers, G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% * Note new Address, Telephone Fax numbers from 6th April 2006 * %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson ECRC ENSIS [t] +44 (0)20 7679 0522 UCL Department of Geography [f] +44 (0)20 7679 0565 Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street [w] http://www.ucl.ac.uk/~ucfagls/cv/ London, UK. [w] http://www.ucl.ac.uk/~ucfagls/ WC1E 6BT. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] Running R from Perl program
A quick search of the archives (http://finzi.psych.upenn.edu/nmz.html) produces several hits. Just one example: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/24327.html Sean On May 10, 2005, at 7:26 AM, Tarun Kumar Singh wrote: Hi all, Is it possoble to include an R function in a Perl program? I would like to use the limma library for microarray analysis, and have no clue how this can be done. Thanks in Advance -Tarun __ 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Running R from Perl program
Well, after reviewing all the available options about 2 years ago, I decided on the traditional perl option of opening up a pipe to R from within perl and simply firing commands at it. This worked for me because all I wanted to do was create images. If you want to get back the results of an analysis, say from topTable() in limma, then you can write the results of that out to a temporary file and read that in using perl. All very cumbersome, but it works :-) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis Sent: 10 May 2005 12:39 To: Tarun Kumar Singh Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Running R from Perl program A quick search of the archives (http://finzi.psych.upenn.edu/nmz.html) produces several hits. Just one example: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/24327.html Sean On May 10, 2005, at 7:26 AM, Tarun Kumar Singh wrote: Hi all, Is it possoble to include an R function in a Perl program? I would like to use the limma library for microarray analysis, and have no clue how this can be done. Thanks in Advance -Tarun __ 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 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R from CD?
On Mon, 22 Nov 2004, Prof Brian Ripley wrote: [...] BTW, I believe running R 2.0.x from a CD will be a lot slower than 1.9.1 because of lazy loading and frequent file accesses: that's a theoretical issue we intend to address for 2.1.0, but not one anyone has yet commented that it is a problem. I collected some data (under Windows XP). On a modern desktop, running R from a CD-R or from a USB 2.0 thumbdrive was perfectably acceptable, with startup times of about 5 secs and little delay when running. On a 2.5year old laptop with a USB 1.1 port (but the same thumbdrive) it took about 15secs to start and with frequent delays the first time an object was used -- I would not find that tolerable. The laptop's CD drive was slower than the desktop and there were delays when it powered down, but it was acceptable. This was less performance penalty than I was expecting, and less than I have seen on a high-latency network file system. So it looks as if all we can do is trade a slower startup time (by caching files) for removing hiatuses when running. (Caching the pkg.rdb and pkg.rdx files when a package is opened would probably only take up a little over 1Mb in a typical session.) Writing to the thumbdrive took about 20mins, as R has so many small files and the drive has a VFAT file system. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R from CD?
On Mon, 2004-11-22 at 02:41, bogdan romocea wrote: Better install and run R from a USB flash drive. This will save you the trouble of re-writing the CD as you upgrade and install new packages. Also, you can simply copy the R installation on your work computer (no install rights needed); R will run. I think there is a niche (= a hole in the wall) for a live CD: it is cheaper to distribute 20 copies of CD's to your audience than 20 USB memory sticks. Instructions would be welcome. From: Hans van Walen hans_at_vanwalen.com At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Check the file Getting-Started-with-the-Rcmdr.pdf in John Fox's Rcmdr package. You should be able to reach this package by launching help.start(), and then browsing its directory in the help browser window. Go to chapter 7. Some Suggestions for Instructors which tells you how to make a live CD of R in Windows. I haven't tried this, since I don't have Windows, but I sure will when I got to be an instructor in a Windows class. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] 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] Running R from CD?
Dear Jari, When I distribute an R Windows CD/ROM to students, I generally include both the installer and an installed version. This allows students who don't want to or can't install the software to use it. They pay a big penalty in speed, however. A flash drive would provide better performance if this is a viable option. It's not really necessary to do anything as elaborate as in my Rcmdr instructions if the CD is for one's own use: Just install to the CD (copy over installed versions of whatever contributed packages you want to use) and run rgui.exe from it. Regards, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jari Oksanen Sent: Monday, November 22, 2004 3:42 AM To: bogdan romocea Cc: [EMAIL PROTECTED]; R-News Subject: Re: [R] Running R from CD? On Mon, 2004-11-22 at 02:41, bogdan romocea wrote: Better install and run R from a USB flash drive. This will save you the trouble of re-writing the CD as you upgrade and install new packages. Also, you can simply copy the R installation on your work computer (no install rights needed); R will run. I think there is a niche (= a hole in the wall) for a live CD: it is cheaper to distribute 20 copies of CD's to your audience than 20 USB memory sticks. Instructions would be welcome. From: Hans van Walen hans_at_vanwalen.com At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Check the file Getting-Started-with-the-Rcmdr.pdf in John Fox's Rcmdr package. You should be able to reach this package by launching help.start(), and then browsing its directory in the help browser window. Go to chapter 7. Some Suggestions for Instructors which tells you how to make a live CD of R in Windows. I haven't tried this, since I don't have Windows, but I sure will when I got to be an instructor in a Windows class. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] 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] Running R from CD?
Let's be a little careful here. An R for Windows installation is relocatable, so you can just install it into a temporary directory and burn a copy of that onto CD. (That may not be true after installing packages into a non-default library.) It is not true of a Unix or MacOS X installation, as far as I am aware, for they have absolute paths coded into the files. However, an R session does need to be able to write to a temporary directory, and also needs a `home' directory and at a last resort the latter defaults to the current directory. So you do need to be running on a machine on which you have a writable area. A policy that says you cannot install a program, but you can run from a CD and you can let such a program write to your area seems full of holes to me. (Ours does not allow low-privilege users to run programs from a CD.) Also, many organizations ban the use of USB drives for security reasons. BTW, I believe running R 2.0.x from a CD will be a lot slower than 1.9.1 because of lazy loading and frequent file accesses: that's a theoretical issue we intend to address for 2.1.0, but not one anyone has yet commented that it is a problem. On Mon, 22 Nov 2004, Jari Oksanen wrote: On Mon, 2004-11-22 at 02:41, bogdan romocea wrote: Better install and run R from a USB flash drive. This will save you the trouble of re-writing the CD as you upgrade and install new packages. Also, you can simply copy the R installation on your work computer (no install rights needed); R will run. I think there is a niche (= a hole in the wall) for a live CD: it is cheaper to distribute 20 copies of CD's to your audience than 20 USB memory sticks. Instructions would be welcome. From: Hans van Walen hans_at_vanwalen.com At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Check the file Getting-Started-with-the-Rcmdr.pdf in John Fox's Rcmdr package. You should be able to reach this package by launching help.start(), and then browsing its directory in the help browser window. Go to chapter 7. Some Suggestions for Instructors which tells you how to make a live CD of R in Windows. I haven't tried this, since I don't have Windows, but I sure will when I got to be an instructor in a Windows class. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Running R from CD?
I have noticed that R 2.0 did run slower than I thought it should. It's only now that you've raised the issue that I realise how much slower. However since I only use the CD when I am working on other people's machines I can't really say if there are other factors impacting upon the performance. I'll dig up the old disk, make some comparisons and forward the results. The bottom line is that it is not a big issue for me. Tom Mulholland -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] ... Subject: Re: [R] Running R from CD? ... BTW, I believe running R 2.0.x from a CD will be a lot slower than 1.9.1 because of lazy loading and frequent file accesses: that's a theoretical issue we intend to address for 2.1.0, but not one anyone has yet commented that it is a problem. __ [EMAIL PROTECTED] 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] Running R from CD?
Better install and run R from a USB flash drive. This will save you the trouble of re-writing the CD as you upgrade and install new packages. Also, you can simply copy the R installation on your work computer (no install rights needed); R will run. HTH, b. From: Hans van Walen hans_at_vanwalen.com Date: Fri 27 Aug 2004 - 23:54:53 EST At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Thank you for your help, Hans van Walen __ [EMAIL PROTECTED] 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] Running R on a grid engine
See comments below.
On Thu, 2004-10-28 at 18:49, S Peri wrote:
Dear Group,
I am using DEAL package for modeling signal
transduction nets. This process is deal slow on a
SunFire server with 8 gigs ram.
we have a grid that can process much faster that one
individual server.
However, to start the process in Grid, I have to give
a command or submit a batch process.
Is there any way, I can run R in bach process.
I tried the following:
R CMD | library(deal) | data -
data.frame(read.table('file1',header=TRUE,
row.names=1))
Something like this works in *NIX
echo print(mean(rnorm(10))) | R --no-save
HOWEVER you will run into nightmares soon trying to backslash all the
quotes and other special characters. And try to recall a long sequence
of commands you typed in a few days ago ...
Better to put all your codes into a file, say script.R and do
R --no-save script.R log_script.R
See help(BATCH).
Here I do not know know :
1. How can I point my data files to a function.
Two ways :
1) Hard code the path inside the script.R
2) Take advantage of commandArgs().
Example. If your script.R contains
data.path - as.character( commandArgs()[3] )
print(data.path)
load (data.path) # or read.delim or whatever
Then you can pass the path to test.rda via command line
R --no-save script.R /home/speri/data/test.rda log_script.R
One thing to keep in mind is to pass the absolute paths and not relative
paths (e.g. ../../data/test.rda). Using relative path may not always
work.
2. creating a function (other than in R environment)
Huh ? You can put all your functions into a file, say functions.R, and
you can source(/path/to/functions.R) in your script.R/
Could any one help me.
Thank you in advance.
Cheers
Peri.
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RE: [R] Running R on a grid engine
Does the grid process faster because there is more than one machine or
because each machine (or at least one machine) is faster? If the former,
you're asking about splitting an R process into several processes (to take
advantage of the grid), and you will want to look at the various R packages
to facilitate that: Snow, Rmpi, Rpvm, TaskPR and perhaps others (browse
cran.rproject.org).
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Adaikalavan Ramasamy
Sent: Thursday, October 28, 2004 2:41 PM
To: S Peri
Cc: R-help
Subject: Re: [R] Running R on a grid engine
See comments below.
On Thu, 2004-10-28 at 18:49, S Peri wrote:
Dear Group,
I am using DEAL package for modeling signal
transduction nets. This process is deal slow on a
SunFire server with 8 gigs ram.
we have a grid that can process much faster that one
individual server.
However, to start the process in Grid, I have to give
a command or submit a batch process.
Is there any way, I can run R in bach process.
I tried the following:
R CMD | library(deal) | data -
data.frame(read.table('file1',header=TRUE,
row.names=1))
Something like this works in *NIX
echo print(mean(rnorm(10))) | R --no-save
HOWEVER you will run into nightmares soon trying to backslash all the
quotes and other special characters. And try to recall a long sequence
of commands you typed in a few days ago ...
Better to put all your codes into a file, say script.R and do
R --no-save script.R log_script.R
See help(BATCH).
Here I do not know know :
1. How can I point my data files to a function.
Two ways :
1) Hard code the path inside the script.R
2) Take advantage of commandArgs().
Example. If your script.R contains
data.path - as.character( commandArgs()[3] )
print(data.path)
load (data.path) # or read.delim or whatever
Then you can pass the path to test.rda via command line
R --no-save script.R /home/speri/data/test.rda log_script.R
One thing to keep in mind is to pass the absolute paths and not relative
paths (e.g. ../../data/test.rda). Using relative path may not always
work.
2. creating a function (other than in R environment)
Huh ? You can put all your functions into a file, say functions.R, and
you can source(/path/to/functions.R) in your script.R/
Could any one help me.
Thank you in advance.
Cheers
Peri.
__
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
[EMAIL PROTECTED] mailing list
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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] Running R from CD?
You can simply start a Linux live distribution including R (for example bio-knoppix) from CD, but you have to restart pc with cd inside. A.S. Alessandro Semeria Models and Simulations Laboratory Montecatini Environmental Research Center (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] 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] Running R from CD?
On Fri, 27 Aug 2004, Hans van Walen wrote: At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Yes, for a suitable definition of `CD'. (You need the extensions which allow long file names and lower-case chars.) You will need some disc area where you unpack the files from the R installer. Then just write the top-level directory (rw1091 or whatever) and all its contents to CD-R. The Windows installation (but not the Unix one) is relocatable as it only uses relative file paths. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R from CD?
Hi! Make a isntallation of R on a PC where it is allowed. Install all packages you need. Burn the installation folder (rw1091) on the CD. Start R by clicking on Rgui.exe in the bin folder (rw1091/bin). Or set a path on the command line to (CD drive letter) :\rw1091\bin Or create a shortcut. This should work. Hope it helps. Eryk Ps. If you need to install afterwards package you have to set R_LIBS to a writable drive. *** REPLY SEPARATOR *** On 8/27/2004 at 3:54 PM Hans van Walen wrote: At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Thank you for your help, Hans van Walen __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] 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] running R UNIX in a mac computer
On Fri, 2004-06-11 at 03:49, Tiago R Magalhaes wrote: Hi to you all My question is: there is a package written in UNIX for which there is no Mac version. I would like to know if it's possible to install the R UNIX version on the MacOSX and run that UNIX package on my Mac (through this UNIX R Vresion on a Mac) I have seen a porfile for r version 1.8.1 on darwin: http://r.darwinports.com/ is that it? aother question related to that if it's possible to use UNIX R in Mac, does anyone know how fast or how slow that is? Tiago, If it is a CRAN package *without* MacOS version, there obviously is a reason for this handicap, and you cannot run the package. If it is a stray package, its developer probably just doesn't have opportunity or will to build a Mac binary, but you can build it yourself if you're lucky. Check the FAQ and ReadMe files with your R/Aqua version to see what you need. With little trouble you can easily use source packages with your Mac R. Many tools are already installed in your OS (perl at least). If the package has only R files, you may be able to install a source package directly. If it has C source code, you should first install MacOS X Developer tools (XCode): it comes with your OS installation CD/DVD, but it is not installed by default. If the package has Fortran source code, you got to find external Fortran compiler: MacOS X ships with C compiler, but without Fortran compiler. See the Mac R FAQ for the best alternatives to find the compiler (this FAQ is installed with your R). Installing a Darwin R orobably won't help you. It needs and uses exactly the same tools to build the packages as R/Aqua. If you can't install a source package in R/Aqua, you cannot install it in R/Darwin, and vice versa. The toolset is the decisive part, not the R shell. I assume that both versions of R are just as fast (or slow). R/Aqua uses highly optimized BLAS for numeric functions, and if R/Darwin uses the same library, it is just as fast. If it doesn't use optimized BLAS, it will be clearly slower. I have installed Linux in Mac, but I found out that R was clearly (20%) slower in Linux than in MacOS in the very same piece of hardware. The main reason seemed to be that Linux R didn't have optimized BLAS because the largest differences were in functions calling svd and qr (I used YellowDog Linux) -- the Linux version took 150%(!) longer to run the same svd-heavy test code. Another reason seemed to be that the Fortran compiler produces much slower code in Linux than in MacOS X (difference about 20%). cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [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] running R UNIX in a mac computer
Hi: Please tell us: which Mac OS are you using? If you are using any of the 10.x, then you should download R-1.9.0 at: http://cran.us.r-project.org/bin/macosx If you have anything older (MacOS 9 or lower), then you should visit: http://cran.us.r-project.org/bin/macos Regards... On Thu, 10 Jun 2004, Tiago R Magalhaes wrote: Hi to you all My question is: there is a package written in UNIX for which there is no Mac version. I would like to know if it's possible to install the R UNIX version on the MacOSX and run that UNIX package on my Mac (through this UNIX R Vresion on a Mac) I have seen a porfile for r version 1.8.1 on darwin: http://r.darwinports.com/ is that it? aother question related to that if it's possible to use UNIX R in Mac, does anyone know how fast or how slow that is? thanks for any help! __ [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 -- Ulises M. Alvarez LAB. DE ONDAS DE CHOQUE FISICA APLICADA Y TECNOLOGIA AVANZADA UNAM [EMAIL PROTECTED] __ [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] running R UNIX in a mac computer
Hola ulisses thank you very much for replying to my posting I am using the last Mac Version: OS X 10.3 Panther I use R in the Mac and it works fine The thing is that I want to use a package that was made in UNIX and I wanted to know how easy it would be to run the UNIX version of R in the Mac so that I can use this package for UNIX... shouldn't you be watching soccer? some of my UNAM friends are nuts for a couple of days already! On Thu, 10 Jun 2004, Ulises Mora Alvarez wrote: Hi: Please tell us: which Mac OS are you using? If you are using any of the 10.x, then you should download R-1.9.0 at: http://cran.us.r-project.org/bin/macosx If you have anything older (MacOS 9 or lower), then you should visit: http://cran.us.r-project.org/bin/macos Regards... On Thu, 10 Jun 2004, Tiago R Magalhaes wrote: Hi to you all My question is: there is a package written in UNIX for which there is no Mac version. I would like to know if it's possible to install the R UNIX version on the MacOSX and run that UNIX package on my Mac (through this UNIX R Vresion on a Mac) I have seen a porfile for r version 1.8.1 on darwin: http://r.darwinports.com/ is that it? aother question related to that if it's possible to use UNIX R in Mac, does anyone know how fast or how slow that is? thanks for any help! __ [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 -- Ulises M. Alvarez LAB. DE ONDAS DE CHOQUE FISICA APLICADA Y TECNOLOGIA AVANZADA UNAM [EMAIL PROTECTED] __ [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] running R UNIX in a mac computer
Hola! If you are already using Panther with R.dmg, then is pretty straight forward to use a Unix package (panther it's a kind of Unix). If the package is already on CRAN, all you have to do is to search the package (either from the command line or from the menus) and then install. If what you are looking for isn't not on CRAN, but it's available as a *.tgz or tar.gz or as a collection of files, you can use Install from local files in the Packages menu. Good look. PS. Yes, I should be watching soccer (I'm getting my degree at the UNAM), but I decided to sacrifice the first half... After all, the final match will be on Sunday and the meeting with my committee is close, very close... Best regards. On Thu, 10 Jun 2004, Tiago R Magalhaes wrote: Hola ulisses thank you very much for replying to my posting I am using the last Mac Version: OS X 10.3 Panther I use R in the Mac and it works fine The thing is that I want to use a package that was made in UNIX and I wanted to know how easy it would be to run the UNIX version of R in the Mac so that I can use this package for UNIX... shouldn't you be watching soccer? some of my UNAM friends are nuts for a couple of days already! On Thu, 10 Jun 2004, Ulises Mora Alvarez wrote: Hi: Please tell us: which Mac OS are you using? If you are using any of the 10.x, then you should download R-1.9.0 at: http://cran.us.r-project.org/bin/macosx If you have anything older (MacOS 9 or lower), then you should visit: http://cran.us.r-project.org/bin/macos Regards... On Thu, 10 Jun 2004, Tiago R Magalhaes wrote: Hi to you all My question is: there is a package written in UNIX for which there is no Mac version. I would like to know if it's possible to install the R UNIX version on the MacOSX and run that UNIX package on my Mac (through this UNIX R Vresion on a Mac) I have seen a porfile for r version 1.8.1 on darwin: http://r.darwinports.com/ is that it? aother question related to that if it's possible to use UNIX R in Mac, does anyone know how fast or how slow that is? thanks for any help! __ [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 -- Ulises M. Alvarez LAB. DE ONDAS DE CHOQUE FISICA APLICADA Y TECNOLOGIA AVANZADA UNAM [EMAIL PROTECTED] -- Ulises M. Alvarez LAB. DE ONDAS DE CHOQUE FISICA APLICADA Y TECNOLOGIA AVANZADA UNAM [EMAIL PROTECTED] __ [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] running R command in the background
This cannot presently be done, as the R internals do not multitask. I am not sure what you would want to happen if the background and foreground commands both tried to write a new version of object `foo', BTW. Allowing multiple execution threads and setReader() as described in the Green Book is a design goal and has been since 2001 at least, so don't expect it soon. It is hard (lots of the code used, e.g. LINPACK, is not reentrant and so needs to be semaphored) and if achieved will need vigilance to keep working. On Fri, 4 Jun 2004, Bickel, David wrote: Is there a way to call an R function to work in the background within the same R session? What I have in mind is the equivalent of adding '' at the end of a UNIX command, so that R can process an intensive command while I execute other R commands. I want to do this in the same R session, rather than with multiple calls to R, so that all my modified objects will stay in the same workspace. I would appreciate any help with this. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R command in the background
You could try looking at the library fork. However, this generally sounds like a bad idea and if you do this, you're kind of asking for trouble with threading issues, as R is not thread-safe. I'm not sure if fork works on all platforms, since I believe it works by running a unix shell command. But it's worth a shot. Best regards, -Andrew --- Prof Brian Ripley [EMAIL PROTECTED] wrote: This cannot presently be done, as the R internals do not multitask. I am not sure what you would want to happen if the background and foreground commands both tried to write a new version of object `foo', BTW. Allowing multiple execution threads and setReader() as described in the Green Book is a design goal and has been since 2001 at least, so don't expect it soon. It is hard (lots of the code used, e.g. LINPACK, is not reentrant and so needs to be semaphored) and if achieved will need vigilance to keep working. On Fri, 4 Jun 2004, Bickel, David wrote: Is there a way to call an R function to work in the background within the same R session? What I have in mind is the equivalent of adding '' at the end of a UNIX command, so that R can process an intensive command while I execute other R commands. I want to do this in the same R session, rather than with multiple calls to R, so that all my modified objects will stay in the same workspace. I would appreciate any help with this. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [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] running R command in the background
By library I of course mean package. -Andrew --- Andrew Young [EMAIL PROTECTED] wrote: You could try looking at the library fork. However, this generally sounds like a bad idea and if you do this, you're kind of asking for trouble with threading issues, as R is not thread-safe. I'm not sure if fork works on all platforms, since I believe it works by running a unix shell command. But it's worth a shot. Best regards, -Andrew --- Prof Brian Ripley [EMAIL PROTECTED] wrote: This cannot presently be done, as the R internals do not multitask. I am not sure what you would want to happen if the background and foreground commands both tried to write a new version of object `foo', BTW. Allowing multiple execution threads and setReader() as described in the Green Book is a design goal and has been since 2001 at least, so don't expect it soon. It is hard (lots of the code used, e.g. LINPACK, is not reentrant and so needs to be semaphored) and if achieved will need vigilance to keep working. On Fri, 4 Jun 2004, Bickel, David wrote: Is there a way to call an R function to work in the background within the same R session? What I have in mind is the equivalent of adding '' at the end of a UNIX command, so that R can process an intensive command while I execute other R commands. I want to do this in the same R session, rather than with multiple calls to R, so that all my modified objects will stay in the same workspace. I would appreciate any help with this. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [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 __ [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] running R command in the background
Did you try actually reading the request (let alone the informed repsonse you included) ... I want to do this in the same session, rather than with multiple calls to R, whereas package fork's DESCRIPTION says Description: These functions provides simple wrappers around the Unix process management API calls: fork, wait, waitpid, kill, and _exit. This enables construction of programs that utilize multiple concurrent processes. exactly what was *not* asked for. On Fri, 4 Jun 2004, Andrew Young wrote: By library I of course mean package. -Andrew --- Andrew Young [EMAIL PROTECTED] wrote: You could try looking at the library fork. However, this generally sounds like a bad idea and if you do this, you're kind of asking for trouble with threading issues, as R is not thread-safe. I'm not sure if fork works on all platforms, since I believe it works by running a unix shell command. But it's worth a shot. Only for zero marks. Best regards, -Andrew --- Prof Brian Ripley [EMAIL PROTECTED] wrote: This cannot presently be done, as the R internals do not multitask. I am not sure what you would want to happen if the background and foreground commands both tried to write a new version of object `foo', BTW. Allowing multiple execution threads and setReader() as described in the Green Book is a design goal and has been since 2001 at least, so don't expect it soon. It is hard (lots of the code used, e.g. LINPACK, is not reentrant and so needs to be semaphored) and if achieved will need vigilance to keep working. On Fri, 4 Jun 2004, Bickel, David wrote: Is there a way to call an R function to work in the background within the same R session? What I have in mind is the equivalent of adding '' at the end of a UNIX command, so that R can process an intensive command while I execute other R commands. I want to do this in the same R session, rather than with multiple calls to R, so that all my modified objects will stay in the same workspace. I would appreciate any help with this. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [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 __ [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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
Perhaps this is a interesting starting point for you? http://steve.stat.tku.edu.tw/R_PHP/doR.html regards,christian Am Dienstag, 3. Februar 2004 03:26 schrieb [EMAIL PROTECTED]: I would like to construct a PHP script that runs R to generate a graphics file. Running R itself is no problem. However, it seems impossible to instantiate one of the graphics devices to create output. For example, the normal bitmap devices (e.g., jpeg, png, etc.) are derived from X11, which requires a display. This seems true, even if no output is ever directed to a real display. For some reason, the postscript device seems to suffer from similar problems. Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? Thanks for your help. Cheers, Brook __ [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 __ [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] running R from PHP
[EMAIL PROTECTED] writes: Below are 2 scripts (png.R and pdf.R) I am trying to run in R from PHP. # png.R x11(display=:5) png(filename=g.png) plot(1:5) graphics.off() # pdf.R pdf(file=g.pdf) plot(1:5) graphics.off() Both run from terminals and png.R will run without a normal X server if Xvfb is running. Neither runs under PHP, though (when invoked as R --no-save xxx.R). They yield the following errors (with the R startup banner deleted for compactness): x11(display=:5) png(filename=g.png) Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: could not open PNG file `g.png' Execution halted and pdf(file=/usr/pkg/share/httpd/htdocs/test-R/g.pdf) Error in PDF(file, old$family, old$encoding, old$bg, old$fg, width, height, : unable to start device pdf In addition: Warning message: cannot open `pdf' file argument `/usr/pkg/share/httpd/htdocs/test-R/g.pdf' Execution halted For reference, the R banner information includes the following: R : Copyright 2003, The R Development Core Team Version 1.6.2 (2003-01-10) Any help on how to get these scripts to work is greatly appreciated. Your R version is about a year out of date, but that's hardly the issue. I don't do PHP, but the error message in both cases has to do with file opening, so how about checking permissions on your current directory: Try sticking this into your script system(id; pwd; ls -la) Also notice that web applications often take special security measures and may change one or all of the following: working directory, root directory, user id, and group id. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [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] running R from PHP
[EMAIL PROTECTED] wrote: Both run from terminals and png.R will run without a normal X server if Xvfb is running. Neither runs under PHP, though (when invoked as R --no-save xxx.R). They yield the following errors (with the R startup banner deleted for compactness): could not open PNG file `g.png' cannot open `pdf' file argument `/usr/pkg/share/httpd/htdocs/test-R/g.pdf' From the evidence above, I'd guess a file permission error. The web server probably runs as the user apache or something similar -- does that user have write permission to the place where you are trying to create the images? Try writing to /tmp/g.png and /tmp/g.pdf and see if the files get created. HTH, Joe __ [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] running R from PHP
On Tue, 3 Feb 2004, Philippe Glaziou wrote: @biology.nmsu.edu [EMAIL PROTECTED] wrote: I would like to construct a PHP script that runs R to generate a graphics file. Running R itself is no problem. However, it seems impossible to instantiate one of the graphics devices to create output. For example, the normal bitmap devices (e.g., jpeg, png, etc.) are derived from X11, which requires a display. This seems true, even if no output is ever directed to a real display. It _is_ documented on the help page, and output _is_ directed to a real display: you just mever see it. It is possible make use a virtual display such as that provided by Xvfb. For some reason, the postscript device seems to suffer from similar problems. Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? If you need a bitmap graphic file, I would suggest the use of ImageMagick: You may as well use the bitmap() device built into R, which is also a wrapper for the use of ghostscript. That too is described on the help page. I have never seen a reported problem with getting postscript output from a script. After reading the posting guide, please give us some useful details of what happened. cunegonde:~/tmp ls foo cunegonde:~/tmp cat foo pdf(file=g.pdf) plot(1:5) dev.off() cunegonde:~/tmp R --no-save foo/dev/null convert g.pdf g.png cunegonde:~/tmp ls -g -rw---1 glaziou 3374 2004-02-03 11:58 g.pdf -rw---1 glaziou 4115 2004-02-03 11:58 g.png -rw---1 glaziou80 2004-02-03 11:58 foo This works from a unix console without X running (the postcript device works similarly on my machine). R can easily be fed this way with a file and parameters passed from a php script. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
[EMAIL PROTECTED] wrote: Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? Look for Xvfb (X virtual frame buffer). Not sure what OS you are running, but on RH9 and Fedora, at least, there is a package called XFree86-Xvfb. I use Xvfb with the following command: /usr/X11R6/bin/Xvfb :5 -screen 0 1024x768x16 More specifically I wrote an init script and set Xvfb up to start as a service on boot. Then in R I use: x11(display=:5) HTH, Joe __ [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] running R from PHP
@biology.nmsu.edu [EMAIL PROTECTED] wrote: I would like to construct a PHP script that runs R to generate a graphics file. Running R itself is no problem. However, it seems impossible to instantiate one of the graphics devices to create output. For example, the normal bitmap devices (e.g., jpeg, png, etc.) are derived from X11, which requires a display. This seems true, even if no output is ever directed to a real display. For some reason, the postscript device seems to suffer from similar problems. Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? If you need a bitmap graphic file, I would suggest the use of ImageMagick: cunegonde:~/tmp ls foo cunegonde:~/tmp cat foo pdf(file=g.pdf) plot(1:5) dev.off() cunegonde:~/tmp R --no-save foo/dev/null convert g.pdf g.png cunegonde:~/tmp ls -g -rw---1 glaziou 3374 2004-02-03 11:58 g.pdf -rw---1 glaziou 4115 2004-02-03 11:58 g.png -rw---1 glaziou80 2004-02-03 11:58 foo This works from a unix console without X running (the postcript device works similarly on my machine). R can easily be fed this way with a file and parameters passed from a php script. -- Philippe Glaziou, MD Epidemiologist Institut Pasteur du Cambodge __ [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]Running R remotely in Windows Environment? Thanks!
Thanks to Prof Ripley, Arne, Andy Bill for unambiguous suggestions!
Linux box is on order.
I'll take notes on our experience post a follow-up
in a few weeks. May be useful to other folks stuck in the Windows world.
-Jim
At 06:24 AM 1/29/2004, Pikounis, Bill wrote:
Jim,
I would really like to reiterate Professor Ripley's and Arne Henningsen
comments. The problem goes for any analytic software or system you might
want to use, not just R. My impression is that at least for part of it, you
want the individual users to use R as they would on their own desktops. (If
that is not the case, much of the rest of this note is pure FYI.) Even in
its most advanced 2003 Server edition, Windows is simply not designed to be
a multi-user system. Sure, it can reliably host a web server that may need
to run quick bursts of R batch-type jobs (analytics) and return results to
a client (e.g. web browser), but that does not sound like what you are
looking for (at least in part). And beyond the technical limitations, use of
Windows Terminal Server (Remote Desktop) / Citrix, etc. will cost much money
and implementation hassle and probably even legal headaches. We have had
colleagues here at Merck (over my and Andy Liaw's disbelief) that have tried
to shoehorn Windows this way, and even the speed of single, small jobs by 1
logged-on took longer on the server than on their much less powerful
laptops.
A Linux solution is very flexible, in our experiences (we have Windows XP as
corporate desktop standard). As stated, with Samba, you can map directories
that look like just another drive in Windows Explorer. Printing is just as
transparent in either direction. VNC (Virtual Network Computing) is very,
very nice to provide the individual user's Linux environment as just another
window on their Windows desktop. With the free utility of autocutsel,
clipboards can be synchronized for ease of cutting and pasting. And KDE, one
of several window manager analogues to Windows, is very sophisticated and
shares a lot in common with the Windows GUI from a user operations
standpoint. While it may sound like a hassle to get up and running now if
your shop is currently 99% Windows, the benefit will absolutely be clear
later.
Hope that helps,
Bill
Bill Pikounis, Ph.D.
Biometrics Research Department
Merck Research Laboratories
PO Box 2000, MailDrop RY33-300
126 E. Lincoln Avenue
Rahway, New Jersey 07065-0900
USA
Phone: 732 594 3913
Fax: 732 594 1565
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Arne Henningsen
Sent: Thursday, January 29, 2004 3:45 AM
To: Jim Porzak
Cc: [EMAIL PROTECTED]
Subject: Re: [R]Running R remotely in Windows Environment?
Hi,
I also suggest to use a Linux Server. You can work on this
machine via ssh
(e.g. with PuTTY) and transfer the input and output files
with scp or a samba
server (which is easy to install and very convenient to use
for windows
users).
Arne
On Thursday 29 January 2004 08:53, Prof Brian Ripley wrote:
On Wed, 28 Jan 2004, Jim Porzak wrote:
We are considering setting up a fast, RAM loaded machine
as an R-server
to handle the big problems not suitable for individual
desktops and,
also, to process ad hoc analysis requests via our portal.
We are 99% a
Windows shop, so first choice is a windows server. We'll
use (D)COM for
the portal interface and understand that.
What has me stumped is how to easily interface individual
analyst's
Windows desktops to the R-server. I haven't seen anything in the
archives, but I can't imagine this hasn't been done. What
am I missing?
R is not designed to be client-server on Windows. People I
know who do
this use Windows Terminal Server or Citrix.
I would question the value of this approach. Unless you
propose to run
64-bit Windows, a `RAM loaded' machine isn't `loaded', and
R under Windows
handles large amounts of memory much less effectively than
under Linux.
64-bit Windows is uncharted territory for R, whereas 64-bit
Unix/Linux is
well trodden.
--
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
[EMAIL PROTECTED]
http://www.uni-kiel.de/agrarpol/ahenningsen/
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Re: [R]Running R remotely in Windows Environment?
On Wed, 28 Jan 2004, Jim Porzak wrote: We are considering setting up a fast, RAM loaded machine as an R-server to handle the big problems not suitable for individual desktops and, also, to process ad hoc analysis requests via our portal. We are 99% a Windows shop, so first choice is a windows server. We'll use (D)COM for the portal interface and understand that. What has me stumped is how to easily interface individual analyst's Windows desktops to the R-server. I haven't seen anything in the archives, but I can't imagine this hasn't been done. What am I missing? R is not designed to be client-server on Windows. People I know who do this use Windows Terminal Server or Citrix. I would question the value of this approach. Unless you propose to run 64-bit Windows, a `RAM loaded' machine isn't `loaded', and R under Windows handles large amounts of memory much less effectively than under Linux. 64-bit Windows is uncharted territory for R, whereas 64-bit Unix/Linux is well trodden. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R]Running R remotely in Windows Environment?
Hi, I also suggest to use a Linux Server. You can work on this machine via ssh (e.g. with PuTTY) and transfer the input and output files with scp or a samba server (which is easy to install and very convenient to use for windows users). Arne On Thursday 29 January 2004 08:53, Prof Brian Ripley wrote: On Wed, 28 Jan 2004, Jim Porzak wrote: We are considering setting up a fast, RAM loaded machine as an R-server to handle the big problems not suitable for individual desktops and, also, to process ad hoc analysis requests via our portal. We are 99% a Windows shop, so first choice is a windows server. We'll use (D)COM for the portal interface and understand that. What has me stumped is how to easily interface individual analyst's Windows desktops to the R-server. I haven't seen anything in the archives, but I can't imagine this hasn't been done. What am I missing? R is not designed to be client-server on Windows. People I know who do this use Windows Terminal Server or Citrix. I would question the value of this approach. Unless you propose to run 64-bit Windows, a `RAM loaded' machine isn't `loaded', and R under Windows handles large amounts of memory much less effectively than under Linux. 64-bit Windows is uncharted territory for R, whereas 64-bit Unix/Linux is well trodden. -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ [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]Running R remotely in Windows Environment?
I would also give my votes to Linux. That's essentially the main function
of our Linux boxes, and some of the boxes are `RAM loaded'. We just use VNC
to connect from the Windoze desktop to the Linux boxes. We can mount the
Windows shared drives on the Linux boxes for file sharing. One of my former
interns ran all her R sessions from a Windows shared drive on a Linux box.
Andy
From: Jim Porzak
We are considering setting up a fast, RAM loaded machine as
an R-server
to handle the big problems not suitable for individual
desktops and, also,
to process ad hoc analysis requests via our portal. We are
99% a Windows
shop, so first choice is a windows server. We'll use (D)COM
for the portal
interface and understand that.
What has me stumped is how to easily interface individual
analyst's Windows
desktops to the R-server. I haven't seen anything in the
archives, but I
can't imagine this hasn't been done. What am I missing?
TIA!
Jim Porzak
Director of Analytics
Loyalty Matrix, Inc.
www.LoyaltyMatrix.com
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RE: [R]Running R remotely in Windows Environment?
Jim,
I would really like to reiterate Professor Ripley's and Arne Henningsen
comments. The problem goes for any analytic software or system you might
want to use, not just R. My impression is that at least for part of it, you
want the individual users to use R as they would on their own desktops. (If
that is not the case, much of the rest of this note is pure FYI.) Even in
its most advanced 2003 Server edition, Windows is simply not designed to be
a multi-user system. Sure, it can reliably host a web server that may need
to run quick bursts of R batch-type jobs (analytics) and return results to
a client (e.g. web browser), but that does not sound like what you are
looking for (at least in part). And beyond the technical limitations, use of
Windows Terminal Server (Remote Desktop) / Citrix, etc. will cost much money
and implementation hassle and probably even legal headaches. We have had
colleagues here at Merck (over my and Andy Liaw's disbelief) that have tried
to shoehorn Windows this way, and even the speed of single, small jobs by 1
logged-on took longer on the server than on their much less powerful
laptops.
A Linux solution is very flexible, in our experiences (we have Windows XP as
corporate desktop standard). As stated, with Samba, you can map directories
that look like just another drive in Windows Explorer. Printing is just as
transparent in either direction. VNC (Virtual Network Computing) is very,
very nice to provide the individual user's Linux environment as just another
window on their Windows desktop. With the free utility of autocutsel,
clipboards can be synchronized for ease of cutting and pasting. And KDE, one
of several window manager analogues to Windows, is very sophisticated and
shares a lot in common with the Windows GUI from a user operations
standpoint. While it may sound like a hassle to get up and running now if
your shop is currently 99% Windows, the benefit will absolutely be clear
later.
Hope that helps,
Bill
Bill Pikounis, Ph.D.
Biometrics Research Department
Merck Research Laboratories
PO Box 2000, MailDrop RY33-300
126 E. Lincoln Avenue
Rahway, New Jersey 07065-0900
USA
Phone: 732 594 3913
Fax: 732 594 1565
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Arne Henningsen
Sent: Thursday, January 29, 2004 3:45 AM
To: Jim Porzak
Cc: [EMAIL PROTECTED]
Subject: Re: [R]Running R remotely in Windows Environment?
Hi,
I also suggest to use a Linux Server. You can work on this
machine via ssh
(e.g. with PuTTY) and transfer the input and output files
with scp or a samba
server (which is easy to install and very convenient to use
for windows
users).
Arne
On Thursday 29 January 2004 08:53, Prof Brian Ripley wrote:
On Wed, 28 Jan 2004, Jim Porzak wrote:
We are considering setting up a fast, RAM loaded machine
as an R-server
to handle the big problems not suitable for individual
desktops and,
also, to process ad hoc analysis requests via our portal.
We are 99% a
Windows shop, so first choice is a windows server. We'll
use (D)COM for
the portal interface and understand that.
What has me stumped is how to easily interface individual
analyst's
Windows desktops to the R-server. I haven't seen anything in the
archives, but I can't imagine this hasn't been done. What
am I missing?
R is not designed to be client-server on Windows. People I
know who do
this use Windows Terminal Server or Citrix.
I would question the value of this approach. Unless you
propose to run
64-bit Windows, a `RAM loaded' machine isn't `loaded', and
R under Windows
handles large amounts of memory much less effectively than
under Linux.
64-bit Windows is uncharted territory for R, whereas 64-bit
Unix/Linux is
well trodden.
--
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
[EMAIL PROTECTED]
http://www.uni-kiel.de/agrarpol/ahenningsen/
__
[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
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Re: [R] Running R remotely in Windows Environment? - Xemacs and ssh
On Thu, Jan 29, 2004 at 04:17:48PM -0800, Vadim Ogranovich wrote:
Hi,
While we are on the topic of Running R remotely in Windows Environment
maybe someone could help with the following specific problem. I run R on
a Linux box from my WindowsXP laptop. I do so via Exceed, which for some
reasons is inconvenient for me.
As an alternative I tried to ssh into the linux machine and then run R.
This worked fine from Cygwin's bash window, but not from under XEmacs
(native Windows port). After starting ssh Xemacs complained:
Pseudo-terminal will not be allocated because stdin is not a terminal
and didn't show the prompt. Did anyone figure out how to remotely run R
from under (X)Emacs on Windows using ssh?
Cygwin can now run an X11 server for you, and it can do it such that the
normal win2k/xp/... window manager controls things -- you need a special
switch the name of which I cannot recall right now (and the windoze system
is at work). Look into the supplied startxin.{bat,sh} which has the line
commented.
So with X11 running on windows machine, you can get via 'ssh -X host' and
get any X11-compliant app back to your windows system.
Hth, Dirk
--
The relationship between the computed price and reality is as yet unknown.
-- From the pac(8) manual page
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Re: [R] Running R-program as queue jobs
Hi! On Thu, Nov 13, 2003 at 09:59:48AM +, Arne Gjuvsland wrote: I have a problem with running my R programs as queue jobs. When I try to submit a batch file to the queue with qsub I get the following error message: /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared libraries: libpcre.so.0: cannot load shared object file: No such file or directory When executed from the command prompt the batch file does its job. Did you run the script on the same machine in both cases? I got burnt a couple of times with different machines running different versions of the OS, non-identical versions of shared libraries etc... cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Running R-program as queue jobs
Jason Turner [EMAIL PROTECTED] writes: Philipp Pagel wrote: Hi! On Thu, Nov 13, 2003 at 09:59:48AM +, Arne Gjuvsland wrote: I have a problem with running my R programs as queue jobs. When I try to submit a batch file to the queue with qsub I get the following error message: /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared libraries: libpcre.so.0: cannot load shared object file: No such file or directory When executed from the command prompt the batch file does its job. Did you run the script on the same machine in both cases? I got burnt a couple of times with different machines running different versions of the OS, non-identical versions of shared libraries etc... In addition to Philipp's good sugestion, I've been burnt on the same machine, but with the batch job running as a different user. When environment variables are needed, or private libraries need to be loaded, things go bad very quickly. Also, environment variables may be set differently between interactive and batch shells. E.g. my crontab file looks like this CVS_RSH=ssh 35 0 * * * $HOME/scripts/r-bugs-commit /dev/null ... for a reason. In Arne's case, I'd suspect the setting of LD_LIBRARY_PATH. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Running R-program as queue jobs
On 13 Nov 2003, Peter Dalgaard wrote: Jason Turner [EMAIL PROTECTED] writes: Philipp Pagel wrote: Hi! On Thu, Nov 13, 2003 at 09:59:48AM +, Arne Gjuvsland wrote: I have a problem with running my R programs as queue jobs. When I try to submit a batch file to the queue with qsub I get the following error message: /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared libraries: libpcre.so.0: cannot load shared object file: No such file or directory When executed from the command prompt the batch file does its job. Did you run the script on the same machine in both cases? I got burnt a couple of times with different machines running different versions of the OS, non-identical versions of shared libraries etc... In addition to Philipp's good sugestion, I've been burnt on the same machine, but with the batch job running as a different user. When environment variables are needed, or private libraries need to be loaded, things go bad very quickly. Also, environment variables may be set differently between interactive and batch shells. E.g. my crontab file looks like this CVS_RSH=ssh 35 0 * * * $HOME/scripts/r-bugs-commit /dev/null ... for a reason. In Arne's case, I'd suspect the setting of LD_LIBRARY_PATH. (The R script will include in R_LD_LIBRARY_PATH the settings used at configure time, so we do try to workaround that one. For example my 64-bit Solaris build has sparcv9 library paths in.) As an aside, from the next non-patch release PCRE, BZLIB and ZLIB will be statically linked into R in a vanilla configuration to help avoid such problems. (For some reason my RH8.0 system has a dynamic pcreposix but only a static pcre, although the current PCRE default build makes both versions of each.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Running R-program as queue jobs
A search on Google shows that libpcre.so.0 is a Perl-compatible regular expression library. Does R use that, or is it the queue script? Have you checked /usr/lib for that library? Maybe you need to install the library or rerun ldconfig. You can get info about shared libraries with the ldd command. That was some ideas, but no shrink wrapped solutions! Hilsen Jesper -Original Message- From: Arne Gjuvsland [mailto:[EMAIL PROTECTED] Sent: Thursday, November 13, 2003 5:00 AM To: [EMAIL PROTECTED] Subject: [R] Running R-program as queue jobs I have a problem with running my R programs as queue jobs. When I try to submit a batch file to the queue with qsub I get the following error message: /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared libraries: libpcre.so.0: cannot load shared object file: No such file or directory When executed from the command prompt the batch file does its job. Any ideas? Arne __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Running R-program as queue jobs - problem solved
At 11:56 13.11.2003 +, Prof Brian Ripley wrote: On 13 Nov 2003, Peter Dalgaard wrote: Jason Turner [EMAIL PROTECTED] writes: Philipp Pagel wrote: Hi! On Thu, Nov 13, 2003 at 09:59:48AM +, Arne Gjuvsland wrote: I have a problem with running my R programs as queue jobs. When I try to submit a batch file to the queue with qsub I get the following error message: /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared libraries: libpcre.so.0: cannot load shared object file: No such file or directory When executed from the command prompt the batch file does its job. Did you run the script on the same machine in both cases? I got burnt a couple of times with different machines running different versions of the OS, non-identical versions of shared libraries etc... In addition to Philipp's good sugestion, I've been burnt on the same machine, but with the batch job running as a different user. When environment variables are needed, or private libraries need to be loaded, things go bad very quickly. Also, environment variables may be set differently between interactive and batch shells. E.g. my crontab file looks like this CVS_RSH=ssh 35 0 * * * $HOME/scripts/r-bugs-commit /dev/null ... for a reason. In Arne's case, I'd suspect the setting of LD_LIBRARY_PATH. (The R script will include in R_LD_LIBRARY_PATH the settings used at configure time, so we do try to workaround that one. For example my 64-bit Solaris build has sparcv9 library paths in.) As an aside, from the next non-patch release PCRE, BZLIB and ZLIB will be statically linked into R in a vanilla configuration to help avoid such problems. (For some reason my RH8.0 system has a dynamic pcreposix but only a static pcre, although the current PCRE default build makes both versions of each.) -- 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 Thanks for helpful advice, the R_LD_LIBRARY_PATH in the R script did not contain the path of the library. Now the script is in the queue, waiting for some quality CPU-time. Arne __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] running R inside of e-macs
Have you installed ESS (Emacs Speak Statistics) ? If not look at http://www.sciviews.org/_rgui/ Bye! A. S. |+| |Alessandro Semeria |Tel. +39 544 536811 | |+| |Models and Simulation Laboratory|Fax. +39 544 538663 | |+| |The Environment Research Center - || |Montecatini (Edison Group),Via || |Ciro Menotti 48,|E-mail: [EMAIL PROTECTED] | |48023 Marina di Ravenna (RA), Italy || |+| __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
