Re: [R] switching to Linux, suggestions?
Again, I have to tell... Take a look at Ubuntu http://www.ubuntulinux.org/ When I get tired of MAC OSX, I installed the ppc version of Ubuntu on my IBook. It's great and it's based on Debian. On Mon, 2004-12-13 at 12:35 -0500, doktora v wrote: I'm using SUSE with success on intel laptop and AMD desktop. You get the best of both worlds: rpm and source. I can easily get the rpm packages i need, and compile on my own the things that i can spend time on (such as R 2.0.1 -- compiles out of the box on suse). BTW, I'm looking to switch to Mac platform. Anyone had any experience with that? I'm expecting on a power G4 laptop later this week hope R behaves... -- doktora On Mon, 13 Dec 2004 09:05:54 -0800 (PST), bogdan romocea [EMAIL PROTECTED] wrote: Before choosing a GNU/Linux distribution look into the package management issue. http://distrowatch.com/ I would suggest that you avoid all RPM-based distributions (Mandrake, Fedora, SuSE), and consider Debian (+ those based on it) the source-based distributions (such as Gentoo). I've been using Mandrake for a couple of years but got tired of RPM. HTH, b. -Original Message- From: Thomas W Volscho [mailto:[EMAIL PROTECTED] Sent: Sunday, December 12, 2004 3:24 PM To: [EMAIL PROTECTED] Subject: [R] switching to Linux, suggestions? Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [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 __ Dress up your holiday email, Hollywood style. Learn more. __ [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 __ [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] switching to Linux, suggestions?
A little bit late, but I have to tell... Take a look at Ubuntu http://www.ubuntulinux.org Is both comfortable to install and maintain; plus easy to expand. __ [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] switching to Linux, suggestions?
Yuandan Zhang [EMAIL PROTECTED] writes: I have both desktop and laptop with Fedora core 3. R 2.0.1 are working well on all PCs. There is a problem with Fedora core 3 on HP nx500 laptop. The display resolution is 1024x768 according to HP's description. However, during the installation, there were only two options on display resolution 800x600 640x480. I tried various ways, but can't set it to 1024x768. any one have fix for this. You may want to set the bits per pixel first (you can reconfigure the screen via the control panel as far as I recall). Anyways, this works fine on other laptops, and is not at all R related, so you should probably ask elsewhere... -- 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://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] switching to Linux, suggestions?
Hello, Thomas W Volscho schrieb: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? R is developed on Linux, so there shouldn't be too much restrictions on whatever distri you're going to use! If running a new shiny Desktop you might consider other aspects than using R, which should run with every Linux distribution. If you're looking for something comfortable to install and maintain you might give Quatian a try (http://dirk.eddelbuettel.com/quantian.html). This is a somewhat modified Knoppix trimmed to statistical analysis (not entirely, though) regards Thomas __ [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] switching to Linux, suggestions?
Before choosing a GNU/Linux distribution look into the package management issue. http://distrowatch.com/ I would suggest that you avoid all RPM-based distributions (Mandrake, Fedora, SuSE), and consider Debian (+ those based on it) the source-based distributions (such as Gentoo). I've been using Mandrake for a couple of years but got tired of RPM. HTH, b. -Original Message- From: Thomas W Volscho [mailto:[EMAIL PROTECTED] Sent: Sunday, December 12, 2004 3:24 PM To: [EMAIL PROTECTED] Subject: [R] switching to Linux, suggestions? Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [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 __ Dress up your holiday email, Hollywood style. Learn more. __ [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] switching to Linux, suggestions?
I'm using SUSE with success on intel laptop and AMD desktop. You get the best of both worlds: rpm and source. I can easily get the rpm packages i need, and compile on my own the things that i can spend time on (such as R 2.0.1 -- compiles out of the box on suse). BTW, I'm looking to switch to Mac platform. Anyone had any experience with that? I'm expecting on a power G4 laptop later this week hope R behaves... -- doktora On Mon, 13 Dec 2004 09:05:54 -0800 (PST), bogdan romocea [EMAIL PROTECTED] wrote: Before choosing a GNU/Linux distribution look into the package management issue. http://distrowatch.com/ I would suggest that you avoid all RPM-based distributions (Mandrake, Fedora, SuSE), and consider Debian (+ those based on it) the source-based distributions (such as Gentoo). I've been using Mandrake for a couple of years but got tired of RPM. HTH, b. -Original Message- From: Thomas W Volscho [mailto:[EMAIL PROTECTED] Sent: Sunday, December 12, 2004 3:24 PM To: [EMAIL PROTECTED] Subject: [R] switching to Linux, suggestions? Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [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 __ Dress up your holiday email, Hollywood style. Learn more. __ [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] switching to Linux, suggestions?
Fedora uses yum as well as rpm. I haven't installed an RPM in months, except for R. Yum is great. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [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] switching to Linux, suggestions?
The newest production release of Fedora is Core 3. I would use this one if I were you. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Thomas Schönhoff [EMAIL PROTECTED] nfo.org To Sent by: R User-Liste [EMAIL PROTECTED] [EMAIL PROTECTED] at.math.ethz.chcc Subject 12/13/2004 10:22 Re: [R] switching to Linux, AMsuggestions? Hello, Thomas W Volscho schrieb: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? R is developed on Linux, so there shouldn't be too much restrictions on whatever distri you're going to use! If running a new shiny Desktop you might consider other aspects than using R, which should run with every Linux distribution. If you're looking for something comfortable to install and maintain you might give Quatian a try (http://dirk.eddelbuettel.com/quantian.html). This is a somewhat modified Knoppix trimmed to statistical analysis (not entirely, though) regards Thomas __ [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] switching to Linux, suggestions?
You have installed RPM's, just under the covers. YUM is just a smart front-end to installing rpms. Regards, --Mike On Mon, 13 Dec 2004 12:52:58 -0500 Jonathan Baron [EMAIL PROTECTED] wrote: Fedora uses yum as well as rpm. I haven't installed an RPM in months, except for R. Yum is great. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [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 -- Mike Meyer, Seattle WA __ [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] switching to Linux, suggestions?
Jonathan Baron [EMAIL PROTECTED] writes: Fedora uses yum as well as rpm. I haven't installed an RPM in months, except for R. Yum is great. Actually, Martyn set up CRAN as a yum repository. I have $ more /etc/yum.repos.d/R.repo [R] name=CRAN Fedora $releasever - $basearch baseurl=http://cran.r-project.org/bin/linux/redhat/fc$releasever/$basearch/ enabled=1 gpgcheck=1 whereafter I could just say yum install R, and in due course I presume yum update R. -- 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://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] switching to Linux, suggestions?
doktora v wrote: I'm using SUSE with success on intel laptop and AMD desktop. You get the best of both worlds: rpm and source. I can easily get the rpm packages i need, and compile on my own the things that i can spend time on (such as R 2.0.1 -- compiles out of the box on suse). BTW, I'm looking to switch to Mac platform. Anyone had any experience with that? I'm expecting on a power G4 laptop later this week hope R behaves... Hello: There is one issue about SuSE Linux: The Professional version and the Standard distribution. The professional version cost a tad more. The advantage of the professional version: you get always the header files too in some cases. I once had SuSE Linux 8 on my old Celeron laptop. At that time I tried to install Numerics on Python. But with no avail because the Standard SuSE distribution lacks some additional header files and you get always the bare minimum only. That said: the normal SuSE distribution will always let you aft-install all the things you need. Regards, S. Gonzi PS: I hope I am not saying somthing outragiuous wrong now: but there exists a free Fortran 95 compiler from INTEL for Linux. As far as I know it is the one and only free Fortran 95 compiler out there (okay gnu g95 is on its way). However, it is hard to get INTEL Fortran 95 running on Debian Linux a colleague told me. I for myslef can only say that I had had no problems in installing Fortran 95 from INTEL on SuSE. __ [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] switching to Linux, suggestions?
On Mon, 2004-12-13 at 23:59 +0100, Peter Dalgaard wrote: Jonathan Baron [EMAIL PROTECTED] writes: Fedora uses yum as well as rpm. I haven't installed an RPM in months, except for R. Yum is great. Actually, Martyn set up CRAN as a yum repository. I have $ more /etc/yum.repos.d/R.repo [R] name=CRAN Fedora $releasever - $basearch baseurl=http://cran.r-project.org/bin/linux/redhat/fc$releasever/$basearch/ enabled=1 gpgcheck=1 whereafter I could just say yum install R, and in due course I presume yum update R. You can also configure up2date - the slightly annoying pulsating red icon on the panel - to get automatic notification of updates from CRAN. Instructions are in the ReadMe file in the same directory as the Fedora Core 3 RPMS. Martyn __ [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] switching to Linux, suggestions?
haha debian vs rpm again... everywhere.. On Tue, 14 Dec 2004 10:30:07 +0100, Siegfried Gonzi [EMAIL PROTECTED] wrote: doktora v wrote: I'm using SUSE with success on intel laptop and AMD desktop. You get the best of both worlds: rpm and source. I can easily get the rpm packages i need, and compile on my own the things that i can spend time on (such as R 2.0.1 -- compiles out of the box on suse). BTW, I'm looking to switch to Mac platform. Anyone had any experience with that? I'm expecting on a power G4 laptop later this week hope R behaves... Hello: There is one issue about SuSE Linux: The Professional version and the Standard distribution. The professional version cost a tad more. The advantage of the professional version: you get always the header files too in some cases. I once had SuSE Linux 8 on my old Celeron laptop. At that time I tried to install Numerics on Python. But with no avail because the Standard SuSE distribution lacks some additional header files and you get always the bare minimum only. That said: the normal SuSE distribution will always let you aft-install all the things you need. Regards, S. Gonzi PS: I hope I am not saying somthing outragiuous wrong now: but there exists a free Fortran 95 compiler from INTEL for Linux. As far as I know it is the one and only free Fortran 95 compiler out there (okay gnu g95 is on its way). However, it is hard to get INTEL Fortran 95 running on Debian Linux a colleague told me. I for myslef can only say that I had had no problems in installing Fortran 95 from INTEL on SuSE. __ [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] switching to Linux, suggestions?
El dom, 12-12-2004 a las 15:23 -0500, Thomas W Volscho escribió: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho I used R in the susseccive Fedora Core release (at the moment I use R 2.0.0 + FC3) with satisfaction. best, Juan Antonio Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [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 -- Juan Antonio Caballero Molina /\ASCII Ribbon Campaign Universidad de Córdoba \ /Respect for open standards Looking for fine softwareX No HTML/RTF in email and/or writing? / \No M$ Word docs in email http://counter.li.org Linux user number 346272 __ [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] switching to Linux, suggestions?
Have you tried Qunatian? http://dirk.eddelbuettel.com/quantian.html Not only does it have R 2.0.1, but it's got a whole bunch of other programs already installed, including emacs, TeX, kile, and many more apps. It's debian and based on clusterKnoppix. You can run it live or install it to hard drive. - Mohamed -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Thomas W Volscho Sent: 12 December 2004 15:24 To: [EMAIL PROTECTED] Subject: [R] switching to Linux, suggestions? Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [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] switching to Linux, suggestions?
I have both desktop and laptop with Fedora core 3. R 2.0.1 are working well on all PCs. There is a problem with Fedora core 3 on HP nx500 laptop. The display resolution is 1024x768 according to HP's description. However, during the installation, there were only two options on display resolution 800x600 640x480. I tried various ways, but can't set it to 1024x768. any one have fix for this. Yuandan On Sun, 12 Dec 2004 15:23:40 -0500 Thomas W Volscho [EMAIL PROTECTED] wrote: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [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] switching to Linux, suggestions?
Hi,
recently, i installed Gentoo in addition to SuSE on my Laptop.
In order to see whether it was worth the effort, i did a small
benchmark for R under SuSE and Gentoo.
I guess, that the benchmarks under SuSE are also approximately
valid for other binary distributions.
As a consequence, depending on your Unix/Linux experience,
i would recommend Gentoo for optimal performance.
If you are new to Linux and want to avoid the relatively complicated
Gentoo setup, i recommend that you should least compile R from source,
which should be easy also for a Linux newbie.
The benchmark (see below for the script) consisted of
i) Generating random normals and plotting density plots.
ii) Cox model
iii) Inverting random 200x200 matrices.
I used different versions of R, since 2.0.1 is not yet included in the
Gentoo portage tree. Here are my results:
A) SuSE 9.2, R 2.0.1 (from i586 rpm):
benchmark cpu.user cpu.system
1benchmark.density 222.22 6.76
11 benchmark.survival 133.69 0.27
12 benchmark.linearalgebra 365.25 3.64
B) R 1.9.0 compiled under SuSE 9.2, without additional CFLAGS
(i.e. using CFLAGS from the configure script):
benchmark cpu.user cpu.system
1benchmark.density 217.31 6.12
11 benchmark.survival 101.77 0.14
12 benchmark.linearalgebra 165.49 3.34
C) R 1.9.0 compiled under SuSE 9.2, using the same CFLAGS
as in Gentoo (see below for my CFLAGS):
benchmark cpu.user cpu.system
1benchmark.density 199.16 5.96
11 benchmark.survival94.26 0.15
12 benchmark.linearalgebra 159.17 4.93
D) R 1.9.0-r1 under Gentoo, using the CFLAGS for the whole system,
not just for R.
benchmark cpu.user cpu.system
1benchmark.density 176.08 6.10
11 benchmark.survival84.20 0.14
12 benchmark.linearalgebra 134.72 6.54
My CFLAGS (for a centrino) are:
CFLAGS=-pipe -O3 -march=pentium4 -mmmx -msse -msse2 -mfpmath=sse,387
-maccumulate-outgoing-args -mno-align-stringops -fomit-frame-pointer
-ffast-math -fsched-spec-load -fprefetch-loop-arrays -ftracer
-fmove-all-movables
Question to the Gurus: Would it be allowed, to use
-funsafe-math-optimizations?
Here is my benchmark script:
--
require(survival)
benchmark.density - function()
{
for (i in 1:1000)
{
x - rnorm(10)
plot(density(x), type=l, xlim=c(-10,10), main=i)
}
}
benchmark.survival - function()
{
for (i in 1:1000)
{
time - c(rexp(800, 1), rexp(800, 0.8), rexp(800, 0.9),
rexp(800, 0.7), rexp(800, 0.5))
time - round(time, digits=2) # introduce ties
event - as.integer(time = 1)
time[time 1] - 1
group - c(rep(0, 800), rep(1, 800), rep(2, 800),
rep(3, 800), rep(4, 800))
plot(survfit(Surv(time,event) ~ group), xlim=c(0,1))
title(main=i)
dummy - coxph(Surv(time,event) ~ group)
}
}
benchmark.linearalgebra - function()
{
for (i in 1:1000)
{
A - matrix(rnorm(200*200), nrow=200, ncol=200)
AI - solve(A)
residual - A %*% AI - diag(1, 200)
hist(residual, main=i)
}
}
my.benchmark - function(func)
{
funcname - (as.character(sys.call()[[2]]))
cat(funcname, \n)
times - system.time(func())
return(data.frame(benchmark=funcname,
cpu.user=times[1],
cpu.system=times[2]))
}
result - my.benchmark(benchmark.density)
result - rbind(result, my.benchmark(benchmark.survival))
result - rbind(result, my.benchmark(benchmark.linearalgebra))
sink(benchmark.out)
cat(Sys.info(), \n)
print(result)
sink()
--
Christian
Dear List,
I have acquired a new desktop and wanted to put a free OS on it. I am
trying Fedora Core 1, but not sure what the best Linux OS is for using R
2.0.1?
Thank you in advance for your input,
Tom Volscho
Thomas W. Volscho
Graduate Student
Dept. of Sociology U-2068
University of Connecticut
Storrs, CT 06269
Phone: (860) 486-3882
http://vm.uconn.edu/~twv1
__
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
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