Re: [R] Installing packages...
I have the exact same problem as you had when I customerized some package: the way I go around this is using install.packages(~/Documents/projects/R_customerized_packages/supclust_1.0-5.tar.gz, repos=NULL, type=source) in which supclust_... is built from R CMD build supclust and in your case, you just need to download the package if you insist on using downloaded package. HTH, Weiwei On 1/23/07, Nüzhet Dalfes [EMAIL PROTECTED] wrote: Hi, I am a total newbie to R. I am using R (2.4.1) on Mac OS X 10.4.8 and trying to install some packages using GUI Packages Data/Package Installer interface... Every time I get: trying URL 'http://umfragen.sowi.uni-mainz.de/CRAN/bin/macosx/universal/contrib/2.4/neural_1.4.1.tgz' Content type 'application/x-tar' length 18920 bytes opened URL == downloaded 18Kb Error in gzfile(file, r) : unable to open connection In addition: Warning message: cannot open compressed file 'neural/DESCRIPTION' What am I doing wrong? Any help will be much appreciated. Nüzhet Dalfes Istanbul Tech. Univ. __ 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing packages.
Dear, I'm not getting Installing packages: install.packages(c(exactRankTests)) trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 26129 bytes opened URL downloaded 25Kb trying URL `http://cran.r- project.org/bin/windows/contrib/2.0/exactRankTests_0.8-10.zip' Content type `application/zip' length 187723 bytes opened URL downloaded 183Kb package 'exactRankTests' successfully unpacked and MD5 sums checked Delete downloaded files (y/N)? y updating HTML package descriptions ? exactRankTests No documentation for 'exactRankTests' in specified packages and libraries: you could try 'help.search(exactRankTests)' How do I do? Thanks a lot. Marcus Vinicius [[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.
Re: [R] Installing packages.
require(exactRankTests) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 29/06/07, Marcus Vinicius [EMAIL PROTECTED] wrote: Dear, I'm not getting Installing packages: install.packages(c(exactRankTests)) trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 26129 bytes opened URL downloaded 25Kb trying URL `http://cran.r- project.org/bin/windows/contrib/2.0/exactRankTests_0.8-10.zip' Content type `application/zip' length 187723 bytes opened URL downloaded 183Kb package 'exactRankTests' successfully unpacked and MD5 sums checked Delete downloaded files (y/N)? y updating HTML package descriptions ? exactRankTests No documentation for 'exactRankTests' in specified packages and libraries: you could try 'help.search(exactRankTests)' How do I do? Thanks a lot. Marcus Vinicius [[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. [[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.
Re: [R] Installing packages.
Marcus Vinicius wrote: Dear, I'm not getting Installing packages: install.packages(c(exactRankTests)) trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 26129 bytes opened URL downloaded 25Kb This means you are using R-2.0.x? This is really ancient. Please upgrade to a more recent version of R. Before using function from the installed package, you have to load it: library(exactRankTests) Uwe Ligges trying URL `http://cran.r- project.org/bin/windows/contrib/2.0/exactRankTests_0.8-10.zip' Content type `application/zip' length 187723 bytes opened URL downloaded 183Kb package 'exactRankTests' successfully unpacked and MD5 sums checked Delete downloaded files (y/N)? y updating HTML package descriptions ? exactRankTests No documentation for 'exactRankTests' in specified packages and libraries: you could try 'help.search(exactRankTests)' How do I do? Thanks a lot. Marcus Vinicius [[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. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing packages
hie how do l install R packages .L'm using windows xp.plus is there a dipository for the packages that one can browse to find out what packages are available. thanks. - Be a PS3 game guru. [[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.
Re: [R] installing packages
Menu Packages Install Packages works well for me. --- raymond chiruka [EMAIL PROTECTED] wrote: hie how do l install R packages .L'm using windows xp.plus is there a dipository for the packages that one can browse to find out what packages are available. thanks. - Be a PS3 game guru. [[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. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages from command line on Linux RHEL4
Assuming the R packages have been downloaded locally and end with
tar.gz, then how about simply changing to where the files are located
and typing the following command?
ls *.tar.gz | while read x; do echo R CMD INSTALL $x; done | bash
Alternatively, you can use the install.packages() function in R.
Regards, Adai
Kermit Short wrote:
Dirk-
Many thanks for your reply. As I mentioned, I know very little
about programming in 'R' and what I've got is a BASH script. If needs be,
I'll look up how to read in a text file through R and add that into your
script in lieu of the (argv) stuff, but you wouldn't happen to know how to
accomplish the same thing using the
R CMD INSTALL
Shell command?
Thanks!
-Kermit
-Original Message-
From: Dirk Eddelbuettel [mailto:[EMAIL PROTECTED]
Sent: Monday, May 21, 2007 12:00 PM
To: [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Installing packages from command line on Linux RHEL4
Hi Kernit,
On 21 May 2007 at 11:37, Kermit Short wrote:
| Greetings.
|
|I am a System Administrator, and thus have very little knowledge of R
| itself. I have been asked to install a list of some 200 packages (from
| CRAM) to R. Rather than installing each package manually, I was hoping I
| could script this. I've written a BASH script that hopefully will do
this,
| but I'm wondering about the Mirror Selection portion of the installation
| process. I've looked and can't find anywhere a parameter to supply that
| specifies a mirror to use so that I don't have to manually select it for
| each package I want to install. In this case, with nearly 200 packages to
| install, this could become quite tedious. Does anyone have any
| suggestions?
The narrow answer is try adding
repos=http://cran.us.r-project.org;
Also, and if I may, the littler front-end (essentially #! shebang support
for R)
helps there:
basebud:~ cat bin/installPackages.r
#!/usr/bin/env r
#
# a simple example to install all the listed arguments as packages
if (is.null(argv)) {
cat(Usage: installPackages.r pkg1 [pkg2 [pkg3 [...]]]\n)
q()
}
for (pkg in argv) {
install.packages(pkg, lib=/usr/local/lib/R/site-library, depend=TRUE)
}
You would still need to add repos=... there. I tend to do that in my
~/.Rprofile.
Hth, Dirk
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Installing packages from command line on Linux RHEL4
Greetings. I am a System Administrator, and thus have very little knowledge of R itself. I have been asked to install a list of some 200 packages (from CRAM) to R. Rather than installing each package manually, I was hoping I could script this. I've written a BASH script that hopefully will do this, but I'm wondering about the Mirror Selection portion of the installation process. I've looked and can't find anywhere a parameter to supply that specifies a mirror to use so that I don't have to manually select it for each package I want to install. In this case, with nearly 200 packages to install, this could become quite tedious. Does anyone have any suggestions? Thanks! -Kermit Short [EMAIL PROTECTED] [[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.
Re: [R] Installing packages from command line on Linux RHEL4
Dirk-
Many thanks for your reply. As I mentioned, I know very little
about programming in 'R' and what I've got is a BASH script. If needs be,
I'll look up how to read in a text file through R and add that into your
script in lieu of the (argv) stuff, but you wouldn't happen to know how to
accomplish the same thing using the
R CMD INSTALL
Shell command?
Thanks!
-Kermit
-Original Message-
From: Dirk Eddelbuettel [mailto:[EMAIL PROTECTED]
Sent: Monday, May 21, 2007 12:00 PM
To: [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Installing packages from command line on Linux RHEL4
Hi Kernit,
On 21 May 2007 at 11:37, Kermit Short wrote:
| Greetings.
|
|I am a System Administrator, and thus have very little knowledge of R
| itself. I have been asked to install a list of some 200 packages (from
| CRAM) to R. Rather than installing each package manually, I was hoping I
| could script this. I've written a BASH script that hopefully will do
this,
| but I'm wondering about the Mirror Selection portion of the installation
| process. I've looked and can't find anywhere a parameter to supply that
| specifies a mirror to use so that I don't have to manually select it for
| each package I want to install. In this case, with nearly 200 packages to
| install, this could become quite tedious. Does anyone have any
| suggestions?
The narrow answer is try adding
repos=http://cran.us.r-project.org;
Also, and if I may, the littler front-end (essentially #! shebang support
for R)
helps there:
basebud:~ cat bin/installPackages.r
#!/usr/bin/env r
#
# a simple example to install all the listed arguments as packages
if (is.null(argv)) {
cat(Usage: installPackages.r pkg1 [pkg2 [pkg3 [...]]]\n)
q()
}
for (pkg in argv) {
install.packages(pkg, lib=/usr/local/lib/R/site-library, depend=TRUE)
}
You would still need to add repos=... there. I tend to do that in my
~/.Rprofile.
Hth, Dirk
--
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
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages from command line on Linux RHEL4
Hi Kernit,
On 21 May 2007 at 11:37, Kermit Short wrote:
| Greetings.
|
|I am a System Administrator, and thus have very little knowledge of R
| itself. I have been asked to install a list of some 200 packages (from
| CRAM) to R. Rather than installing each package manually, I was hoping I
| could script this. I've written a BASH script that hopefully will do this,
| but I'm wondering about the Mirror Selection portion of the installation
| process. I've looked and can't find anywhere a parameter to supply that
| specifies a mirror to use so that I don't have to manually select it for
| each package I want to install. In this case, with nearly 200 packages to
| install, this could become quite tedious. Does anyone have any
| suggestions?
The narrow answer is try adding
repos=http://cran.us.r-project.org;
Also, and if I may, the littler front-end (essentially #! shebang support for
R)
helps there:
basebud:~ cat bin/installPackages.r
#!/usr/bin/env r
#
# a simple example to install all the listed arguments as packages
if (is.null(argv)) {
cat(Usage: installPackages.r pkg1 [pkg2 [pkg3 [...]]]\n)
q()
}
for (pkg in argv) {
install.packages(pkg, lib=/usr/local/lib/R/site-library, depend=TRUE)
}
You would still need to add repos=... there. I tend to do that in my
~/.Rprofile.
Hth, Dirk
--
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
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages from command line on Linux RHEL4
Kermit, On 21 May 2007 at 12:05, Kermit Short wrote: | Dirk- | Many thanks for your reply. As I mentioned, I know very little | about programming in 'R' and what I've got is a BASH script. If needs be, | I'll look up how to read in a text file through R and add that into your | script in lieu of the (argv) stuff, but you wouldn't happen to know how to | accomplish the same thing using the | | R CMD INSTALL | | Shell command? I'm confused. Your 1st email asked about the mirror selection. Now you want to install from local files. Those are two different problems. Please consult the 'R Admin' manual, or go back to the list with preferably concrete questions, or reproducible examples. Hth, Dirk -- 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing packages and windows vista
Opening R by right clicking and choosing run as administrator' worked. Was able to run install packages without a problem. I have not tested the other methods suggested. thank you. Dan O'Shea -- Original message -- From: Duncan Murdoch [EMAIL PROTECTED] On 2/6/2007 10:33 AM, Daniel O'Shea wrote: I installed R (R-2.4.1-win32.exe) on a new computer with Windows Vista and a 64 bit operating system (hp dv9000 with intel core t7200). The base R runs fine, but I can not get any of the packages to load. From within R I choose install packages choose a site then a package. I tried installing 2 packages and get similar errors (see below), I just copied and pasted lines from R. Can anyone offer any suggestions? Thank you. I believe that on Vista you need to do like other OS's, and run package installs at a higher security level than the default. I don't have Vista so I've never done this, but I've been told you do it by right clicking on the R icon and choosing Run as administrator. I'd be interested in hearing if this is true of all package installs, or only installs to C:/Program files. Can you have a local library for your user, with only user permissions needed to modify packages there? You'd test this by creating a library directory in your own file space, then using .libPaths() to add it to the library location list. By default new installs would go there. Duncan Murdoch Dan O'Shea utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- also installing the dependencies 'scatterplot3d', 'rgl', 'ellipse' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/scatterplot3d_0.3-24.zip' Content type 'application/zip' length 540328 bytes opened URL downloaded 527Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/ellipse_0.3-4.zip' Content type 'application/zip' length 91877 bytes opened URL downloaded 89Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/vegan_1.8-5.zip' Content type 'application/zip' length 1176434 bytes opened URL downloaded 1148Kb Error in zip.unpack(pkg, tmpDir) : cannot open file 'C:/Program Files (x86)/R/R-2.4.1/library/file60bf5753/scatterplot3d/chtml/scatterplot3d.chm' utils:::menuInstallPkgs() also installing the dependencies 'akima', 'gam', 'RColorBrewer', 'sm', 'deldir', 'sp', 'maps', 'spatstat', 'PBSmapping', 'gpclib', 'RArcInfo', 'tkrplot', 'maptools', 'mapproj', 'rgl', 'qcc', 'sgeostat', 'acepack', 'TeachingDemos', 'chron', 'Hmisc' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/akima_0.5-1.zip' Content type 'application/zip' length 128809 bytes opened URL downloaded 125Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gam_0.98.zip' Content type 'application/zip' length 238008 bytes opened URL downloaded 232Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RColorBrewer_0.2-3.zip' Content type 'application/zip' length 39787 bytes opened URL downloaded 38Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sm_2.1-0.zip' Content type 'application/zip' length 400621 bytes opened URL downloaded 391Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/deldir_0.0-5.zip' Content type 'application/zip' length 108656 bytes opened URL downloaded 106Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sp_0.9-4.zip' Content type 'application/zip' length 747542 bytes opened URL downloaded 730Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maps_2.0-33.zip' Content type 'application/zip' length 2219136 bytes opened URL downloaded 2167Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/spatstat_1.11-0.zip' Content type 'application/zip' length 4558460 bytes opened URL downloaded 4451Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/PBSmapping_2.09.zip' Content type 'application/zip' length 6725596 bytes opened URL downloaded 6567Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gpclib_1.3-3.zip' Content type 'application/zip' length 95120 bytes opened URL downloaded 92Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RArcInfo_0.4-7.zip' Content type 'application/zip' length 374375 bytes opened URL downloaded 365Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/tkrplot_0.0-16.zip' Content type 'application/zip' length 24119 bytes opened URL downloaded 23Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maptools_0.6-6.zip' Content type 'application/zip' length 679963 bytes opened URL downloaded 664Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/mapproj_1.1-7.1.zip'
Re: [R] installing packages and windows vista
Thank you Dan! I dunno if I would have ever found that. Thanks! Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, February 07, 2007 9:49 AM To: Duncan Murdoch; [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] installing packages and windows vista Opening R by right clicking and choosing run as administrator' worked. Was able to run install packages without a problem. I have not tested the other methods suggested. thank you. Dan O'Shea -- Original message -- From: Duncan Murdoch [EMAIL PROTECTED] On 2/6/2007 10:33 AM, Daniel O'Shea wrote: I installed R (R-2.4.1-win32.exe) on a new computer with Windows Vista and a 64 bit operating system (hp dv9000 with intel core t7200). The base R runs fine, but I can not get any of the packages to load. From within R I choose install packages choose a site then a package. I tried installing 2 packages and get similar errors (see below), I just copied and pasted lines from R. Can anyone offer any suggestions? Thank you. I believe that on Vista you need to do like other OS's, and run package installs at a higher security level than the default. I don't have Vista so I've never done this, but I've been told you do it by right clicking on the R icon and choosing Run as administrator. I'd be interested in hearing if this is true of all package installs, or only installs to C:/Program files. Can you have a local library for your user, with only user permissions needed to modify packages there? You'd test this by creating a library directory in your own file space, then using .libPaths() to add it to the library location list. By default new installs would go there. Duncan Murdoch Dan O'Shea utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- also installing the dependencies 'scatterplot3d', 'rgl', 'ellipse' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/scatterplot3d_0.3-24.zip' Content type 'application/zip' length 540328 bytes opened URL downloaded 527Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/ellipse_0.3-4.zip' Content type 'application/zip' length 91877 bytes opened URL downloaded 89Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/vegan_1.8-5.zip' Content type 'application/zip' length 1176434 bytes opened URL downloaded 1148Kb Error in zip.unpack(pkg, tmpDir) : cannot open file 'C:/Program Files (x86)/R/R-2.4.1/library/file60bf5753/scatterplot3d/chtml/scatterplot3d.chm' utils:::menuInstallPkgs() also installing the dependencies 'akima', 'gam', 'RColorBrewer', 'sm', 'deldir', 'sp', 'maps', 'spatstat', 'PBSmapping', 'gpclib', 'RArcInfo', 'tkrplot', 'maptools', 'mapproj', 'rgl', 'qcc', 'sgeostat', 'acepack', 'TeachingDemos', 'chron', 'Hmisc' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/akima_0.5-1.zip' Content type 'application/zip' length 128809 bytes opened URL downloaded 125Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gam_0.98.zip' Content type 'application/zip' length 238008 bytes opened URL downloaded 232Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RColorBrewer_0.2-3.zip' Content type 'application/zip' length 39787 bytes opened URL downloaded 38Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sm_2.1-0.zip' Content type 'application/zip' length 400621 bytes opened URL downloaded 391Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/deldir_0.0-5.zip' Content type 'application/zip' length 108656 bytes opened URL downloaded 106Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sp_0.9-4.zip' Content type 'application/zip' length 747542 bytes opened URL downloaded 730Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maps_2.0-33.zip' Content type 'application/zip' length 2219136 bytes opened URL downloaded 2167Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/spatstat_1.11-0.zip' Content type 'application/zip' length 4558460 bytes opened URL downloaded 4451Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/PBSmapping_2.09.zip' Content type 'application/zip' length 6725596 bytes opened URL downloaded 6567Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gpclib_1.3-3.zip' Content type 'application/zip' length 95120 bytes opened URL downloaded 92Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RArcInfo_0.4-7.zip' Content type 'application/zip' length
[R] installing packages and windows vista
I installed R (R-2.4.1-win32.exe) on a new computer with Windows Vista and a 64 bit operating system (hp dv9000 with intel core t7200). The base R runs fine, but I can not get any of the packages to load. From within R I choose install packages choose a site then a package. I tried installing 2 packages and get similar errors (see below), I just copied and pasted lines from R. Can anyone offer any suggestions? Thank you. Dan O'Shea utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- also installing the dependencies 'scatterplot3d', 'rgl', 'ellipse' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/scatterplot3d_0.3-24.zip' Content type 'application/zip' length 540328 bytes opened URL downloaded 527Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/ellipse_0.3-4.zip' Content type 'application/zip' length 91877 bytes opened URL downloaded 89Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/vegan_1.8-5.zip' Content type 'application/zip' length 1176434 bytes opened URL downloaded 1148Kb Error in zip.unpack(pkg, tmpDir) : cannot open file 'C:/Program Files (x86)/R/R-2.4.1/library/file60bf5753/scatterplot3d/chtml/scatterplot3d.chm' utils:::menuInstallPkgs() also installing the dependencies 'akima', 'gam', 'RColorBrewer', 'sm', 'deldir', 'sp', 'maps', 'spatstat', 'PBSmapping', 'gpclib', 'RArcInfo', 'tkrplot', 'maptools', 'mapproj', 'rgl', 'qcc', 'sgeostat', 'acepack', 'TeachingDemos', 'chron', 'Hmisc' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/akima_0.5-1.zip' Content type 'application/zip' length 128809 bytes opened URL downloaded 125Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gam_0.98.zip' Content type 'application/zip' length 238008 bytes opened URL downloaded 232Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RColorBrewer_0.2-3.zip' Content type 'application/zip' length 39787 bytes opened URL downloaded 38Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sm_2.1-0.zip' Content type 'application/zip' length 400621 bytes opened URL downloaded 391Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/deldir_0.0-5.zip' Content type 'application/zip' length 108656 bytes opened URL downloaded 106Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sp_0.9-4.zip' Content type 'application/zip' length 747542 bytes opened URL downloaded 730Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maps_2.0-33.zip' Content type 'application/zip' length 2219136 bytes opened URL downloaded 2167Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/spatstat_1.11-0.zip' Content type 'application/zip' length 4558460 bytes opened URL downloaded 4451Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/PBSmapping_2.09.zip' Content type 'application/zip' length 6725596 bytes opened URL downloaded 6567Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gpclib_1.3-3.zip' Content type 'application/zip' length 95120 bytes opened URL downloaded 92Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RArcInfo_0.4-7.zip' Content type 'application/zip' length 374375 bytes opened URL downloaded 365Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/tkrplot_0.0-16.zip' Content type 'application/zip' length 24119 bytes opened URL downloaded 23Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maptools_0.6-6.zip' Content type 'application/zip' length 679963 bytes opened URL downloaded 664Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/mapproj_1.1-7.1.zip' Content type 'application/zip' length 64188 bytes opened URL downloaded 62Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/qcc_1.2.zip' Content type 'application/zip' length 314782 bytes opened URL downloaded 307Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sgeostat_1.0-20.zip' Content type 'application/zip' length 140584 bytes opened URL downloaded 137Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/acepack_1.3-2.2.zip' Content type 'application/zip' length 55675 bytes opened URL downloaded 54Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/TeachingDemos_1.4.zip' Content type 'application/zip' length 383599 bytes opened URL downloaded 374Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/chron_2.3-9.zip' Content type 'application/zip' length 112830 bytes opened URL downloaded 110Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/Hmisc_3.1-2.zip' Content type 'application/zip' length 2079032 bytes opened URL downloaded 2030Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/Design_2.0-12.zip' Content type
Re: [R] installing packages and windows vista
On 2/6/2007 10:33 AM, Daniel O'Shea wrote: I installed R (R-2.4.1-win32.exe) on a new computer with Windows Vista and a 64 bit operating system (hp dv9000 with intel core t7200). The base R runs fine, but I can not get any of the packages to load. From within R I choose install packages choose a site then a package. I tried installing 2 packages and get similar errors (see below), I just copied and pasted lines from R. Can anyone offer any suggestions? Thank you. I believe that on Vista you need to do like other OS's, and run package installs at a higher security level than the default. I don't have Vista so I've never done this, but I've been told you do it by right clicking on the R icon and choosing Run as administrator. I'd be interested in hearing if this is true of all package installs, or only installs to C:/Program files. Can you have a local library for your user, with only user permissions needed to modify packages there? You'd test this by creating a library directory in your own file space, then using .libPaths() to add it to the library location list. By default new installs would go there. Duncan Murdoch Dan O'Shea utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- also installing the dependencies 'scatterplot3d', 'rgl', 'ellipse' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/scatterplot3d_0.3-24.zip' Content type 'application/zip' length 540328 bytes opened URL downloaded 527Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/ellipse_0.3-4.zip' Content type 'application/zip' length 91877 bytes opened URL downloaded 89Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/vegan_1.8-5.zip' Content type 'application/zip' length 1176434 bytes opened URL downloaded 1148Kb Error in zip.unpack(pkg, tmpDir) : cannot open file 'C:/Program Files (x86)/R/R-2.4.1/library/file60bf5753/scatterplot3d/chtml/scatterplot3d.chm' utils:::menuInstallPkgs() also installing the dependencies 'akima', 'gam', 'RColorBrewer', 'sm', 'deldir', 'sp', 'maps', 'spatstat', 'PBSmapping', 'gpclib', 'RArcInfo', 'tkrplot', 'maptools', 'mapproj', 'rgl', 'qcc', 'sgeostat', 'acepack', 'TeachingDemos', 'chron', 'Hmisc' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/akima_0.5-1.zip' Content type 'application/zip' length 128809 bytes opened URL downloaded 125Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gam_0.98.zip' Content type 'application/zip' length 238008 bytes opened URL downloaded 232Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RColorBrewer_0.2-3.zip' Content type 'application/zip' length 39787 bytes opened URL downloaded 38Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sm_2.1-0.zip' Content type 'application/zip' length 400621 bytes opened URL downloaded 391Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/deldir_0.0-5.zip' Content type 'application/zip' length 108656 bytes opened URL downloaded 106Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sp_0.9-4.zip' Content type 'application/zip' length 747542 bytes opened URL downloaded 730Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maps_2.0-33.zip' Content type 'application/zip' length 2219136 bytes opened URL downloaded 2167Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/spatstat_1.11-0.zip' Content type 'application/zip' length 4558460 bytes opened URL downloaded 4451Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/PBSmapping_2.09.zip' Content type 'application/zip' length 6725596 bytes opened URL downloaded 6567Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gpclib_1.3-3.zip' Content type 'application/zip' length 95120 bytes opened URL downloaded 92Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RArcInfo_0.4-7.zip' Content type 'application/zip' length 374375 bytes opened URL downloaded 365Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/tkrplot_0.0-16.zip' Content type 'application/zip' length 24119 bytes opened URL downloaded 23Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maptools_0.6-6.zip' Content type 'application/zip' length 679963 bytes opened URL downloaded 664Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/mapproj_1.1-7.1.zip' Content type 'application/zip' length 64188 bytes opened URL downloaded 62Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/qcc_1.2.zip' Content type 'application/zip' length 314782 bytes opened URL downloaded 307Kb trying URL
Re: [R] installing packages and windows vista
Daniel O'Shea wrote: I installed R (R-2.4.1-win32.exe) on a new computer with Windows Vista and a 64 bit operating system (hp dv9000 with intel core t7200). The base R runs fine, but I can not get any of the packages to load. From within R I choose install packages choose a site then a package. I tried installing 2 packages and get similar errors (see below), I just copied and pasted lines from R. Can anyone offer any suggestions? Thank you. Hmm. As you might realize, there is as yet very little experience with Vista to go around. Prepare to be quizzed... The immediate suspicions would be permission problems. You might consider changing directory to My Documents/R or whatever the equivalent is on Vista, before you start installation (make sure it exists, of course). You might also try something like install.packages(ISwR, lib=mylib) Again, first make sure that the directory exists. (Reason for suggesting ISwR is that I know that that package has no uninstalled dependencies, so it simplifies the issue.) One more thing to try would be to download the package as a local Zip file and install from that. -pd Dan O'Shea utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- also installing the dependencies 'scatterplot3d', 'rgl', 'ellipse' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/scatterplot3d_0.3-24.zip' Content type 'application/zip' length 540328 bytes opened URL downloaded 527Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/ellipse_0.3-4.zip' Content type 'application/zip' length 91877 bytes opened URL downloaded 89Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/vegan_1.8-5.zip' Content type 'application/zip' length 1176434 bytes opened URL downloaded 1148Kb Error in zip.unpack(pkg, tmpDir) : cannot open file 'C:/Program Files (x86)/R/R-2.4.1/library/file60bf5753/scatterplot3d/chtml/scatterplot3d.chm' utils:::menuInstallPkgs() also installing the dependencies 'akima', 'gam', 'RColorBrewer', 'sm', 'deldir', 'sp', 'maps', 'spatstat', 'PBSmapping', 'gpclib', 'RArcInfo', 'tkrplot', 'maptools', 'mapproj', 'rgl', 'qcc', 'sgeostat', 'acepack', 'TeachingDemos', 'chron', 'Hmisc' trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/akima_0.5-1.zip' Content type 'application/zip' length 128809 bytes opened URL downloaded 125Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gam_0.98.zip' Content type 'application/zip' length 238008 bytes opened URL downloaded 232Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RColorBrewer_0.2-3.zip' Content type 'application/zip' length 39787 bytes opened URL downloaded 38Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sm_2.1-0.zip' Content type 'application/zip' length 400621 bytes opened URL downloaded 391Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/deldir_0.0-5.zip' Content type 'application/zip' length 108656 bytes opened URL downloaded 106Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/sp_0.9-4.zip' Content type 'application/zip' length 747542 bytes opened URL downloaded 730Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maps_2.0-33.zip' Content type 'application/zip' length 2219136 bytes opened URL downloaded 2167Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/spatstat_1.11-0.zip' Content type 'application/zip' length 4558460 bytes opened URL downloaded 4451Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/PBSmapping_2.09.zip' Content type 'application/zip' length 6725596 bytes opened URL downloaded 6567Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/gpclib_1.3-3.zip' Content type 'application/zip' length 95120 bytes opened URL downloaded 92Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/RArcInfo_0.4-7.zip' Content type 'application/zip' length 374375 bytes opened URL downloaded 365Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/tkrplot_0.0-16.zip' Content type 'application/zip' length 24119 bytes opened URL downloaded 23Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/maptools_0.6-6.zip' Content type 'application/zip' length 679963 bytes opened URL downloaded 664Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/mapproj_1.1-7.1.zip' Content type 'application/zip' length 64188 bytes opened URL downloaded 62Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/rgl_0.70.zip' Content type 'application/zip' length 838137 bytes opened URL downloaded 818Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.4/qcc_1.2.zip' Content type 'application/zip' length 314782 bytes opened URL downloaded 307Kb trying URL
[R] Installing packages...
Hi, I am a total newbie to R. I am using R (2.4.1) on Mac OS X 10.4.8 and trying to install some packages using GUI Packages Data/Package Installer interface... Every time I get: trying URL 'http://umfragen.sowi.uni-mainz.de/CRAN/bin/macosx/universal/contrib/2.4/neural_1.4.1.tgz' Content type 'application/x-tar' length 18920 bytes opened URL == downloaded 18Kb Error in gzfile(file, r) : unable to open connection In addition: Warning message: cannot open compressed file 'neural/DESCRIPTION' What am I doing wrong? Any help will be much appreciated. Nüzhet Dalfes Istanbul Tech. Univ. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages...
well, i don't use RGui, but trying: install.packages(neural, type=source) ## from the R command line i could not reproduce the error (which may be a problem with the copy on the mirror you're using)... b On Jan 23, 2007, at 3:09 PM, Nüzhet Dalfes wrote: Hi, I am a total newbie to R. I am using R (2.4.1) on Mac OS X 10.4.8 and trying to install some packages using GUI Packages Data/Package Installer interface... Every time I get: trying URL 'http://umfragen.sowi.uni-mainz.de/CRAN/bin/macosx/universal/ contrib/2.4/neural_1.4.1.tgz' Content type 'application/x-tar' length 18920 bytes opened URL == downloaded 18Kb Error in gzfile(file, r) : unable to open connection In addition: Warning message: cannot open compressed file 'neural/DESCRIPTION' What am I doing wrong? Any help will be much appreciated. Nüzhet Dalfes Istanbul Tech. Univ. __ 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] Installing packages...
2007/1/23, Nüzhet Dalfes [EMAIL PROTECTED]: Hi, I am a total newbie to R. I am using R (2.4.1) on Mac OS X 10.4.8 and trying to install some packages using GUI Packages Data/Package Installer interface... Every time I get: trying URL ' http://umfragen.sowi.uni-mainz.de/CRAN/bin/macosx/universal/contrib/2.4/neural_1.4.1.tgz ' Content type 'application/x-tar' length 18920 bytes opened URL == downloaded 18Kb Error in gzfile(file, r) : unable to open connection In addition: Warning message: cannot open compressed file 'neural/DESCRIPTION' What am I doing wrong? Any help will be much appreciated. Nüzhet Dalfes Istanbul Tech. Univ. __ 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. Dear Mr. Dalfes, I have same opinion with Benilton. I think that you should use the command lines mentioned by him to install packages exclusively. Beside, i don't know the Mac OS X but there may be some problem about your security constraints of your system. -- Ýbrahim Mutlay Ankara, Turkey. [[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.
Re: [R] Installing packages...
why not just type in console: install.packages(neural) and see what happens. On 1/23/07, Nüzhet Dalfes [EMAIL PROTECTED] wrote: Hi, I am a total newbie to R. I am using R (2.4.1) on Mac OS X 10.4.8 and trying to install some packages using GUI Packages Data/Package Installer interface... Every time I get: trying URL 'http://umfragen.sowi.uni-mainz.de/CRAN/bin/macosx/universal/contrib/2.4/neural_1.4.1.tgz' Content type 'application/x-tar' length 18920 bytes opened URL == downloaded 18Kb Error in gzfile(file, r) : unable to open connection In addition: Warning message: cannot open compressed file 'neural/DESCRIPTION' What am I doing wrong? Any help will be much appreciated. Nüzhet Dalfes Istanbul Tech. Univ. __ 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages...
On 24/01/2007, at 7:09 AM, Nüzhet Dalfes wrote: Hi, I am a total newbie to R. I am using R (2.4.1) on Mac OS X 10.4.8 and trying to install some packages using GUI Packages Data/Package Installer interface... Every time I get: trying URL 'http://umfragen.sowi.uni-mainz.de/CRAN/bin/macosx/universal/ contrib/2.4/neural_1.4.1.tgz' Content type 'application/x-tar' length 18920 bytes opened URL == downloaded 18Kb Error in gzfile(file, r) : unable to open connection In addition: Warning message: cannot open compressed file 'neural/DESCRIPTION' What am I doing wrong? Any help will be much appreciated. Nüzhet Dalfes Istanbul Tech. Univ. This looks like a permissions problem, possibly your account doesn't have Administrator privileges. Try selecting At User level for the Install Location in the install packages dialog. There is a special mailling list for mac problems, at https:// stat.ethz.ch/mailman/listinfo/r-sig-mac which may provide a better answer. Ken __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing packages without being a root?
Hi, I have a problem with installing packages without being a superuser(root) in Linux(Suse 10.0 64bit). I've read the entire FAQ and R-admin but I couldn't find a solution to my problem. I'm the admin of the computer but I want other users to install whatever packages they want. Do you think that I have a problem with user priviliges / directory accessin permissions? Thanks, [EMAIL PROTECTED] [[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.
Re: [R] installing packages without being a root?
How about try: R CMD INSTALL -l R_pkg_lib R_pkg ahmet rasit wrote: Hi, I have a problem with installing packages without being a superuser(root) in Linux(Suse 10.0 64bit). I've read the entire FAQ and R-admin but I couldn't find a solution to my problem. I'm the admin of the computer but I want other users to install whatever packages they want. Do you think that I have a problem with user priviliges / directory accessin permissions? Thanks, [EMAIL PROTECTED] [[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. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing packages with R v.2.3.1 on MAC OS X -- Error: Cannot chdir: No such file or directory
Dear all, I'm working on MAC OS X 10.4.7 using R version 2.3.1 (June 2006) and platform powerpc-apple-darwin8.6.0. Since I installed the new version of R I cannot install packages any more (but it worked fine before) and get the following message every time. I can, however, install packages from the command line if I get them as precompiled binaries. -- install.packages(foreign, lib=~/libs/Rlibs) trying URL 'http://www.biometrics.mtu.edu/CRAN/bin/macosx/powerpc/ contrib/2.3/foreign_0.8-15.tgz' Content type 'application/x-gzip' length 268096 bytes opened URL == downloaded 261Kb tar: ~/libs/Rlibs/file77a4044d: Cannot chdir: No such file or directory tar: Error is not recoverable: exiting now gzip: stdout: Broken pipe Error in sprintf(gettext(fmt, domain = domain), ...) : argument is missing, with no default --- The command did create the directory (i.e. ~/libs/Rlibs/file77a4044d) on my system and has open priviledges (i.e. drwxr-xr-x) but is empty. I've tried 'sudo R' but that does not help and cannot find anything helpful on this in the R-help archives or FAQ. Thanks in advance for your help, I would really appreciate any help in solving this, best regards, Snaebjorn __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages with R v.2.3.1 on MAC OS X -- Error: Cannot chdir: No such file or directory
Are you trying to install a package from source? Try adding type='source' when you call install.packages(). The help page for install.packages() indicates the need for this on a Mac. You might also check and see if ~/libs exists, and you have write privileges, but take care of the source vs. binary issue first. Notice the 'bin' in the URL path it mentions. -Don At 12:16 PM -0400 9/21/06, Snaebjorn Gunnsteinsson wrote: Dear all, I'm working on MAC OS X 10.4.7 using R version 2.3.1 (June 2006) and platform powerpc-apple-darwin8.6.0. Since I installed the new version of R I cannot install packages any more (but it worked fine before) and get the following message every time. I can, however, install packages from the command line if I get them as precompiled binaries. -- install.packages(foreign, lib=~/libs/Rlibs) trying URL 'http://www.biometrics.mtu.edu/CRAN/bin/macosx/powerpc/ contrib/2.3/foreign_0.8-15.tgz' Content type 'application/x-gzip' length 268096 bytes opened URL == downloaded 261Kb tar: ~/libs/Rlibs/file77a4044d: Cannot chdir: No such file or directory tar: Error is not recoverable: exiting now gzip: stdout: Broken pipe Error in sprintf(gettext(fmt, domain = domain), ...) : argument is missing, with no default --- The command did create the directory (i.e. ~/libs/Rlibs/file77a4044d) on my system and has open priviledges (i.e. drwxr-xr-x) but is empty. I've tried 'sudo R' but that does not help and cannot find anything helpful on this in the R-help archives or FAQ. Thanks in advance for your help, I would really appreciate any help in solving this, best regards, Snaebjorn __ 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. -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages with R v.2.3.1 on MAC OS X -- Error: Cannot chdir: No such file or directory
Hi Don, type=source solved the problem. Thanks very much for your help, best, Snaebjorn On Sep 21, 2006, at 3:59 PM, Don MacQueen wrote: Are you trying to install a package from source? Try adding type='source' when you call install.packages(). The help page for install.packages() indicates the need for this on a Mac. You might also check and see if ~/libs exists, and you have write privileges, but take care of the source vs. binary issue first. Notice the 'bin' in the URL path it mentions. -Don At 12:16 PM -0400 9/21/06, Snaebjorn Gunnsteinsson wrote: Dear all, I'm working on MAC OS X 10.4.7 using R version 2.3.1 (June 2006) and platform powerpc-apple-darwin8.6.0. Since I installed the new version of R I cannot install packages any more (but it worked fine before) and get the following message every time. I can, however, install packages from the command line if I get them as precompiled binaries. - --- -- install.packages(foreign, lib=~/libs/Rlibs) trying URL 'http://www.biometrics.mtu.edu/CRAN/bin/macosx/powerpc/ contrib/2.3/foreign_0.8-15.tgz' Content type 'application/x-gzip' length 268096 bytes opened URL == downloaded 261Kb tar: ~/libs/Rlibs/file77a4044d: Cannot chdir: No such file or directory tar: Error is not recoverable: exiting now gzip: stdout: Broken pipe Error in sprintf(gettext(fmt, domain = domain), ...) : argument is missing, with no default - --- --- The command did create the directory (i.e. ~/libs/Rlibs/ file77a4044d) on my system and has open priviledges (i.e. drwxr-xr- x) but is empty. I've tried 'sudo R' but that does not help and cannot find anything helpful on this in the R-help archives or FAQ. Thanks in advance for your help, I would really appreciate any help in solving this, best regards, Snaebjorn __ 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. -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing packages without clicking
I need to install several (too many) packages from local *.zip files. is there any form to do it without clicking? I'm asking for a R code that allow me perform these task. --- Mario Alfonso Morales Rivera. Profesor Asistente. Departamento de Matemáticas y estadística. Universidad de Córdoba. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages without clicking
On Tue, 14 Feb 2006, Mario Alfonso Morales Rivera wrote: I need to install several (too many) packages from local *.zip files. is there any form to do it without clicking? I'm asking for a R code that allow me perform these task. See ?install.packages. You seem to be using Windows (you did not say). So the help page says repos: character vector, the base URL(s) of the repositories to use, i.e., the URL of the CRAN master such as 'http://cran.r-project.org;' or its Statlib mirror, 'http://lib.stat.cmu.edu/R/CRAN;'. Can be 'NULL' to install from local '.zip' files. and so all you need is install.packages(c(my1.zip, my2.zip), repos = NULL) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages without clicking
I need to install several (too many) packages from local *.zip files. Are you aware of being able to select multiple .zip files at one time using SHIFT-click or CTRL-click? is there any form to do it without clicking? I'm asking for a R code that allow me perform these task. You could just do what the clicking does, i.e. call the function install.packages() with appropriate parameters. See utils:::menuInstallLocal Hope this helps, Ray Brownrigg __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing packages into updated R
A minor inconvenience in updating an R installation is remembering which packages were installed previously. Has anyone written a script to inspect a previous installation, then get install the same packages into the new installation? -- Michael Prager NOAA Center for Coastal Fisheries and Habitat Research Beaufort, North Carolina 28516 Opinions expressed are personal, not official. No government endorsement of any product is made or implied. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages into updated R
In http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip are two Windows XP batch files: movedir.bat copydir.bat which will move the packages (which is much faster and suitable if you don't need the old version of R any more) or copy the packages (which takes longer but preserves the old version). On 12/20/05, Michael H. Prager [EMAIL PROTECTED] wrote: A minor inconvenience in updating an R installation is remembering which packages were installed previously. Has anyone written a script to inspect a previous installation, then get install the same packages into the new installation? -- Michael Prager NOAA Center for Coastal Fisheries and Habitat Research Beaufort, North Carolina 28516 Opinions expressed are personal, not official. No government endorsement of any product is made or implied. __ 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] Installing packages into updated R
Michael H. Prager wrote: A minor inconvenience in updating an R installation is remembering which packages were installed previously. Has anyone written a script to inspect a previous installation, then get install the same packages into the new installation? x - installed.packages()[,1] install.packages(x) Uwe Ligges __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages into updated R
This is one reason we normally recommend that you install into a separate library. Then update.packages(checkBuilt = TRUE) is all that is needed. However, foo - installed.packages() as.vector(foo[is.na(foo[, Priority]), 1]) will give you a character vector which you can feed to install.packages(), so it's not complex to do manually. On Tue, 20 Dec 2005, Michael H. Prager wrote: A minor inconvenience in updating an R installation is remembering which packages were installed previously. Has anyone written a script to inspect a previous installation, then get install the same packages into the new installation? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages into updated R
On Ti, 2005-12-20, 16:11, Michael H. Prager skrev: A minor inconvenience in updating an R installation is remembering which packages were installed previously. Has anyone written a script to inspect a previous installation, then get install the same packages into the new installation? If the previous installation is still alive, fire it up and pS - packageStatus() pkgs - pS$inst$Package[!pS$inst$Priority %in% c(base, recommended)] save(pkgs, file = foo) In the new installation, load(foo) install.packages(pkgs) HTH Henric __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing packages, again
Hi again, I've just uninstalled R2.01 and installed the new R2.10 on my WindowsXP machine. I then attempted to install the vegan package from source files, as I learned to do last week, with the help of some of you. I have updated my path variable to the new R directory (R/rw2010/bin instead of R/rw2001pat/bin), and I've still got the HTMLHelpWorkshop files installed, as well as Perl and the MinGW compiler. I didn't change anything in those files, and everything is stored in directories without spaces in the name. I had trouble with the install, so I deleted the rtools folder and reinstalled it. Still, the package won't install. Following R CMD INSTALL vegan I get the error: no rule to make target 'C:/R/rw2001pat/include/R.h', needed by 'goffactor.o'. Stop. So it looks like I've still got something pointing to the old rw2001pat directory, instead of the new rw2010 directory. Can anyone tell me what I've overlooked? I have also gone into Mkrules and updated all the paths that I could. Thanks again, Tyler -- Tyler Smith PhD Candidate Department of Plant Science McGill University [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages, again
On Mon, 25 Apr 2005, Tyler Smith wrote: I've just uninstalled R2.01 and installed the new R2.10 on my WindowsXP machine. I then attempted to install the vegan package from source files, as I learned to do last week, with the help of some of you. I have updated my path variable to the new R directory (R/rw2010/bin instead of R/rw2001pat/bin), and I've still got the HTMLHelpWorkshop files installed, as well as Perl and the MinGW compiler. I didn't change anything in those files, and everything is stored in directories without spaces in the name. I had trouble with the install, so I deleted the rtools folder and reinstalled it. Still, the package won't install. Following R CMD INSTALL vegan I get the error: no rule to make target 'C:/R/rw2001pat/include/R.h', needed by 'goffactor.o'. Stop. So it looks like I've still got something pointing to the old rw2001pat directory, instead of the new rw2010 directory. Can anyone tell me what I've overlooked? I have also gone into Mkrules and updated all the paths that I could. Create a file in the 'vegan' package directory named '.Rbuildignore' and add the text 'Makedeps' on a line by itself. See if that fixes your problem. You're picking up the dependencies from previous version's last compilation. You could also delete this file since it'll be recreated anyway. IMO, the file 'Makedeps' should be added to the list of files R ignores by default. -- SIGSIG -- signature too long (core dumped) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing packages, again
Thanks! I tried adding the .Rbuildignore file, but that didn't work out. So I found the Makedeps file in the vegan/src folder and deleted it. That solved the problem. Tyler -- Tyler Smith PhD Candidate Department of Plant Science [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Installing packages from source on WindowsXP
I recall having this problem. I think I had a version that didn't work. Did you download the htmlhelp.exe from http://www.murdoch-sutherland.com/Rtools/ . The path does not matter as I have it in a folder on it's own. I think that I also had a path to the version that didn't work and I had to get my IT people to let me put my location first. Tom -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Tyler Smith Sent: Friday, 22 April 2005 1:27 PM To: R-Help Subject: [R] Installing packages from source on WindowsXP Hi, I'm having some problems installing packages from the source files on Windows, using R CMD INSTALL pkg. I'm running WindowsXP, and I've followed the instructions as per the README.packages file from the R installation. I ran into a hitch, with the install failing following a hhc: not found warning. I figured out that this was related to the html help workshop. Adding the HHW folder to the Path variable didn't help. README.packages mentions that HHW should be in the same drive as the other tools, which it is, but in a different folder. So I put a copy of hhc.exe in the Rtools/bin folder and everything seems to have worked out. My question is, is this going to cause me problems later on? Should I transfer all the HHW files to the Rtools/bin? Is there a better way to arrange the HHW files? I'm installing from source files instead of using the automated GUI feature because I want to read the original code to see how experienced users write functions. I'm using version 2.0.1 Patched (2005-04-16). Thanks for your time, Tyler -- Tyler Smith PhD Candidate Department of Plant Science McGill University [EMAIL PROTECTED] __ 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] Installing packages from source on WindowsXP
Tyler Smith wrote: Hi, I'm having some problems installing packages from the source files on Windows, using R CMD INSTALL pkg. I'm running WindowsXP, and I've followed the instructions as per the README.packages file from the R installation. I ran into a hitch, with the install failing following a hhc: not found warning. I figured out that this was related to the html help workshop. Adding the HHW folder to the Path variable didn't help. README.packages mentions that HHW should be in the same drive as the other tools, which it is, but in a different folder. So I put a copy of hhc.exe in the Rtools/bin folder and everything seems to have worked out. My question is, is this going to cause me problems later on? Should I No, only if you want to update and forget to update that file as well. Uwe Ligges transfer all the HHW files to the Rtools/bin? Is there a better way to arrange the HHW files? I'm installing from source files instead of using the automated GUI feature because I want to read the original code to see how experienced users write functions. I'm using version 2.0.1 Patched (2005-04-16). Thanks for your time, Tyler __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing packages from source on WindowsXP
Ok, I uninstalled my copy of HHW (and deleted the extra file from the Rtools/bin folder), and reinstalled from the murdoch-sutherland site. From what I read there I think it's the same version, and I actually get a warning that I already have a newer version installed on my machine (1.3.1) anyways. Just for good measure I installed it to C:\HTMLHelpWorkshop, instead of the default location in Program Files\HTML Help Workshop, in case the spaces in the folder names was an issue. I updated the Path variable and voila, everything seems to be working fine. So, whatever the actual problem was, it's gone now. Magic. Thanks!! On a related note, now that I seem to be on top of installing packages from source files, is there any advantage to installing the R software itself from source files? From the help files that sounds even trickier... Tyler -- Tyler Smith PhD Candidate Department of Plant Science McGill University CANADA [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages from source on WindowsXP
Tyler Smith wrote: Ok, I uninstalled my copy of HHW (and deleted the extra file from the Rtools/bin folder), and reinstalled from the murdoch-sutherland site. From what I read there I think it's the same version, and I actually get a warning that I already have a newer version installed on my machine (1.3.1) anyways. Just for good measure I installed it to C:\HTMLHelpWorkshop, instead of the default location in Program Files\HTML Help Workshop, in case the spaces in the folder names was an issue. I updated the Path variable and voila, everything seems to be working fine. So, whatever the actual problem was, it's gone now. Magic. Thanks!! On a related note, now that I seem to be on top of installing packages from source files, is there any advantage to installing the R software itself from source files? From the help files that sounds even trickier... Yes, there some advantages, for example: - if you want to change something in the sources - if you want to link against some CPU optimized linear algebra system such as Goto's BLAS, etc. But if you want to use R as is anyway (as most several users do), you won't have advantages from my point of view. Uwe Ligges Tyler __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages from source on WindowsXP
On Fri, 2005-04-22 at 09:46 -0400, Tyler Smith wrote: Ok, I uninstalled my copy of HHW (and deleted the extra file from the Rtools/bin folder), and reinstalled from the murdoch-sutherland site. From what I read there I think it's the same version, and I actually get a warning that I already have a newer version installed on my machine (1.3.1) anyways. Just for good measure I installed it to C:\HTMLHelpWorkshop, instead of the default location in Program Files\HTML Help Workshop, in case the spaces in the folder names was an issue. I updated the Path variable and voila, everything seems to be working fine. So, whatever the actual problem was, it's gone now. Magic. Thanks!! On a related note, now that I seem to be on top of installing packages from source files, is there any advantage to installing the R software itself from source files? From the help files that sounds even trickier... Tyler R Windows FAQ 2.17 R can't find my file, but I know it is there! ... Another possible source of grief is spaces in folder names. ... Also, from the R Admin Manual (page 35): Do not use filepaths containing spaces If you want to compile from source, be sure to completely review the R Admin Manual for details on this process under Windows. There are some potential advantages relative to using optimized libraries (ie. BLAS). These are mentioned in the Admin Manual. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing packages from source code
Hi everybody,
I have trouble in installing packages from source code by following Section
5.1 in manual R-admin.pdf . I am using R 2.1.0 and Win NT.
Following the Windows toolset section in the manual, I download the tool
set package from: http://www.murdoch-sutherland.com/Rtools/tools.zip
and unzip under C:\tools
I also downloaded Perl (Windows Port) and installed it.
I downloaded source code of abind package (abind.1.1-0.tar.gz) to C:\, as
an example.
1. I tried to install abind package in Rgui by typing in:
install.packages(repos=NULL, pkgs='c:/abind.1.1-0.tar.gz', type='source', lib =
'c:/program files/r/rw2010/library/')
Warning message:
installation of package 'c:/abind.1.1-0.tar.gz' had non-zero exit status in:
install.packages(repos = NULL, pkgs = c:/abind.1.1-0.tar.gz,
2. I then tried to install abind package in CMD:
r cmd install -l c:/progra~1/r/rw2010/library/ c:/abind.1.1-0.tar.gz
ARGUMENT 'cmd' __ignored__
ARGUMENT 'install' __ignored__
WARNING: unknown option -l
ARGUMENT 'c:/progra~1/r/rw2010/library/'
ARGUMENT 'c:/abind.1.1-0.tar.gz' __ignor
R : Copyright 2004, The R Foundation for
Version 2.0.1 (2004-11-15), ISBN 3-9000
R is free software and comes with ABSOLU
You are welcome to redistribute it under
Type 'license()' or 'licence()' for dist
R is a collaborative project with many c
Type 'contributors()' for more informati
'citation()' on how to cite R or R packa
Type 'demo()' for some demos, 'help()' f
'help.start()' for a HTML browser interf
Type 'q()' to quit R.
[Previously saved workspace restored]
The purpose of installing package from source code is that I hope it can create
those rds files in meta directory automatically.
I wonder if I miss anything here. Can anyone help me out please?
Thanks alot,
Huan
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[R] Installing packages from source on WindowsXP
Hi, I'm having some problems installing packages from the source files on Windows, using R CMD INSTALL pkg. I'm running WindowsXP, and I've followed the instructions as per the README.packages file from the R installation. I ran into a hitch, with the install failing following a hhc: not found warning. I figured out that this was related to the html help workshop. Adding the HHW folder to the Path variable didn't help. README.packages mentions that HHW should be in the same drive as the other tools, which it is, but in a different folder. So I put a copy of hhc.exe in the Rtools/bin folder and everything seems to have worked out. My question is, is this going to cause me problems later on? Should I transfer all the HHW files to the Rtools/bin? Is there a better way to arrange the HHW files? I'm installing from source files instead of using the automated GUI feature because I want to read the original code to see how experienced users write functions. I'm using version 2.0.1 Patched (2005-04-16). Thanks for your time, Tyler -- Tyler Smith PhD Candidate Department of Plant Science McGill University [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installing Packages on an Athlon 64 Linux System
I installed FC 2 X86-64 on an Athlon 64 system. I then installed R 2.0.0. It runs fine except when I try to install or update packages using either install.packages or update.packages. I get the following types of errors: gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c block.c -o block.o cc1: error: CPU you selected does not support x86-64 instruction set cc1: error: CPU you selected does not support x86-64 instruction set make: *** [block.o] Error 1 ERROR: compilation failed for package 'gstat' ** Removing '/usr/lib/R/library/gstat' ** Restoring previous '/usr/lib/R/library/gstat' How can I fix this? Rick B. __ [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] Installing Packages on an Athlon 64 Linux System
rab [EMAIL PROTECTED] writes: I installed FC 2 X86-64 on an Athlon 64 system. I then installed R 2.0.0. It runs fine except when I try to install or update packages using either install.packages or update.packages. I get the following types of errors: gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c block.c -o block.o cc1: error: CPU you selected does not support x86-64 instruction set cc1: error: CPU you selected does not support x86-64 instruction set Well it doesn't. So what is -march=i386 -mcpu=i686 doing in the CFLAGS? Sounds like you are using a 386-compiled R in compatibility mode and are getting bitten by the fact that your gcc is not a cross compiler. Did you use Martyn's RPMs? If so, I'd try a local rebuild (look up the docs for rpmbuild) of R from the SRPM. Another option might be that you need to set up a 32 bit build environment. I don't know FC3 but on SuSE you have the linux32 prefix to configure c. -- 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] Installing Packages on an Athlon 64 Linux System
On our SLES8 for amd64 installation, GCC 3.2.x (forgot what x is) is the default, and does not support -mcpu=k8. GCC 3.3.x is installed in /opt/gcc33, and does support that flag. Andy From: Peter Dalgaard rab [EMAIL PROTECTED] writes: I installed FC 2 X86-64 on an Athlon 64 system. I then installed R 2.0.0. It runs fine except when I try to install or update packages using either install.packages or update.packages. I get the following types of errors: gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c block.c -o block.o cc1: error: CPU you selected does not support x86-64 instruction set cc1: error: CPU you selected does not support x86-64 instruction set Well it doesn't. So what is -march=i386 -mcpu=i686 doing in the CFLAGS? Sounds like you are using a 386-compiled R in compatibility mode and are getting bitten by the fact that your gcc is not a cross compiler. Did you use Martyn's RPMs? If so, I'd try a local rebuild (look up the docs for rpmbuild) of R from the SRPM. Another option might be that you need to set up a 32 bit build environment. I don't know FC3 but on SuSE you have the linux32 prefix to configure c. -- 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 __ [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] Installing Packages on an Athlon 64 Linux System
On Sat, 6 Nov 2004, rab wrote: I installed FC 2 X86-64 on an Athlon 64 system. I then installed R 2.0.0. It runs fine except when I try to install or update packages using either install.packages or update.packages. I get the following types of errors: gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c block.c -o block.o cc1: error: CPU you selected does not support x86-64 instruction set cc1: error: CPU you selected does not support x86-64 instruction set make: *** [block.o] Error 1 ERROR: compilation failed for package 'gstat' ** Removing '/usr/lib/R/library/gstat' ** Restoring previous '/usr/lib/R/library/gstat' How can I fix this? How did you get -pipe -march=i386 -mcpu=i686? That was not put there by R, and is the problem. If you did not build R from the sources on that machine, please do so -- if this was a binary install it is for the wrong architecture. -- 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] Installing Packages on an Athlon 64 Linux System
But this is FC2, not FC3 (not released until tomorrow) and not SuSE. gcc 3.3.3 and 64-bit builds are the default on FC2, and R build out of the box (unsuprising as it is one of our standard test platforms). I have offered Martyn an RPM for FC2 on x86_64, but not had a reply. On Sat, 6 Nov 2004, Liaw, Andy wrote: On our SLES8 for amd64 installation, GCC 3.2.x (forgot what x is) is the default, and does not support -mcpu=k8. GCC 3.3.x is installed in /opt/gcc33, and does support that flag. Andy From: Peter Dalgaard rab [EMAIL PROTECTED] writes: I installed FC 2 X86-64 on an Athlon 64 system. I then installed R 2.0.0. It runs fine except when I try to install or update packages using either install.packages or update.packages. I get the following types of errors: gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c block.c -o block.o cc1: error: CPU you selected does not support x86-64 instruction set cc1: error: CPU you selected does not support x86-64 instruction set Well it doesn't. So what is -march=i386 -mcpu=i686 doing in the CFLAGS? Sounds like you are using a 386-compiled R in compatibility mode and are getting bitten by the fact that your gcc is not a cross compiler. Did you use Martyn's RPMs? If so, I'd try a local rebuild (look up the docs for rpmbuild) of R from the SRPM. Another option might be that you need to set up a 32 bit build environment. I don't know FC3 but on SuSE you have the linux32 prefix to configure c. -- 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 __ [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
[R] Installing packages on Debian linux
Hello R users!
I am running R on windows and linux (Debian). Until recently I found
the function
install.packages('R-package_name')
which is just great and simple. It is standard for installing packages
for me under windows. Under Debian linux I got used to installing packages
vie apt-get tool and also R CMD INSTALL. As I can see R is using the
same/similiar packaging system (dependencies, ...) as Debian. Is it wise
to mix all three methods?
Which method is prefered for installation of R packages under Debian linux?
- apt-get install R-package_name
- install.packages('R-package_name')
I actually never tried with install.packages under linux. Where does it put
the filesm under /usr/local or standard path?
Thanks!
--
Lep pozdrav / With regards,
Gregor GORJANC
---
University of Ljubljana
Biotechnical Faculty URI: http://www.bfro.uni-lj.si
Zootechnical Departmentemail: gregor.gorjanc at bfro.uni-lj.si
Groblje 3 tel: +386 (0)1 72 17 861
SI-1230 Domzalefax: +386 (0)1 72 41 005
Slovenia
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Re: [R] Installing packages on Debian linux
Gorjanc Gregor wrote:
same/similiar packaging system (dependencies, ...) as Debian. Is it wise
to mix all three methods?
Mixing R CMD and install.packages() doesn't pose any problems, AFAIK, but
mixing any of them with apt-get does. The problem is that apt-get doesn't
know what you're doing with R CMD or install.packages() or remove.packages(),
so you may end up with duplicate packages (possibly in different places, see
below). I generally try to leave as much package management up to the system,
so I choose apt-get whenever possible. However, not all CRAN packages are
available from Debian yet, so you may end up having to use install.packages()
to install some packages.
Which method is prefered for installation of R packages under Debian linux?
- apt-get install R-package_name
- install.packages('R-package_name')
I actually never tried with install.packages under linux. Where does it put
the filesm under /usr/local or standard path?
install.packages() will use /usr/local/lib/R/site-library as default, but you
can change that with the lib argument. apt-get will put them
in /usr/lib/R/site-library.
I have a question to add myself though: is it still necessary to add a line
like:
deb http://cran.r-project.org/bin/linux/debian woody main
to /etc/apt/sources.list, as indicated in the CRAN mirrors? This might be
redundant, as a lot of packages are already available through the Debian
mirrors anyway, but I haven't checked how the list compares with the one in
CRAN.
Dirk? (Dirk Eddelbuettel is the maintainer of R Debian packages)
--
Best wishes,
Sebastian
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Re: [R] Installing packages on OS X
On Wed, 2004-09-08 at 21:25, hadley wickham wrote: On my computer, it seems that (binary?) packages installed through the GUI in RAqua are not used available to the command line version of R, while (source) packages installed with R CMD INSTALL are available to both. This is a problem when I run R CMD CHECK on a package that I am creating that depends on packages I have installed through the gui. Is this a problem with my installation of R, or a known limitation? (there is no mention of this in the Mac OS X faq, however, the entire section entitled Installing packages is blank). It is in some other FAQ... Unfortunately, I don't have a Mac available now, so I can't check. However, seek for environmental variables and setting library paths in some other R FAQ or R Administration/Installation guide. There will you find a description of things you should do. It is just as crystal clear as unix man pages: everything is clear *after* you know what is said there, but you may have hard time noticing this clarity. I solved this problem some months ago after a long search among the official documentation. So it is documented, but well hidden. I may have a look at a machine where I solved this in the evening (UTC+3), if you won't get solution before that. 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] Installing packages on OS X
Here's my guess: R CMD INSTALL installs to .Library, and does not look at R_LIBS unless set in its environment. install.packages() installs at .libPaths()[1], and uses all the library trees available. So if you have R_LIBS set in ~/.Renviron (as I have), or .libPaths() set in .Rprofile or elsewhere, you need to set R_LIBS in your shell before calling R CMD check (l/case). On 9 Sep 2004, Jari Oksanen wrote: On Wed, 2004-09-08 at 21:25, hadley wickham wrote: On my computer, it seems that (binary?) packages installed through the GUI in RAqua are not used available to the command line version of R, while (source) packages installed with R CMD INSTALL are available to both. This is a problem when I run R CMD CHECK on a package that I am creating that depends on packages I have installed through the gui. Is this a problem with my installation of R, or a known limitation? (there is no mention of this in the Mac OS X faq, however, the entire section entitled Installing packages is blank). It is in some other FAQ... Unfortunately, I don't have a Mac available now, so I can't check. However, seek for environmental variables and setting library paths in some other R FAQ or R Administration/Installation guide. There will you find a description of things you should do. It is just as crystal clear as unix man pages: everything is clear *after* you know what is said there, but you may have hard time noticing this clarity. I solved this problem some months ago after a long search among the official documentation. So it is documented, but well hidden. I may have a look at a machine where I solved this in the evening (UTC+3), if you won't get solution before that. cheers, jari oksanen -- 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] Installing packages on OS X
Thanks to you both. Setting R_LIBS='~/Library/R/library/' in ~/.Renviron did the trick. Thanks, Hadley __ [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
[R] Installing packages on OS X
On my computer, it seems that (binary?) packages installed through the GUI in RAqua are not used available to the command line version of R, while (source) packages installed with R CMD INSTALL are available to both. This is a problem when I run R CMD CHECK on a package that I am creating that depends on packages I have installed through the gui. Is this a problem with my installation of R, or a known limitation? (there is no mention of this in the Mac OS X faq, however, the entire section entitled Installing packages is blank). Thanks, Hadley __ [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
[R] Installing packages from ZIP files
I have R 1.9.0 running under Solaris 2.9 ona SunBlade 100, and am very happy with it. I heard about the stuff at www.rmetrics.org and thought it might be worth looking at. However, what I found there is a bunch of .zip files. The entry page suggests that there is some way to install packages from .zip files in R, but I have searched all the documentation I have and cannot find it. _Is_ there a way to install a package from a local .zip file in R 1.9.0 for Unix, and if so, what is it? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages from ZIP files
On Wed, 19 May 2004, Richard A. O'Keefe wrote: I have R 1.9.0 running under Solaris 2.9 ona SunBlade 100, and am very happy with it. I heard about the stuff at www.rmetrics.org and thought it might be worth looking at. However, what I found there is a bunch of .zip files. The entry page suggests that there is some way to install packages from .zip files in R, but I have searched all the documentation I have and cannot find it. _Is_ there a way to install a package from a local .zip file in R 1.9.0 for Unix, and if so, what is it? Unzip it into a suitable dir, then R CMD INSTALL. -- 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] Installing packages from ZIP files
I asked about installing R packages from ZIP files, specifically with respect to the Rmetrics packages. Sean Davis [EMAIL PROTECTED] asked: Have you tried R CMD INSTALL filename.zip? If that didn't work, could you simply unzip filename.zip and install using R CMD INSTALL filename? If you can't unzip the zip files (using command unzip), that may be the problem. Yes, I have tried R CMD INSTALL filename.zip, and it doesn't work. I can unzip the files, and I get perfectly reasonable-looking directory trees when I do this (except for the thrice-accursed MS-DOS carriage returns all over the place, which presumably do R no harm). f% ls -l *.zip -rw-r--r-- 1 ok comsci472733 May 19 13:57 evir_1.0.zip -rw-r--r-- 1 ok comsci 1391119 May 19 14:01 fBasics_190.10051.zip -rw-r--r-- 1 ok comsci255366 May 19 13:56 fExtremes_190.10051.zip -rw-r--r-- 1 ok comsci370293 May 19 13:57 fOptions_190.10051.zip -rw-r--r-- 1 ok comsci938564 May 19 13:59 fSeries_190.10051.zip f% unzip -l evir_1.0.zip Archive: evir_1.0.zip LengthDateTimeName -- 1875 11-21-02 14:24 evir/INDEX 37 11-21-02 14:24 evir/TITLE 2174 11-21-02 14:24 evir/RCHANGES 1923 11-21-02 14:24 evir/README 624 11-21-02 14:24 evir/DESCRIPTION 0 11-21-02 14:24 evir/R/ 49555 11-21-02 14:24 evir/R/evir 0 11-21-02 14:24 evir/demo/ 246 11-21-02 14:24 evir/demo/00Index ... 0 11-21-02 14:24 evir/data/ 367 11-21-02 14:24 evir/data/00Index ... 0 11-21-02 14:24 evir/man/ 41581 11-21-02 14:24 evir/man/evir.Rd ... 0 11-21-02 14:24 evir/help/ 644 11-21-02 14:24 evir/help/AnIndex ... 0 11-21-02 14:24 evir/html/ 4867 11-21-02 14:24 evir/html/00Index.html ... 1165 11-21-02 14:24 evir/html/bmw.html 0 11-21-02 14:24 evir/latex/ 781 11-21-02 14:24 evir/latex/bmw.tex ... 0 11-21-02 14:24 evir/R-ex/ 295 11-21-02 14:24 evir/R-ex/decluster.R ... 4971 11-21-02 14:24 evir/CONTENTS 0 11-21-02 14:24 evir/chtml/ 52043 11-21-02 14:24 evir/chtml/evir.chm 0 11-21-02 14:24 evir/ ----- 1150125161 files But f% /users/local/bin/R CMD INSTALL evir_1.0.zip gzip: evir_1.0.zip has more than one entry--rest ignored tar: tape blocksize error error: cannot extract package from 'evir_1.0.zip': No such file or directory for reading errors. f% /users/local/bin/R CMD INSTALL fBasics_190.10051.zip gzip: fBasics_190.10051.zip has more than one entry--rest ignored tar: blocksize = 0 error: cannot extract package from 'fBasics_190.10051.zip': No such file or directory for reading errors. f% /users/local/bin/R CMD INSTALL fExtremes_190.10051.zip gzip: fExtremes_190.10051.zip has more than one entry--rest ignored tar: blocksize = 0 error: cannot extract package from 'fExtremes_190.10051.zip': No such file or directory for reading errors. R CMD INSTALL --help talks about *making* ZIP files, but says nothing about *using* ZIP files. I would have assumed, on the grounds of silence, that R couldn't install from ZIP files except that www.rmetrics.org evidently think it *can*. The suggestion to unzip the file and then pass the name of the *directory* (not a plain file) to R CMD INSTALL seems to be working. Perhaps one sentence could be added to ?INSTALL or R CMD INSTALL --help saying To install from a ZIP file, first unzip the file and then install the resulting directory. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing packages
Fred J. wrote:
yes, I loged in as admin. and that fixed the problem,
but when I type ?fdim I don't get the help docs, why?
even though I have all the htmls under
C:\Program Files\R\rw1081\library\fdim\html
thanks
Either you forgot to load the package
library(fdim)
or your installation is still broken (please check whether you have got
read permissions) ...
BTW: Without having changed the defaults, you will need the files in
...\fdim\help, those in ...\fdim\html will be displayed after setting
options(htmlhelp=TRUE).
Uwe Ligges
--- Duncan Murdoch [EMAIL PROTECTED] wrote:
On Sat, 6 Mar 2004 13:30:25 -0800 (PST), you wrote:
Error in int.unzip(zipname, NULL, dest) :
destination
does not exist
R tries to build a temporary directory to hold the
files, and it
sounds as though it's failing when it does that.
You can see the sort
of name it is trying to use with this command:
tempfile(,.libPaths()[1])
[1] F:/R/cvs/r-devel/library\\file27447
If you don't have permission to create a directory
with that name,
then the command will fail. I'd guess that's your
problem.
The way around this is to install the library in a
local path, instead
of one where you don't have write access. You can
do this within a
session by calling
.libPaths('c:/newpath')
and on the command line that invoked R by adding the
argument
R_LIBS=c:/newpath.
Notice the use of the forward slash, not a
backslash, in the path
name.
Duncan Murdoch
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RE: [R] Installing packages
local({a - CRAN.packages()
+ install.packages(select.list(a[,1],,TRUE),
.libPaths()[1], available=a)})
trying URL
`http://cran.r-project.org/bin/windows/contrib/1.8/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length
16079 bytes
opened URL
downloaded 15Kb
trying URL
`http://cran.r-project.org/bin/windows/contrib/1.8/fdim_1.0-2.zip'
Content type `application/zip' length 71062 bytes
opened URL
downloaded 69Kb
Error in int.unzip(zipname, NULL, dest) : destination
does not exist
--- Andrew C. Ward [EMAIL PROTECTED] wrote:
You won't have to type anything if you install CRAN
packages through the menu system (Packages-Install
package(s) from CRAN..). Failing that, please tell
us more about what the error was.
Regards,
Andrew C. Ward
56 Azalea Crescent
Fitzgibbon Qld 4018
[EMAIL PROTECTED]
On Saturday, March 06, 2004 3:47 PM, Fred J.
[SMTP:[EMAIL PROTECTED] wrote:
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Re: [R] Installing packages
On Sat, 6 Mar 2004 13:30:25 -0800 (PST), you wrote:
Error in int.unzip(zipname, NULL, dest) : destination
does not exist
R tries to build a temporary directory to hold the files, and it
sounds as though it's failing when it does that. You can see the sort
of name it is trying to use with this command:
tempfile(,.libPaths()[1])
[1] F:/R/cvs/r-devel/library\\file27447
If you don't have permission to create a directory with that name,
then the command will fail. I'd guess that's your problem.
The way around this is to install the library in a local path, instead
of one where you don't have write access. You can do this within a
session by calling
.libPaths('c:/newpath')
and on the command line that invoked R by adding the argument
R_LIBS=c:/newpath.
Notice the use of the forward slash, not a backslash, in the path
name.
Duncan Murdoch
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Re: [R] Installing packages
yes, I loged in as admin. and that fixed the problem,
but when I type ?fdim I don't get the help docs, why?
even though I have all the htmls under
C:\Program Files\R\rw1081\library\fdim\html
thanks
--- Duncan Murdoch [EMAIL PROTECTED] wrote:
On Sat, 6 Mar 2004 13:30:25 -0800 (PST), you wrote:
Error in int.unzip(zipname, NULL, dest) :
destination
does not exist
R tries to build a temporary directory to hold the
files, and it
sounds as though it's failing when it does that.
You can see the sort
of name it is trying to use with this command:
tempfile(,.libPaths()[1])
[1] F:/R/cvs/r-devel/library\\file27447
If you don't have permission to create a directory
with that name,
then the command will fail. I'd guess that's your
problem.
The way around this is to install the library in a
local path, instead
of one where you don't have write access. You can
do this within a
session by calling
.libPaths('c:/newpath')
and on the command line that invoked R by adding the
argument
R_LIBS=c:/newpath.
Notice the use of the forward slash, not a
backslash, in the path
name.
Duncan Murdoch
__
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Re: [R] Installing packages
Fred,
Did you loaded the library before typing ?fdim
?fdim
Error in help(fdim) : No documentation for `fdim' in specified packages
and libraries:
you could try `help.search(fdim)'
library(fdim)
?fdim
fdim package:fdim R Documentation
Calculation of generalizated fractal dimension of Data-Sets.
Description:
Returns the Fractal Dimension of data-frames.
Usage:
fdim(X, BaseR=2, Mnmax=TRUE, nMax=9, NumMinP=1, q=0, Alpha=0.2,
PlotF=FALSE)
Arguments:
Hector
At 12:04 AM 3/7/2004, Fred J. wrote:
yes, I loged in as admin. and that fixed the problem,
but when I type ?fdim I don't get the help docs, why?
even though I have all the htmls under
C:\Program Files\R\rw1081\library\fdim\html
thanks
--- Duncan Murdoch [EMAIL PROTECTED] wrote:
On Sat, 6 Mar 2004 13:30:25 -0800 (PST), you wrote:
Error in int.unzip(zipname, NULL, dest) :
destination
does not exist
R tries to build a temporary directory to hold the
files, and it
sounds as though it's failing when it does that.
You can see the sort
of name it is trying to use with this command:
tempfile(,.libPaths()[1])
[1] F:/R/cvs/r-devel/library\\file27447
If you don't have permission to create a directory
with that name,
then the command will fail. I'd guess that's your
problem.
The way around this is to install the library in a
local path, instead
of one where you don't have write access. You can
do this within a
session by calling
.libPaths('c:/newpath')
and on the command line that invoked R by adding the
argument
R_LIBS=c:/newpath.
Notice the use of the forward slash, not a
backslash, in the path
name.
Duncan Murdoch
__
[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
Héctor L. Ayala-del-Río, Ph.D.
Center for Microbial Ecology
Michigan State University
540 Plant Soil Sciences Building
East Lansing, MI 48824
Tel: 517-353-9021
Fax: 517-353-2917
[EMAIL PROTECTED]
__
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[R] installing packages on MAC os X
Hello, I've just downloaded and installed the RAqua onto my Mac and I have R up and running fine. Now I'm trying to get 'ape' downloaded and installed and having quite the difficulty. I am following the directions specified under 'Installing packages' where packages can be downloaded and installed from within R. I get the following error messages: 1: argument 'lib' is missing: using ~/Library/RAqua/library in: install.packages(ape) 2: Installation of package ape had non-zero exit status in: install.packages(ape) Can you please advise on what I am doing wrong? thanks! Sara Good-Avila Sara V. Good-Avila, http://ace.acadiau.ca/~savila/webpage/ Department of Biology Acadia University Wolfville, Nova Scotia Canada, B4P 2R6 Phone: (902) 585-1798 Fax -1059 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] installing packages on MAC os X
On Mon, 29 Dec 2003, Sara Good-Avila wrote: Hello, I've just downloaded and installed the RAqua onto my Mac and I have R up and running fine. Now I'm trying to get 'ape' downloaded and installed and having quite the difficulty. I am following the directions specified under 'Installing packages' where packages can be downloaded and installed from within R. It would help if you said what you actually did -- I'm not sure which instructions you mean. I get the following error messages: These are actually warning messages, not error messages 1: argument 'lib' is missing: using ~/Library/RAqua/library in: install.packages(ape) This one is unsightly but harmless (it will go away in the next version) 2: Installation of package ape had non-zero exit status in: install.packages(ape) This is the problem, but it doesn't say what the cause is. Try again, but this time also open a `Console' window (look under Applications then Utilities in the Finder). This will show the actual output from the installation, and should give a more informative error message (to us, even if not necessarily to you). Installation of ape works for me in both binary and source forms, so there's something about your setup that is responsible. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Installing packages
Marc Schwartz [EMAIL PROTECTED] writes: On Thu, 2003-11-13 at 12:18, Nathan Leon Pace, MD, MStat wrote: Running under Redhat 7.3 Linux I have installed R Version 1.8.0 (2003-10-08) from a binary download using the rpm manager. Using packageStatus(), I am attempted to upgrade several packages. This is unsuccessful with the following error messages: * Installing *source* package 'MASS' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c MASS.c -o MASS.o gcc: installation problem, cannot exec `cpp0': No such file or directory make: *** [MASS.o] Error 1 ERROR: compilation failed for package 'MASS' gcc version 2.96 2731 (Red Hat Linux 7.3 2.96-113) is installed. I have checked the R archives and FAQ and admin manual for help. My knowledge of c compiling is limited. Any pointers for debugging this problem would be appreciated. Nathan Not sure if you have received any other replies yet, but it appears that you may be getting bitten by the infamous Red Hat 7.x gcc 2.96 problem. Without getting into details, this is a known issue with this version of gcc that was improperly released by RH. The official note on this issue from gnu.org is here: http://gcc.gnu.org/gcc-2.96.html To my knowledge RH released updates to that version, but I believe that the only real fix is to either revert to gcc 2.95.x or upgrade to a version 3.x series release. Martyn Plummer, the RH maintainer for R may have more detailed information on this and I am cc'ing him on this reply. Hmm, the symptoms don't quite usually look like that, and most of them got fixed in the 2.96-N releases where N was somewhere in the 80's IIRC. This claims to be an installation error where the preprocessor cpp0 is not found, so my first try would be to go look for it, i.e. (on RH8) $ locate cpp0 /usr/lib/gcc-lib/i386-redhat-linux/3.2/tradcpp0 /usr/lib/gcc-lib/i386-redhat-linux/3.2/cpp0 It seems to live in the cpp package, $ rpm -qf /usr/lib/gcc-lib/i386-redhat-linux/3.2/cpp0 cpp-3.2-7 so rpm -V cpp should help you check your installation. -- 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] Installing packages
On Fri, 2003-11-14 at 05:37, Peter Dalgaard wrote: Marc Schwartz [EMAIL PROTECTED] writes: On Thu, 2003-11-13 at 12:18, Nathan Leon Pace, MD, MStat wrote: Running under Redhat 7.3 Linux I have installed R Version 1.8.0 (2003-10-08) from a binary download using the rpm manager. Using packageStatus(), I am attempted to upgrade several packages. This is unsuccessful with the following error messages: * Installing *source* package 'MASS' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c MASS.c -o MASS.o gcc: installation problem, cannot exec `cpp0': No such file or directory make: *** [MASS.o] Error 1 ERROR: compilation failed for package 'MASS' gcc version 2.96 2731 (Red Hat Linux 7.3 2.96-113) is installed. I have checked the R archives and FAQ and admin manual for help. My knowledge of c compiling is limited. Any pointers for debugging this problem would be appreciated. Nathan Not sure if you have received any other replies yet, but it appears that you may be getting bitten by the infamous Red Hat 7.x gcc 2.96 problem. Without getting into details, this is a known issue with this version of gcc that was improperly released by RH. The official note on this issue from gnu.org is here: http://gcc.gnu.org/gcc-2.96.html To my knowledge RH released updates to that version, but I believe that the only real fix is to either revert to gcc 2.95.x or upgrade to a version 3.x series release. Martyn Plummer, the RH maintainer for R may have more detailed information on this and I am cc'ing him on this reply. Hmm, the symptoms don't quite usually look like that, and most of them got fixed in the 2.96-N releases where N was somewhere in the 80's IIRC. This claims to be an installation error where the preprocessor cpp0 is not found, so my first try would be to go look for it, i.e. (on RH8) $ locate cpp0 /usr/lib/gcc-lib/i386-redhat-linux/3.2/tradcpp0 /usr/lib/gcc-lib/i386-redhat-linux/3.2/cpp0 It seems to live in the cpp package, $ rpm -qf /usr/lib/gcc-lib/i386-redhat-linux/3.2/cpp0 cpp-3.2-7 so rpm -V cpp should help you check your installation. Peter, Thanks for your comments on this. In checking at RH for 2.96 update announcements, I believe this one: https://rhn.redhat.com/errata/RHBA-2002-200.html is the most recent, which would suggest that the 2.96-113 series of RPMS is the latest for that version. Perhaps the first step toward resolution would be to check the installation of cpp as you suggest. If that shows any problems, starting with [re]installing the cpp-2.96-113.i386.rpm from the above site would make sense and if that does not work or has errors, then re-installing all 9 RPMS under the RH 7.3/i386 section on that page, would be a next step. Marc __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Installing packages
Running under Redhat 7.3 Linux I have installed R Version 1.8.0 (2003-10-08) from a binary download using the rpm manager. Using packageStatus(), I am attempted to upgrade several packages. This is unsuccessful with the following error messages: * Installing *source* package 'MASS' ... ** libs gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c MASS.c -o MASS.o gcc: installation problem, cannot exec `cpp0': No such file or directory make: *** [MASS.o] Error 1 ERROR: compilation failed for package 'MASS' gcc version 2.96 2731 (Red Hat Linux 7.3 2.96-113) is installed. I have checked the R archives and FAQ and admin manual for help. My knowledge of c compiling is limited. Any pointers for debugging this problem would be appreciated. Nathan Nathan Leon Pace, MD, MStat Work:[EMAIL PROTECTED] Department of AnesthesiologyHome:[EMAIL PROTECTED] University of Utah Work:801.581.6393 Salt Lake City, UtahHome:801.467.2925 Fax:801.581.4367 Cell:801.558.3987 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] installing packages not on CRAN
Hi, how to use install.packages to install SimpleR package of J. Verzani? using install.packages with the CRAN packages is simple: install.packages(ineq,contriburl=http://cran.at.r-project.org/bin/windows/contrib/1.8,CRAN=NULL) same with Simple package fails: install.packages(Simple,contriburl=http://www.math.csi.cuny.edu/Statistics/R/simpleR,CRAN=NULL) since there is no file named PACKAGES. My solution is: path-paste(getwd(),simple.zip, sep=/) download.file(http://www.math.csi.cuny.edu/Statistics/R/simpleR/Simple_0.4.zip,path,mode=wb;) install.packages(path,CRAN=NULL) Is there more elegant way to do this in Windows? Vytautas Maniusis, Vilnius University, lithuania __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] installing packages not on CRAN
On Fri, 24 Oct 2003 [EMAIL PROTECTED] wrote: Hi, how to use install.packages to install SimpleR package of J. Verzani? using install.packages with the CRAN packages is simple: install.packages(ineq,contriburl=http://cran.at.r-project.org/bin/windows/contrib/1.8,CRAN=NULL) same with Simple package fails: install.packages(Simple,contriburl=http://www.math.csi.cuny.edu/Statistics/R/simpleR,CRAN=NULL) since there is no file named PACKAGES. My solution is: path-paste(getwd(),simple.zip, sep=/) download.file(http://www.math.csi.cuny.edu/Statistics/R/simpleR/Simple_0.4.zip,path,mode=wb;) install.packages(path,CRAN=NULL) Is there more elegant way to do this in Windows? Download the file and use the menu item to install it, if the above is too complicated for you. -- 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
