Re: [R] install.packages
Aimin Yan wrote:
> I try to type this in my R-winEdt.
GH! Again and again I have to tell that RWinEdt is just some
enhancement for an editor that may help for you R programming, but is
not related to any error messages you receive from R!
> but I got these. Do you know?
Yes, you are not reading any documentation at all, obviously. Please try
to reduce your mail traffic on R-help by simply reading some
documentation (and the posting guide!) from time to time. Thank you.
Uwe Ligges
> Aimin
>
> >
> install.packages('http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip')
> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
> no package
> 'http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip'
>
> at the repositories
>
> __
> 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.
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Re: [R] install.packages
install.packages("plotrix")
b.
On Dec 13, 2006, at 1:42 PM, Aimin Yan wrote:
> I try to type this in my R-winEdt.
> but I got these. Do you know?
>
> Aimin
>
>>
> install.packages('http://rh-mirror.linux.iastate.edu/CRAN/bin/
> windows/contrib/2.4/plotrix_2.1-6.zip')
> Warning in download.packages(pkgs, destdir = tmpd, available =
> available, :
> no package
> 'http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/
> plotrix_2.1-6.zip'
> at the repositories
>
> __
> 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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] install.packages
I try to type this in my R-winEdt.
but I got these. Do you know?
Aimin
>
install.packages('http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip')
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
no package
'http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip'
at the repositories
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] install.packages from local .tar.gz (was 'for local zip') files
On Mon, 17 Jul 2006, Muhammad Subianto wrote:
> On 7/16/06, Daniel Gatti <[EMAIL PROTECTED]> wrote:
> > O/S: Linux
> > R version : 2.2.1
^
That appears to be the problem. As the posting guide asked you to
(***before posting***), please update.
And I presume we really are talking about .tar.gz files here, not 'zip
files' (used on Windows, which did work in 2.2.1).
> install.packages("~/R/packages/contrib/ash_1.0-9.tar.gz", repos=NULL)
works perfectly in current R, but not in the obselete 2.2.1.
> > The R server doesn't have http internet access. And the sys admins will
> > not install the R libraries that I requested. So I have downloaded the
> > packages that I want to intall and have moved them into my home
> > directory on the server. These are a series of *.tar.gz files. I want
> > to install the R libraries in my home directory, but I can't get it to
> > work. According to the install.packages documentation :
> >
> > install.packages(pkgs, lib, repos = getOption("repos"), contriburl =
> > contrib.url(repos, type), method, available = NULL, destdir = NULL,
> > installWithVers = FALSE, dependencies = FALSE, type = getOption("pkgType"))
> >
> > repos: character vector, the base URL(s) of the repositories to use,
> >i.e., Can be 'NULL' to install from local '.tar.gz' files.
> >
> > contriburl: URL(s) of the contrib section of the repositories. ..
> >Can be 'NULL' to install from local '.tar.gz' files.
> >
> >
> > pkgs: character vector of the short names of packages/bundles whose
> > current versions should be downloaded from the repositories.
> > If 'repos = NULL', a character vector of file paths of
> > '.tar.gz' files. These can be source archives or binary
> > package/bundle archive files (as created by 'R CMD build
> > --binary'). ..
> >
> > lib: character vector giving the library directories where to install
> > the packages. Recycled as needed.
> >
> > So I have issued a command like this:
> >
> > > install.packages(pkgs="~/Rdownloads/hgug4112a_1.12.0.tar.gz", lib =
> > "~/Rlib", repos=NULL, contriburl=NULL)
> >
> > Warning in download.packages(pkgs, destdir = tmpd, available =
> > available, :
> > no package '~/Rdownloads/hgug4112a_1.12.0.tar.gz' at the
> > repositories
> >
> > As far as I can tell, I've given it the full path to the zip file, the
> > directory in which to install the library and I've set the repository
> > path to 'NULL' to indicate that I'm installing from an already
> > downloaded zip file. But I'm missing something. Any ideas?
> >
> > Thanks,
> > Dan
> >
> > __
> > 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
> >
>
>
>
> Put your packages, for example, in directory "/dir/of/pkgs"
> library(tools)
> write_PACKAGES("/dir/of/pkgs")
>
> and the package will be installed to "/dir/of/R/libs"
>
> install.packages("NameOfPkgs",
> lib="/dir/of/R/libs",
> repos=NULL,
> dependencies=TRUE,
> contriburl="file:dir/of/pkgs")
>
> Best, Muhammad Subianto
>
> __
> 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
>
--
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
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Re: [R] install.packages for local zip files
On 7/16/06, Daniel Gatti <[EMAIL PROTECTED]> wrote:
> O/S: Linux
> R version : 2.2.1
>
> The R server doesn't have http internet access. And the sys admins will
> not install the R libraries that I requested. So I have downloaded the
> packages that I want to intall and have moved them into my home
> directory on the server. These are a series of *.tar.gz files. I want
> to install the R libraries in my home directory, but I can't get it to
> work. According to the install.packages documentation :
>
> install.packages(pkgs, lib, repos = getOption("repos"), contriburl =
> contrib.url(repos, type), method, available = NULL, destdir = NULL,
> installWithVers = FALSE, dependencies = FALSE, type = getOption("pkgType"))
>
> repos: character vector, the base URL(s) of the repositories to use,
>i.e., Can be 'NULL' to install from local '.tar.gz' files.
>
> contriburl: URL(s) of the contrib section of the repositories. ..
>Can be 'NULL' to install from local '.tar.gz' files.
>
>
> pkgs: character vector of the short names of packages/bundles whose
> current versions should be downloaded from the repositories.
> If 'repos = NULL', a character vector of file paths of
> '.tar.gz' files. These can be source archives or binary
> package/bundle archive files (as created by 'R CMD build
> --binary'). ..
>
> lib: character vector giving the library directories where to install
> the packages. Recycled as needed.
>
> So I have issued a command like this:
>
> > install.packages(pkgs="~/Rdownloads/hgug4112a_1.12.0.tar.gz", lib =
> "~/Rlib", repos=NULL, contriburl=NULL)
>
> Warning in download.packages(pkgs, destdir = tmpd, available =
> available, :
> no package '~/Rdownloads/hgug4112a_1.12.0.tar.gz' at the
> repositories
>
> As far as I can tell, I've given it the full path to the zip file, the
> directory in which to install the library and I've set the repository
> path to 'NULL' to indicate that I'm installing from an already
> downloaded zip file. But I'm missing something. Any ideas?
>
> Thanks,
> Dan
>
> __
> 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
>
Put your packages, for example, in directory "/dir/of/pkgs"
library(tools)
write_PACKAGES("/dir/of/pkgs")
and the package will be installed to "/dir/of/R/libs"
install.packages("NameOfPkgs",
lib="/dir/of/R/libs",
repos=NULL,
dependencies=TRUE,
contriburl="file:dir/of/pkgs")
Best, Muhammad Subianto
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] install.packages for local zip files
O/S: Linux
R version : 2.2.1
The R server doesn't have http internet access. And the sys admins will
not install the R libraries that I requested. So I have downloaded the
packages that I want to intall and have moved them into my home
directory on the server. These are a series of *.tar.gz files. I want
to install the R libraries in my home directory, but I can't get it to
work. According to the install.packages documentation :
install.packages(pkgs, lib, repos = getOption("repos"), contriburl =
contrib.url(repos, type), method, available = NULL, destdir = NULL,
installWithVers = FALSE, dependencies = FALSE, type = getOption("pkgType"))
repos: character vector, the base URL(s) of the repositories to use,
i.e., Can be 'NULL' to install from local '.tar.gz' files.
contriburl: URL(s) of the contrib section of the repositories. ..
Can be 'NULL' to install from local '.tar.gz' files.
pkgs: character vector of the short names of packages/bundles whose
current versions should be downloaded from the repositories.
If 'repos = NULL', a character vector of file paths of
'.tar.gz' files. These can be source archives or binary
package/bundle archive files (as created by 'R CMD build
--binary'). ..
lib: character vector giving the library directories where to install
the packages. Recycled as needed.
So I have issued a command like this:
> install.packages(pkgs="~/Rdownloads/hgug4112a_1.12.0.tar.gz", lib =
"~/Rlib", repos=NULL, contriburl=NULL)
Warning in download.packages(pkgs, destdir = tmpd, available =
available, :
no package '~/Rdownloads/hgug4112a_1.12.0.tar.gz' at the
repositories
As far as I can tell, I've given it the full path to the zip file, the
directory in which to install the library and I've set the repository
path to 'NULL' to indicate that I'm installing from an already
downloaded zip file. But I'm missing something. Any ideas?
Thanks,
Dan
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Re: [R] install.packages saying the car package is not in therepositories
On 10 March 2006 at 19:14, Jeremy Morris wrote: | > Please re-read the entire message I sent you yesterday as it already | > answered this question. (Hint: The answer is in the R FAQ too.) | | I couldn't find anything on the R FAQ's mentioning Debian | specifically. And a simple search for 'upgrade' in the FAQ also Odd -- dumping the lynx output through grep reveals several finds of Debian or debian: [EMAIL PROTECTED]:~> lynx -dump http://cran.us.r-project.org/doc/FAQ/R-FAQ.html | grep -i debian [80]http://buildd.debian.org/build.php?&pkg=r-base), and x86_64 CPUs, Debiani386 stable/oldstable Christian Steigies Debian packages, maintained by Dirk Eddelbuettel and Doug Bates, have long been part of the Debian distribution, and can be accessed through APT, the Debian package maintenance tool. Use e.g. apt-get install deb http://cran.R-project.org/bin/linux/debian stable/ libreadline-dev (Debian) or readline-devel (Red Hat). 80. http://buildd.debian.org/build.php?&pkg=r-base [EMAIL PROTECTED]:~> | turned up nothing. I even used Google to search for a way to upgrade | R using CRAN, with no relevant results. After a little bit of | searching around the CRAN site I found this : | | http://cran.r-project.org/bin/linux/debian/README | | Which was all the information I needed. Thanks for all the help. My pleasure. 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
Re: [R] install.packages saying the car package is not in therepositories
> Please re-read the entire message I sent you yesterday as it already > answered this question. (Hint: The answer is in the R FAQ too.) I couldn't find anything on the R FAQ's mentioning Debian specifically. And a simple search for 'upgrade' in the FAQ also turned up nothing. I even used Google to search for a way to upgrade R using CRAN, with no relevant results. After a little bit of searching around the CRAN site I found this : http://cran.r-project.org/bin/linux/debian/README Which was all the information I needed. Thanks for all the help. Jeremy __ 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] install.packages saying the car package is not in therepositories
On 9 March 2006 at 20:47, Jeremy Morris wrote: | Thank you, this did the trick. | | > In which case | > | > $ apt-get install r-cran-car | > | > is your friend. | | Is there anyway to upgrade my R install through CRAN? Or is there | some Debian repository that has an upgraded version of R? Yes. Please re-read the entire message I sent you yesterday as it already answered this question. (Hint: The answer is in the R FAQ too.) Hope this helps, 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
Re: [R] install.packages saying the car package is not in therepositories
Thank you, this did the trick. > In which case > > $ apt-get install r-cran-car > > is your friend. Is there anyway to upgrade my R install through CRAN? Or is there some Debian repository that has an upgraded version of R? Thanks again. Jeremy __ 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] install.packages saying the car package is not in therepositories
On 9 March 2006 at 02:23, Jeremy Morris wrote: | I am running version 2.1.0 of R on a Debian Linux machine. In which case $ apt-get install r-cran-car is your friend. 2.1.0 is ancient, so you could take advantage of the backport of the current R the Debian stable which Chris Steigies provides -- and that is on every CRAN mirror as detailed in the R FAQ. 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
Re: [R] install.packages saying the car package is not in therepositories
I am running version 2.1.0 of R on a Debian Linux machine. Jeremy __ 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] install.packages saying the car package is not in therepositories
Dear Jeremy,
The car package (version 1.1-0) is certainly on CRAN. I checked a couple of
mirrors, and it's there as well. (I assume that .Library contains the
library location to which you want to install?) What OS and version of R are
you using?
Regards,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Jeremy Morris
> Sent: Wednesday, March 08, 2006 5:22 PM
> To: r-help@stat.math.ethz.ch
> Subject: [R] install.packages saying the car package is not
> in therepositories
>
> I am attempting to install the car package using the command :
>
> > install.packages('car',.Library)
>
> After I have chosen a mirror, I get the following message :
>
> Warning message:
> no package 'car' at the repositories in:
> download.packages(pkgs, destdir = tmpd, available = available,
>
> I used the CRAN.packages() function to see what was going on,
> and the car package is not listed. I have also tried several
> mirrors, all with the same error message. I have tried to
> install other packages, this has been successful.
>
> Any help would be great.
>
> Jeremy
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
__
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[R] install.packages saying the car package is not in the repositories
I am attempting to install the car package using the command :
> install.packages('car',.Library)
After I have chosen a mirror, I get the following message :
Warning message:
no package 'car' at the repositories in: download.packages(pkgs,
destdir = tmpd, available = available,
I used the CRAN.packages() function to see what was going on, and the
car package is not listed. I have also tried several mirrors, all
with the same error message. I have tried to install other packages,
this has been successful.
Any help would be great.
Jeremy
__
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[R] install.packages() failed
I use Mac. I installed R with the download from R-project, so R is in
/usr/bin/R.
My TclTk library is installed via fink (although I don't remember I
intentionally
installed it) so libtk8.4.dylib is in /sw/lib.
I tried to install the HDF5 package from within R:
>install.packages('hdf5')
and it failed like this
---
Loading Tcl/Tk interface ... Error in dyn.load(x, as.logical(local),
as.logical(now))
:
unable to load shared library '/Library/Frameworks/R.framework/
Resources/library/tcltk/libs/tcltk.so':
dlcompat: dyld: /Library/Frameworks/R.framework/Resources/bin/exec/R
can't open library: /usr/local/lib/libtk8.4.dylib (No such file or directory,
errno
= 2)
Error: .onLoad failed in 'loadNamespace' for 'tcltk'
---
Apparently R looks for libtk8.4.dylib in /usr/local/lib and doesn't know it's
in /
sw/lib. How can I tell R about this?
Also, I tried installing the downloaded source with
>R CMD INSTALL hdf5_1.6.0.tar.gz
and it failed because the 'configure' script of the package failed. Anybody had
experience with this? If I can install with 'R CMD INSTALL', that's also good
enough.
Thanks.
Zepu
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Re: [R] install.packages under SuSE 10 behind proxy, R 2.2.0 from source
Hi I figured it out. if I use install.packages(..., method="wget") it works but if I use the default method, it doesn't. Rainer Rainer M. Krug wrote: > Hi > > I installed R 2.2.0 from source and want to use install.packages but it > doesn't work. > > http_proxy is set to http://proxy.sun.ac.za:3128 > > but it still can't connect to the repository. > The mirror is available, I can connect to it via the internet. > > Any help welcome, > > Rainer > > > -- NEW TELEPHONE NUMBER Tel:+27 - (0)72 808 2975 (w) Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [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] install.packages under SuSE 10 behind proxy, R 2.2.0 from source
Hi I installed R 2.2.0 from source and want to use install.packages but it doesn't work. http_proxy is set to http://proxy.sun.ac.za:3128 but it still can't connect to the repository. The mirror is available, I can connect to it via the internet. Any help welcome, Rainer -- NEW TELEPHONE NUMBER Tel:+27 - (0)72 808 2975 (w) Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [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] install.packages parameters
Caveat: I know next to nothing about Mac... That said, my guess is that you installed R from binary, rather than building from source. In that case the compilers and flags, etc., are configured to the machine that the binary is built on. You can look in $RHOME/etc/Makeconf to see the settings, and see if changing them helps. Andy > From: [EMAIL PROTECTED] > > Hello. > > R is having some trouble installing a package because it > passed arguments to > gcc which were non-existent directories and files. It also > didn't find > g77, although it's in a directory in my $PATH; I tricked it > by making a > sym link in /usr/bin. > > What file does R get these parameters from? > I've looked for the parameters in the package source, the > install.packages > help pages, and the R preferences menu, all to no avail. > > I am running R 2.1.0 on Mac 10.3.8, and three days ago I installed a > different package from source where installation involved gcc without > any problems, and nothing has changed since then. The packages I'm > trying to install are Joe Schafer's mix, norm, and cat. > > Thanks, > > Janet > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] install.packages parameters
Hello. R is having some trouble installing a package because it passed arguments to gcc which were non-existent directories and files. It also didn't find g77, although it's in a directory in my $PATH; I tricked it by making a sym link in /usr/bin. What file does R get these parameters from? I've looked for the parameters in the package source, the install.packages help pages, and the R preferences menu, all to no avail. I am running R 2.1.0 on Mac 10.3.8, and three days ago I installed a different package from source where installation involved gcc without any problems, and nothing has changed since then. The packages I'm trying to install are Joe Schafer's mix, norm, and cat. Thanks, Janet __ 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] install.packages and MacOS 10.3.8
Dear Uwe,
That install.binaries() was exactly what I needed...
Thanks a lot.
Uwe Ligges a écrit :
Patrick Giraudoux wrote:
Dear Listers,
I am trying to install packages via install.packages() from MacOS
10.3.8. Installing work fine when run from the menu, but the
following command (useful for setting up each computer of the student
computer room) leads nowhere for some reasons:
pack<-c("ade4","adehabitat","geoR","gstat","KernSmooth","lattice","leaps")
install.packages(pack,dependencies=T)
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 51500 bytes
opened URL
==
downloaded 50Kb
also installing the dependencies 'SparseM', 'gee', 'waveslim',
'splancs', 'maptools', 'spdep', 'pixmap', 'ape', 'tripack'
trying URL `http://cran.r-project.org/src/contrib/SparseM_0.60.tar.gz'
[SNIP]
* Installing *source* package 'SparseM' ...
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
command not found
ERROR: compilation failed for package 'SparseM'
* Installing *source* package 'gee' ...
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
command not found
ERROR: compilation failed for package 'gee'
etc...
Can anybody tell me what goes wrong with this command (which usually
work without any problem with R 2.0.1 and Windows XP).
So at least "make" and probably much more is missing on your machines
(or not in your path or whatever). You might want to try
install.binaries() instead (which is similar to install.packages() on
Windows, since it installs binary packages rather than trying to
compile and install source packages) - or set up your machines with
the required set of tools.
Uwe Ligges
Thanks in advance,
Patrick
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Re: [R] install.packages and MacOS 10.3.8
Patrick Giraudoux wrote:
Dear Listers,
I am trying to install packages via install.packages() from MacOS
10.3.8. Installing work fine when run from the menu, but the following
command (useful for setting up each computer of the student computer
room) leads nowhere for some reasons:
pack<-c("ade4","adehabitat","geoR","gstat","KernSmooth","lattice","leaps")
install.packages(pack,dependencies=T)
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 51500 bytes
opened URL
==
downloaded 50Kb
also installing the dependencies 'SparseM', 'gee', 'waveslim',
'splancs', 'maptools', 'spdep', 'pixmap', 'ape', 'tripack'
trying URL `http://cran.r-project.org/src/contrib/SparseM_0.60.tar.gz'
[SNIP]
* Installing *source* package 'SparseM' ...
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
command not found
ERROR: compilation failed for package 'SparseM'
* Installing *source* package 'gee' ...
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
command not found
ERROR: compilation failed for package 'gee'
etc...
Can anybody tell me what goes wrong with this command (which usually
work without any problem with R 2.0.1 and Windows XP).
So at least "make" and probably much more is missing on your machines
(or not in your path or whatever). You might want to try
install.binaries() instead (which is similar to install.packages() on
Windows, since it installs binary packages rather than trying to compile
and install source packages) - or set up your machines with the required
set of tools.
Uwe Ligges
Thanks in advance,
Patrick
__
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http://www.R-project.org/posting-guide.html
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[R] install.packages and MacOS 10.3.8
Dear Listers,
I am trying to install packages via install.packages() from MacOS
10.3.8. Installing work fine when run from the menu, but the following
command (useful for setting up each computer of the student computer
room) leads nowhere for some reasons:
pack<-c("ade4","adehabitat","geoR","gstat","KernSmooth","lattice","leaps")
install.packages(pack,dependencies=T)
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 51500 bytes
opened URL
==
downloaded 50Kb
also installing the dependencies 'SparseM', 'gee', 'waveslim', 'splancs', 'maptools',
'spdep', 'pixmap', 'ape', 'tripack'
trying URL `http://cran.r-project.org/src/contrib/SparseM_0.60.tar.gz'
Content type `application/x-tar' length 1064262 bytes
opened URL
==
downloaded 1039Kb
trying URL `http://cran.r-project.org/src/contrib/gee_4.13-10.tar.gz'
Content type `application/x-tar' length 49586 bytes
opened URL
==
downloaded 48Kb
trying URL `http://cran.r-project.org/src/contrib/waveslim_1.4.tar.gz'
Content type `application/x-tar' length 358305 bytes
opened URL
==
(etc)
* Installing *source* package 'SparseM' ...
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make: command not
found
ERROR: compilation failed for package 'SparseM'
* Installing *source* package 'gee' ...
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make: command not
found
ERROR: compilation failed for package 'gee'
etc...
Can anybody tell me what goes wrong with this command (which usually
work without any problem with R 2.0.1 and Windows XP).
Thanks in advance,
Patrick
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] install.packages() for local source file
This is not a `definitive bug' but as you have been told repeatedly a
failure on your part to read the help adequately:
contriburl: URL of the contrib section of CRAN.
The good news is that R-devel does support local installation, so R 2.1.0
will.
On Sat, 1 Jan 2005, Paul Roebuck wrote:
On Sat, 1 Jan 2005, Roger D. Peng wrote:
Paul Roebuck wrote:
Wish to install a local source package on Un*x platform from
within R. Same thing as I can accomplish from cmdline as
$ export R_LIBS=~/R/library
$ cd /path/to/pkg
$ R CMD INSTALL -l $R_LIBS
So, how do you go about this anyway?
And isn't this a bug in 'install.packages'?
---
$ R
R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
file.pkg <- "mypkg_0.1.tar.gz"
path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
file.exists(path.pkg)
[1] TRUE
uri.pkg <- paste("file://", path.pkg, sep = "")
install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
Error in file.info(x) : Object "tmpd" not found
traceback()
4: file.info(x)
3: dirTest(destdir)
2: download.packages(pkgs, destdir = tmpd, available = available,
contriburl = contriburl, method = method)
1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
version
_
platform sparc-sun-solaris2.9
arch sparc
os solaris2.9
system sparc, solaris2.9
status
major1
minor9.0
year 2004
month04
day 12
language R
By the way, do you get this error in a recent version of R
(say >= 1.9.1). I believe install.packages() has changed
since 1.9.0. For example, see the thread starting here
https://stat.ethz.ch/pipermail/r-help/2004-July/053001.html
Roger,
Thanks for that link which helped me diagnose the problem.
I observed the same error you observed (.../053047.html). Still
think it's kind of hinky to pass an uninitialized variable (tmpd)
to another method and count on it doing something though.
I wondered if something had changed as well, but noticed no change
glancing at the source for install.packages on 2.0.1 (OS X).
But underneath, the behavior was different since I got a
different error message which noted the lack of a PACKAGES
file. That was enough to get the rest to work...
Hopefully this will help my case for updating to the current
version on our shared Un*x workstations since I can now point
to a definitive bug that impacted my work due to using an
older version of this software.
R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0
parentdir <- file.path(path.expand("~"), "Projects", "cvknn")
uri.parentdir <- paste("file://", parentdir, sep = "")
savewd <- getwd()
setwd(parentdir)
rmsymlink <- FALSE
if (file.exists("PACKAGES") == FALSE) {
file.symlink(file.path("mypkg", "DESCRIPTION"), "PACKAGES")
rmsymlink <- TRUE
}
install.packages("mypkg",
+ contriburl = uri.parentdir,
+ lib = Sys.getenv("R_LIBS"))
if (rmsymlink) file.remove("PACKAGES")
setwd(savewd)
Perhaps the documentation for the 'contriburl' should
specify that it is expecting 'URL of the directory of
the contrib section of CRAN'.
--
SIGSIG -- signature too long (core dumped)
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--
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
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Re: [R] install.packages() for local source file
On Sat, 1 Jan 2005, Roger D. Peng wrote:
> Paul Roebuck wrote:
> > Wish to install a local source package on Un*x platform from
> > within R. Same thing as I can accomplish from cmdline as
> >
> > $ export R_LIBS=~/R/library
> > $ cd /path/to/pkg
> > $ R CMD INSTALL -l $R_LIBS
> >
> >
> > So, how do you go about this anyway?
> > And isn't this a bug in 'install.packages'?
> >
> > ---
> > $ R
> >
> > R : Copyright 2004, The R Foundation for Statistical Computing
> > Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
> >
> >
> >>file.pkg <- "mypkg_0.1.tar.gz"
> >>path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
> >>file.exists(path.pkg)
> >
> > [1] TRUE
> >
> >>uri.pkg <- paste("file://", path.pkg, sep = "")
> >>install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> >
> > Error in file.info(x) : Object "tmpd" not found
> >
> >>traceback()
> >
> > 4: file.info(x)
> > 3: dirTest(destdir)
> > 2: download.packages(pkgs, destdir = tmpd, available = available,
> >contriburl = contriburl, method = method)
> > 1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> >
> >>version
> >
> > _
> > platform sparc-sun-solaris2.9
> > arch sparc
> > os solaris2.9
> > system sparc, solaris2.9
> > status
> > major1
> > minor9.0
> > year 2004
> > month04
> > day 12
> > language R
> >
>
> By the way, do you get this error in a recent version of R
> (say >= 1.9.1). I believe install.packages() has changed
> since 1.9.0. For example, see the thread starting here
>
> https://stat.ethz.ch/pipermail/r-help/2004-July/053001.html
>
Roger,
Thanks for that link which helped me diagnose the problem.
I observed the same error you observed (.../053047.html). Still
think it's kind of hinky to pass an uninitialized variable (tmpd)
to another method and count on it doing something though.
I wondered if something had changed as well, but noticed no change
glancing at the source for install.packages on 2.0.1 (OS X).
But underneath, the behavior was different since I got a
different error message which noted the lack of a PACKAGES
file. That was enough to get the rest to work...
Hopefully this will help my case for updating to the current
version on our shared Un*x workstations since I can now point
to a definitive bug that impacted my work due to using an
older version of this software.
R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0
> parentdir <- file.path(path.expand("~"), "Projects", "cvknn")
> uri.parentdir <- paste("file://", parentdir, sep = "")
> savewd <- getwd()
> setwd(parentdir)
> rmsymlink <- FALSE
> if (file.exists("PACKAGES") == FALSE) {
> file.symlink(file.path("mypkg", "DESCRIPTION"), "PACKAGES")
> rmsymlink <- TRUE
> }
> install.packages("mypkg",
+ contriburl = uri.parentdir,
+ lib = Sys.getenv("R_LIBS"))
> if (rmsymlink) file.remove("PACKAGES")
> setwd(savewd)
Perhaps the documentation for the 'contriburl' should
specify that it is expecting 'URL of the directory of
the contrib section of CRAN'.
--
SIGSIG -- signature too long (core dumped)
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Re: [R] install.packages() for local source file
By the way, do you get this error in a recent version of R (say >= 1.9.1). I
believe install.packages() has changed since 1.9.0. For example, see the thread
starting here
https://stat.ethz.ch/pipermail/r-help/2004-July/053001.html
-roger
Paul Roebuck wrote:
Wish to install a local source package on Un*x platform from
within R. Same thing as I can accomplish from cmdline as
$ export R_LIBS=~/R/library
$ cd /path/to/pkg
$ R CMD INSTALL -l $R_LIBS
So, how do you go about this anyway?
And isn't this a bug in 'install.packages'?
---
$ R
R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
file.pkg <- "mypkg_0.1.tar.gz"
path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
file.exists(path.pkg)
[1] TRUE
uri.pkg <- paste("file://", path.pkg, sep = "")
install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
Error in file.info(x) : Object "tmpd" not found
traceback()
4: file.info(x)
3: dirTest(destdir)
2: download.packages(pkgs, destdir = tmpd, available = available,
contriburl = contriburl, method = method)
1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
version
_
platform sparc-sun-solaris2.9
arch sparc
os solaris2.9
system sparc, solaris2.9
status
major1
minor9.0
year 2004
month04
day 12
language R
--
SIGSIG -- signature too long (core dumped)
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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RE: [R] install.packages() for local source file
On Sat, 1 Jan 2005, Liaw, Andy wrote:
> > From: Paul Roebuck
> >
> > > Please read ?install.packages. It's most definitely not a bug for a
> > > function that works as documented. If you want, you might take the
> > > source for install.packages and strip it down to do what you want,
> > > say something called installLocalPackages.
> >
> > Well, I called myself having read it but it still wasn't obvious
> > to me; hence I posted the question here. Exactly which part should
> > I have read more carefully? I will grant that I left out one thing
> > when I did my cut'n'paste but it doesn't change the result.
> > My attempt to install my local package should have read:
> >
> > > install.packages("mypkg",
> >contriburl = uri.pkg,
> >lib = Sys.getenv("R_LIBS"))
> >
> > Looking at the source, 'tmpd' is only set if the protocol
> > is not "file:". Since I use that protocol, it would seem
> > to me that passing 'NULL' instead of 'tempfile("Rinstdir")'
> > would constitute a bug.
>
> The version of ?install.packages (in R-2.0.1) I've read never said
> it could install local source packages, so why would it be
> considered a bug not being able to do something that is never
> claimed? You seem to expect the function to do something that
> it is never designed to do.
The name of the routine made the claim, not I.
One could be forgiven for assuming it could since the
'contriburl' argument implies it could use a CD. I've
used it in the past for local installs by simulating
the CRAN directory structure and overriding the 'CRAN'
argument but that's kind of a hassle for something quick.
Perhaps it should be renamed 'install.packages.from.CRAN'
since the current name implies something different to me.
The programmer in me would still call the current situation
a bug - the if statement around the 'localcran' variable
is missing the else case to handle this scenario. Assuming
so, I really don't see why this [w|c]ouldn't handle local source
installs. And if it can't (and never could be made to do so),
then the code should have a 'stop("local install unimplemented")'
there so no one else ever has to ask again.
--
SIGSIG -- signature too long (core dumped)
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RE: [R] install.packages() for local source file
The version of ?install.packages (in R-2.0.1) I've read never said it could
install local source packages, so why would it be considered a bug not being
able to do something that is never claimed? You seem to expect the function
to do something that it is never designed to do.
Andy
> From: Paul Roebuck
>
> On Sat, 1 Jan 2005, Liaw, Andy wrote:
>
> > > From: Paul Roebuck
> > >
> > > Wish to install a local source package on Un*x platform from
> > > within R. Same thing as I can accomplish from cmdline as
> > >
> > > $ export R_LIBS=~/R/library
> > > $ cd /path/to/pkg
> > > $ R CMD INSTALL -l $R_LIBS
> > >
> > >
> > > So, how do you go about this anyway?
> > > And isn't this a bug in 'install.packages'?
> > >
> > > ---
> > > $ R
> > >
> > > R : Copyright 2004, The R Foundation for Statistical Computing
> > > Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
> > >
> > > > file.pkg <- "mypkg_0.1.tar.gz"
> > > > path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
> > > > file.exists(path.pkg)
> > > [1] TRUE
> > > > uri.pkg <- paste("file://", path.pkg, sep = "")
> > > > install.packages(contriburl = uri.pkg, lib =
> Sys.getenv("R_LIBS"))
> > > Error in file.info(x) : Object "tmpd" not found
> > > > traceback()
> > > 4: file.info(x)
> > > 3: dirTest(destdir)
> > > 2: download.packages(pkgs, destdir = tmpd, available = available,
> > >contriburl = contriburl, method = method)
> > > 1: install.packages(contriburl = uri.pkg, lib =
> Sys.getenv("R_LIBS"))
> > > > version
> > > _
> > > platform sparc-sun-solaris2.9
> > > arch sparc
> > > os solaris2.9
> > > system sparc, solaris2.9
> > > status
> > > major1
> > > minor9.0
> > > year 2004
> > > month04
> > > day 12
> > > language R
> >
> > Please read ?install.packages. It's most definitely not a bug for a
> > function that works as documented. If you want, you might take the
> > source for install.packages and strip it down to do what you want,
> > say something called installLocalPackages.
>
> Well, I called myself having read it but it still wasn't obvious
> to me; hence I posted the question here. Exactly which part should
> I have read more carefully? I will grant that I left out one thing
> when I did my cut'n'paste but it doesn't change the result.
> My attempt to install my local package should have read:
>
> > install.packages("mypkg",
>contriburl = uri.pkg,
>lib = Sys.getenv("R_LIBS"))
>
> Looking at the source, 'tmpd' is only set if the protocol
> is not "file:". Since I use that protocol, it would seem
> to me that passing 'NULL' instead of 'tempfile("Rinstdir")'
> would constitute a bug.
>
> --
> 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
>
>
__
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RE: [R] install.packages() for local source file
On Sat, 1 Jan 2005, Liaw, Andy wrote:
> > From: Paul Roebuck
> >
> > Wish to install a local source package on Un*x platform from
> > within R. Same thing as I can accomplish from cmdline as
> >
> > $ export R_LIBS=~/R/library
> > $ cd /path/to/pkg
> > $ R CMD INSTALL -l $R_LIBS
> >
> >
> > So, how do you go about this anyway?
> > And isn't this a bug in 'install.packages'?
> >
> > ---
> > $ R
> >
> > R : Copyright 2004, The R Foundation for Statistical Computing
> > Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
> >
> > > file.pkg <- "mypkg_0.1.tar.gz"
> > > path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
> > > file.exists(path.pkg)
> > [1] TRUE
> > > uri.pkg <- paste("file://", path.pkg, sep = "")
> > > install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> > Error in file.info(x) : Object "tmpd" not found
> > > traceback()
> > 4: file.info(x)
> > 3: dirTest(destdir)
> > 2: download.packages(pkgs, destdir = tmpd, available = available,
> >contriburl = contriburl, method = method)
> > 1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> > > version
> > _
> > platform sparc-sun-solaris2.9
> > arch sparc
> > os solaris2.9
> > system sparc, solaris2.9
> > status
> > major1
> > minor9.0
> > year 2004
> > month04
> > day 12
> > language R
>
> Please read ?install.packages. It's most definitely not a bug for a
> function that works as documented. If you want, you might take the
> source for install.packages and strip it down to do what you want,
> say something called installLocalPackages.
Well, I called myself having read it but it still wasn't obvious
to me; hence I posted the question here. Exactly which part should
I have read more carefully? I will grant that I left out one thing
when I did my cut'n'paste but it doesn't change the result.
My attempt to install my local package should have read:
> install.packages("mypkg",
contriburl = uri.pkg,
lib = Sys.getenv("R_LIBS"))
Looking at the source, 'tmpd' is only set if the protocol
is not "file:". Since I use that protocol, it would seem
to me that passing 'NULL' instead of 'tempfile("Rinstdir")'
would constitute a bug.
--
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
RE: [R] install.packages() for local source file
Please read ?install.packages. It's most definitely not a bug for a
function that works as documented. If you want, you might take the source
for install.packages and strip it down to do what you want, say something
called installLocalPackages.
Andy
> From: Paul Roebuck
>
> Wish to install a local source package on Un*x platform from
> within R. Same thing as I can accomplish from cmdline as
>
> $ export R_LIBS=~/R/library
> $ cd /path/to/pkg
> $ R CMD INSTALL -l $R_LIBS
>
>
> So, how do you go about this anyway?
> And isn't this a bug in 'install.packages'?
>
> ---
> $ R
>
> R : Copyright 2004, The R Foundation for Statistical Computing
> Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
>
> > file.pkg <- "mypkg_0.1.tar.gz"
> > path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
> > file.exists(path.pkg)
> [1] TRUE
> > uri.pkg <- paste("file://", path.pkg, sep = "")
> > install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> Error in file.info(x) : Object "tmpd" not found
> > traceback()
> 4: file.info(x)
> 3: dirTest(destdir)
> 2: download.packages(pkgs, destdir = tmpd, available = available,
>contriburl = contriburl, method = method)
> 1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> > version
> _
> platform sparc-sun-solaris2.9
> arch sparc
> os solaris2.9
> system sparc, solaris2.9
> status
> major1
> minor9.0
> year 2004
> month04
> day 12
> language R
>
>
> --
> SIGSIG -- signature too long (core dumped)
>
> __
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[R] install.packages() for local source file
Wish to install a local source package on Un*x platform from
within R. Same thing as I can accomplish from cmdline as
$ export R_LIBS=~/R/library
$ cd /path/to/pkg
$ R CMD INSTALL -l $R_LIBS
So, how do you go about this anyway?
And isn't this a bug in 'install.packages'?
---
$ R
R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
> file.pkg <- "mypkg_0.1.tar.gz"
> path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
> file.exists(path.pkg)
[1] TRUE
> uri.pkg <- paste("file://", path.pkg, sep = "")
> install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
Error in file.info(x) : Object "tmpd" not found
> traceback()
4: file.info(x)
3: dirTest(destdir)
2: download.packages(pkgs, destdir = tmpd, available = available,
contriburl = contriburl, method = method)
1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
> version
_
platform sparc-sun-solaris2.9
arch sparc
os solaris2.9
system sparc, solaris2.9
status
major1
minor9.0
year 2004
month04
day 12
language R
--
SIGSIG -- signature too long (core dumped)
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Re: [R] install.packages() vs. update.packages()
Gorjanc Gregor bfro.uni-lj.si> writes: : : Hello! : : Is there virtually any difference if one uses install.packages() or : update.packages() for updating/upgrading of R packages? update.packages calls install.packages to do the installation. Check out the source. __ 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] install.packages() vs. update.packages()
Hello! Is there virtually any difference if one uses install.packages() or update.packages() for updating/upgrading of R packages? -- Lep pozdrav / With regards, Gregor GORJANC --- University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si Zootechnical Departmentemail: gregor.gorjanc bfro.uni-lj.si Groblje 3 tel: +386 (0)1 72 17 861 SI-1230 Domzalefax: +386 (0)1 72 17 888 Slovenia __ 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] install.packages, bundles, pmatch, and Rprofile...
On Tue, 2 Nov 2004, Andy Bunn wrote: > Hi, > > Somebody asked me to make sure that all the machines running the in our lab > (XP and Linux, both running 2.0) have R installed and that A) All the > packages are installed and B) kept up-to-date. > > Obediently, I began to modify a shared Rprofile so that once a week it > checks for new packages and updates to the current version of the installed > packages on CRAN. Sounds simple enough. Plus some general conditioning > statements to make sure that this runs only once a week or so the logic I'm > following is: > > > myPackages <- installed.packages() > CRANsPackages <- CRAN.packages() > missingPackages <- CRANsPackages[is.na(match(CRANsPackages[,1], > myPackages[,1])),1] > install.packages(missingPackages) > > > Now this might be trivial, but, missingPackages includes bundled packages > which are already installed (e.g., dse, VR) in addition to those packages > that are truly missing. I know I have to match myPackages with the Contains > column in CRANsPackages and probably use pmatch to do it, but the syntax > eludes me. You do want an exact match. The code you need is in packageStatus(), so you don't need to reinvent this particular wheel. Look at its summary() method (and output) to see how to get what you want. -- 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] install.packages, bundles, pmatch, and Rprofile...
Hi,
Somebody asked me to make sure that all the machines running the in our lab
(XP and Linux, both running 2.0) have R installed and that A) All the
packages are installed and B) kept up-to-date.
Obediently, I began to modify a shared Rprofile so that once a week it
checks for new packages and updates to the current version of the installed
packages on CRAN. Sounds simple enough. Plus some general conditioning
statements to make sure that this runs only once a week or so the logic I'm
following is:
myPackages <- installed.packages()
CRANsPackages <- CRAN.packages()
missingPackages <- CRANsPackages[is.na(match(CRANsPackages[,1],
myPackages[,1])),1]
install.packages(missingPackages)
Now this might be trivial, but, missingPackages includes bundled packages
which are already installed (e.g., dse, VR) in addition to those packages
that are truly missing. I know I have to match myPackages with the Contains
column in CRANsPackages and probably use pmatch to do it, but the syntax
eludes me.
So, an example:
# Install a bundled package
install.packages("gregmisc")
# Get the installed package matrix
myPackages <- installed.packages()
# See if gregmisc is really there
myPackages[grep("gregmisc", myPackages[,5]),]
# Get the matrix of all the packages on CRAN
CRANsPackages <- CRAN.packages()
# Find the missing packages
missingPackages <- CRANsPackages[is.na(match(CRANsPackages[,1],
myPackages[,1])),1]
# Whoops, gregmisc is in there even though its bundles are in myPackages...
missingPackages[grep("gregmisc", missingPackages)]
# Here are the bundles as a string in CRANsPackages...
CRANsPackages[grep("gregmisc", CRANsPackages[,1]),8]
I've looked through R-admin and searched CRAN. What I'm after is a
semi-permanent fix to maintaining R on multiple machines and across
platforms. Other folks must do this? Are there other useful tips?
Off to the polls,
Andy
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Re: [R] install.packages and warnings
These are probably indicating many files lacking EOL on the last line. It
comes from
echo ".installPackageIndices(\".\", \"${R_PACKAGE_DIR}\")" | \
R_DEFAULT_PACKAGES=tools ${R_EXE} --vanilla >/dev/null
if test ${?} -ne 0; then
error "installing package indices failed"
do_exit_on_error
fi
AFAICS.
On Wed, 21 Apr 2004, Göran Broström wrote:
> When I install packages from CRAN I sometimes get a hint about warnings:
>
> ---
> > install.packages(c("Hmisc", "Design"))
> ..
> which.influence texthtmllatex example
> There were 14 warnings (use warnings() to see them)
> * DONE (Design)
>
> Delete downloaded files (y/N)? y
>
> > warnings()
> NULL
> ---
> Where did the warnings go? (R-1.9.0, Debian testing/unstable)
>
> Göran
>
--
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
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[R] install.packages and warnings
When I install packages from CRAN I sometimes get a hint about warnings:
---
> install.packages(c("Hmisc", "Design"))
..
which.influence texthtmllatex example
There were 14 warnings (use warnings() to see them)
* DONE (Design)
Delete downloaded files (y/N)? y
> warnings()
NULL
---
Where did the warnings go? (R-1.9.0, Debian testing/unstable)
Göran
--
Göran Broströmtel: +46 90 786 5223
Department of Statistics fax: +46 90 786 6614
Umeå University http://www.stat.umu.se/egna/gb/
SE-90187 Umeå, Sweden e-mail: [EMAIL PROTECTED]
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Re: [R] install.packages
> "Olivia" == Olivia Lau <[EMAIL PROTECTED]> > on Fri, 16 Apr 2004 12:48:31 -0400 (EDT) writes: . Olivia> One question about the CRAN submission process: Once Olivia> the package is on CRAN, how frequently can we update Olivia> the package (release a new version)? Is it Olivia> basically continuous? I read R-ext carefully, but Olivia> it doesn't seem to say. Well, the CRAN maintainers (at TU Wien) have to do manual work for each submission; but since they ``basically work continuously'' :-) :-) you can update accordingly ;-) Regards, Martin __ [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] install.packages
install.packages works for Linux because the directory structure is not
version dependent, as it is for the Windows download. That should be
fixed as soon as my sys admin consents to install R 1.9.0 so we
can do the cross compile.
Of course, you are right, Martin and Peter, that Zelig should be on CRAN
proper. We just need to write a few .Rd files to be compliant with R
check, and change our documentation to reflect these new installation
instructions. As you can see, the Zelig documentation currently follows
the model rather than the command, and this needs to be revised to pass
R check in a meaningful way. In the meanwhile, Windows users can download
the zip file and do a local installation. I'm sorry about the confusion.
One question about the CRAN submission process: Once the package is on
CRAN, how frequently can we update the package (release a new version)?
Is it basically continuous? I read R-ext carefully, but it doesn't seem
to say.
Thanks,
Olivia Lau
Zelig[[3]]
> > >>>>> "R" == R Heberto Ghezzo <[EMAIL PROTECTED]>
> > >>>>> on Thu, 15 Apr 2004 12:16:03 -0400 writes:
> >
> > R> Hello, I just downloaded RW1090. No problems. My thanks
> > R> to everybody involved in the project. I work in Win98 I
> > R> updated my library, some problems with some files that
> > R> were in the PACKAGES list but not in 1.9/ site, now all
> > R> are. I tried to install "Zelig" from Harvard
> > R> install.packages("Zelig",CRAN="http://gking.harvard.edu";)
> > R> this worked in 1.8.1 but now it appends
> > R> "bin/windows/contrib/1.9" to the address and of course it
> > R> can not find the file and aborts with error 404 Is there
> > R> a way around besides http'ing directly to harvard and
> > R> getting the zip and unzipping it in /library?
> >
> > To my astonishment, it actually works for me (in Linux)
> > with the source package...
> >
> > OTOH, gking.harvard.edu is not really a CRAN mirror, and "GKing"
> > has probably not yet created the bin/windows/contrib/1.9/
> > directory and its contents.
> > As a matter of fact, I believe he should rather submit his
> > package to CRAN proper and you and he wouldn't have to deal with
> > such things as creating now directories when a the version of R
> > is bumped up.
> >
> > As he says on the Zelig web pages, the easy alternative is to
> > download the zip file and install that from the Package menu on
> > Windows.
> >
> > Regards,
> > Martin
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Re: [R] install.packages
Jim Lemon wrote: I hope I will be pardoned for asking what may be a dumb question on this thread. Recently I noticed that when I tried my established method of adding a package to R (i.e. download the *.tar.gz file to a directory of similar files and INSTALL), I was no longer able to do this. I did eventually find the function install.packages() and it worked very nicely, thanks. However, I'd like to know if it is still possible to download packages from CRAN or other sites. For example, I run R on a little old laptop that has no Internet connection whatever, and it will be a bit of a problem keeping it up to date. Downloading the sources and running R INSTALL package_x.y-z.tar.gz should still work (and does for me) ... Which R version / OS are we talking about? Uwe Ligges __ [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] install.packages
I hope I will be pardoned for asking what may be a dumb question on this thread. Recently I noticed that when I tried my established method of adding a package to R (i.e. download the *.tar.gz file to a directory of similar files and INSTALL), I was no longer able to do this. I did eventually find the function install.packages() and it worked very nicely, thanks. However, I'd like to know if it is still possible to download packages from CRAN or other sites. For example, I run R on a little old laptop that has no Internet connection whatever, and it will be a bit of a problem keeping it up to date. Jim __ [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] install.packages
>>>>> "R" == R Heberto Ghezzo <[EMAIL PROTECTED]>
>>>>> on Thu, 15 Apr 2004 12:16:03 -0400 writes:
R> Hello, I just downloaded RW1090. No problems. My thanks
R> to everybody involved in the project. I work in Win98 I
R> updated my library, some problems with some files that
R> were in the PACKAGES list but not in 1.9/ site, now all
R> are. I tried to install "Zelig" from Harvard
R> install.packages("Zelig",CRAN="http://gking.harvard.edu";)
R> this worked in 1.8.1 but now it appends
R> "bin/windows/contrib/1.9" to the address and of course it
R> can not find the file and aborts with error 404 Is there
R> a way around besides http'ing directly to harvard and
R> getting the zip and unzipping it in /library?
To my astonishment, it actually works for me (in Linux)
with the source package...
OTOH, gking.harvard.edu is not really a CRAN mirror, and "GKing"
has probably not yet created the bin/windows/contrib/1.9/
directory and its contents.
As a matter of fact, I believe he should rather submit his
package to CRAN proper and you and he wouldn't have to deal with
such things as creating now directories when a the version of R
is bumped up.
As he says on the Zelig web pages, the easy alternative is to
download the zip file and install that from the Package menu on
Windows.
Regards,
Martin
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Re: [R] install.packages
"R. Heberto Ghezzo" <[EMAIL PROTECTED]> writes:
> Hello,
> I just downloaded RW1090. No problems. My thanks to everybody involved in the
> project. I work in Win98
> I updated my library, some problems with some files that were in the PACKAGES list
> but not in 1.9/ site, now all are.
> I tried to install "Zelig" from Harvard
> install.packages("Zelig",CRAN="http://gking.harvard.edu";)
> this worked in 1.8.1 but now it appends "bin/windows/contrib/1.9" to the address
> and of course it can not find the file and aborts with error 404
> Is there a way around besides http'ing directly to harvard and getting the zip and
> unzipping it in /library?
Well, you can http to harvard, get it and use "Install from local zip
file", which will get it registered correctly.
And, basically, if Gary King wants to pretend that his site is a CRAN
clone with exactly one package, it's up to him to supply the requisite
1.9 dir. It's not a problem with install.packages() that it barfs if
it gets a CRAN argument that isn't a CRAN mirror.
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] install.packages
Hello,
I just downloaded RW1090. No problems. My thanks to everybody involved in the
project. I work in Win98
I updated my library, some problems with some files that were in the PACKAGES list
but not in 1.9/ site, now all are.
I tried to install "Zelig" from Harvard
install.packages("Zelig",CRAN="http://gking.harvard.edu";)
this worked in 1.8.1 but now it appends "bin/windows/contrib/1.9" to the address
and of course it can not find the file and aborts with error 404
Is there a way around besides http'ing directly to harvard and getting the zip and
unzipping it in /library?
Thanks
.
Heberto Ghezzo Ph.D.
McGill University
Montreal - Que - Canada
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Re: [R] install.packages() for a local file
> There is a method to install a package from a local file. > From the unix command line, use >R INSTALL > possibly using >R CMD build > first. Right. I already do this within the function (I need to install the packages from inside of R), but was going through trying to find redundant code and thought this might be a place where I could replace one of my functions with a call to one of R's functions. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] install.packages() for a local file
There is a method to install a package from a local file. From the unix command line, use R INSTALL possibly using R CMD build first. See Writing R Extensions at CRAN for more information. Or R --help at the unix command line. I haven't looked for a way using install.packages(). -Don At 3:09 PM -0500 11/13/03, Jeff Gentry wrote: Hello ... I see that on Windows one can specify a filename as the "pkgs" argument and then set CRAN=NULL when calling install.packages() for a local file. Is there a way to do this on unix? It doesn't appear to be possible, but perhaps I am missing something here. Also, if indeed there is no method to do this on unix, is there a reason behind it or has it just never been implemented? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] install.packages() for a local file
On 13 Nov 2003, Peter Dalgaard wrote: > I suppose the theory is that you might as well just run "R CMD > INSTALL" on the file. That's what I figured here, but wanted to be sure. I had found a block of code of mine where I was basically reinventing the wheel installing local packages and was wondering why I hadn't just used install.packages() on the files. I can at least change the code for the Windows side of things. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] install.packages() for a local file
Jeff Gentry <[EMAIL PROTECTED]> writes: > Hello ... > > I see that on Windows one can specify a filename as the "pkgs" argument > and then set CRAN=NULL when calling install.packages() for a local > file. Is there a way to do this on unix? It doesn't appear to be > possible, but perhaps I am missing something here. > > Also, if indeed there is no method to do this on unix, is there a reason > behind it or has it just never been implemented? Unix doesn't (generally) have binary packages, so has to be different. I suppose the theory is that you might as well just run "R CMD INSTALL" on the file. -- 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
[R] install.packages() for a local file
Hello ... I see that on Windows one can specify a filename as the "pkgs" argument and then set CRAN=NULL when calling install.packages() for a local file. Is there a way to do this on unix? It doesn't appear to be possible, but perhaps I am missing something here. Also, if indeed there is no method to do this on unix, is there a reason behind it or has it just never been implemented? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] install.packages (newbie?) error
If you are using the Carbon version of R (there are *two* ports for MacOS X) then install.packages() is not included. (Where have you been reading about it: under documentation for a different port?) You need to get akima.sit from the /bin/macos/contrib area on CRAN. On Sat, 2 Aug 2003, Åsa Byström wrote: > I recently installed R 1.7.1 on Mac OS 10.2.6, and I now need to > install the akima package. When I use install.packages(akima) or any > variation of that command, I get the following message: > > Error: couldn't find function "install.packages" > > (I haven't had any problems with other commands so far, so I don't > think there's a problem with the R installation. I also threw the whole > thing out and re-installed R from scratch, but that didn't help.) > > I then tried simply downloading, unstuffing, and dragging the package What do you mean by `the package'? The sources, akima*.tar.gz or the MacOS binary akima.sit? > to my library folder. But then, when I tried library(akima), another > error message said the package wasn't properly installed. -- 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
[R] install.packages (newbie?) error
I recently installed R 1.7.1 on Mac OS 10.2.6, and I now need to install the akima package. When I use install.packages(akima) or any variation of that command, I get the following message: Error: couldn't find function "install.packages" (I haven't had any problems with other commands so far, so I don't think there's a problem with the R installation. I also threw the whole thing out and re-installed R from scratch, but that didn't help.) I then tried simply downloading, unstuffing, and dragging the package to my library folder. But then, when I tried library(akima), another error message said the package wasn't properly installed. Any hints? Thanks, Åsa Byström __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
