Re: [R] install package from CRAN
On Jul 28, 2009, at 8:15 PM, cindy Guo wrote:
Hi,
I have a very basic question about install packages from CRAN on
unix. I
only installed on Windows before. Should I use the command
install.package?
The error message I got is
syntax error near unexpected token `mvtnorm'
Is it because I didn't set the path? Which path should I specify?
You should use install.packages (note the last s)... how did you
call that function to get that error you are showing us?
It looks like you're trying to install the 'mvtnorm' package, and
you'd do so like this:
install.packages('mvtnorm')
Is that what you did?
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R] install package from CRAN
Hi, Steve,
Thanks for the response.
I did the same thing:
install.packages('mvtnorm')
-bash: syntax error near unexpected token `'mvtnorm''
I think what may cause difference is that I am using a unix cluster of my
university, so I am not the administrator. Do I need to set the path?
Cindy
On Tue, Jul 28, 2009 at 5:31 PM, Steve Lianoglou
mailinglist.honey...@gmail.com wrote:
On Jul 28, 2009, at 8:15 PM, cindy Guo wrote:
Hi,
I have a very basic question about install packages from CRAN on unix. I
only installed on Windows before. Should I use the command
install.package?
The error message I got is
syntax error near unexpected token `mvtnorm'
Is it because I didn't set the path? Which path should I specify?
You should use install.packages (note the last s)... how did you call
that function to get that error you are showing us?
It looks like you're trying to install the 'mvtnorm' package, and you'd do
so like this:
install.packages('mvtnorm')
Is that what you did?
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
[[alternative HTML version deleted]]
__
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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
and provide commented, minimal, self-contained, reproducible code.
Re: [R] install package from CRAN
Hi,
On Jul 28, 2009, at 8:36 PM, cindy Guo wrote:
Hi, Steve,
Thanks for the response.
I did the same thing:
install.packages('mvtnorm')
-bash: syntax error near unexpected token `'mvtnorm''
I think what may cause difference is that I am using a unix cluster
of my university, so I am not the administrator. Do I need to set
the path?
I think I remember R installing into an alternative lib directory in
your home directory if you didn't have access to your system's R
library directory automatically. I believe R creates a default
directory if you don't specify one, otherwise you can make your own R/
library directory somewhere you have access to and pass that into the
install.packages function, like:
install.packages('mvtnorm', lib='/the/path/to/your/personal/R/library')
I'm not sure, though, this actually looks like a different/worse
problem because the error your get seems to be coming from your unix
shell .. as if R is doing something like a system call but the
command it's sending is malformed.
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
__
R-help@r-project.org 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] install package from CRAN
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of cindy Guo
Sent: Tuesday, July 28, 2009 5:36 PM
To: Steve Lianoglou
Cc: r-help@r-project.org
Subject: Re: [R] install package from CRAN
Hi, Steve,
Thanks for the response.
I did the same thing:
install.packages('mvtnorm')
-bash: syntax error near unexpected token `'mvtnorm''
I think what may cause difference is that I am using a unix cluster of my
university, so I am not the administrator. Do I need to set the path?
Cindy
The error you are getting is from the bash shell. Are you trying to run the
command from the shell, or from inside R? You need to start R and then run
install.packages('mvtnorm') from the R terminal. You still may have permission
problems, and I think you will need to have installed and have access to the
appropriate tools for building packages.
Hope this is helpful,
Dan
Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204
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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 package from CRAN
Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I didn't set the path? Which path should I specify? a) You use install.packages() only from __inside R__. As you got an error from bash, you must have done this from the command prompt. b) At the command prompt, use 'R CMD INSTALL mvtnorm' instead. In either case, you need proper permissions to install in global directories, so if you can run this, try either 'sudo R' to start R so that 'install.packages(mvtnorm)' will succeed, or use 'sudo R CMD INSTALL mvtnorm. Also, if you are on Debian / Ubuntu, you can do sudo apt-get install r-cran-mvtnorm as we provide a prebuild version. Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org 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] install package from CRAN
Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I didn't set the path? Which path should I specify? a) You use install.packages() only from __inside R__. As you got an error from bash, you must have done this from the command prompt. b) At the command prompt, use 'R CMD INSTALL mvtnorm' instead. In either case, you need proper permissions to install in global directories, so if you can run this, try either 'sudo R' to start R so that 'install.packages(mvtnorm)' will succeed, or use 'sudo R CMD INSTALL mvtnorm. Also, if you are on Debian / Ubuntu, you can do sudo apt-get install r-cran-mvtnorm as we provide a prebuild version. Dirk -- Three out of two people have difficulties with fractions. [[alternative HTML version deleted]] __ R-help@r-project.org 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] install package from CRAN
What was the problem- out of curiosity? Stephen Sefick On Tue, Jul 28, 2009 at 9:23 PM, cindy Guocindy.g...@gmail.com wrote: Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I didn't set the path? Which path should I specify? a) You use install.packages() only from __inside R__. As you got an error from bash, you must have done this from the command prompt. b) At the command prompt, use 'R CMD INSTALL mvtnorm' instead. In either case, you need proper permissions to install in global directories, so if you can run this, try either 'sudo R' to start R so that 'install.packages(mvtnorm)' will succeed, or use 'sudo R CMD INSTALL mvtnorm. Also, if you are on Debian / Ubuntu, you can do sudo apt-get install r-cran-mvtnorm as we provide a prebuild version. Dirk -- Three out of two people have difficulties with fractions. [[alternative HTML version deleted]] __ R-help@r-project.org 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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org 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] install package from CRAN
Hi, Thank you for asking. Actually I downloaded the tar.gz file as Mark said and used R CMD INSTALL -l . package.tar.gz to install. I didn't know I can download CRAN packages from the internet. I am not a unix person, so I struggled a lot with the commands on unix and directories especially. I don't know how to deal with it when I don't have enough privilege. Cindy On Tue, Jul 28, 2009 at 7:33 PM, stephen sefick ssef...@gmail.com wrote: What was the problem- out of curiosity? Stephen Sefick On Tue, Jul 28, 2009 at 9:23 PM, cindy Guocindy.g...@gmail.com wrote: Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I didn't set the path? Which path should I specify? a) You use install.packages() only from __inside R__. As you got an error from bash, you must have done this from the command prompt. b) At the command prompt, use 'R CMD INSTALL mvtnorm' instead. In either case, you need proper permissions to install in global directories, so if you can run this, try either 'sudo R' to start R so that 'install.packages(mvtnorm)' will succeed, or use 'sudo R CMD INSTALL mvtnorm. Also, if you are on Debian / Ubuntu, you can do sudo apt-get install r-cran-mvtnorm as we provide a prebuild version. Dirk -- Three out of two people have difficulties with fractions. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis [[alternative HTML version deleted]] __ R-help@r-project.org 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.
