Which packages are installed with the default R installation?

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Which packages are installed with the default R installation?

maya
Hello,

I am a new R user, I have one R version in my Macbook and one in a ubuntu desktop.
I was installing some packages from a secure private source to the R in ubuntu and it replaced some of the existing packages. While the version in my macbook works all ok, in the Ubuntu version of R, I am missing some basic functionalities like:
find.package()
and I can't install new packages which are throwing dependency errors.

> install.packages("ggplot2")
..
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘ggplot2’ is not available

Can you help me with what base packages I may be missing?
Thanks in advance,
D. Isler
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Re: Which packages are installed with the default R installation?

David Winsemius

On Mar 4, 2012, at 4:22 PM, maya wrote:

> Hello,
>
> I am a new R user, I have one R version in my Macbook and one in a  
> ubuntu
> desktop.
> I was installing some packages from a secure private source to the R  
> in
> ubuntu and it replaced some of the existing packages. While the  
> version in
> my macbook works all ok, in the Ubuntu version of R, I am missing  
> some basic
> functionalities like:
> find.package()
> and I can't install new packages which are throwing dependency errors.
>
>> install.packages("ggplot2")
> ..
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘ggplot2’ is not available
>
> Can you help me with what base packages I may be missing?

So far I see no evidence that any base packages are "missing".  
"ggplot2" is certainly not a base package.

--

David Winsemius, MD
West Hartford, CT

______________________________________________
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Re: Which packages are installed with the default R installation?

Joshua Wiley-2
In reply to this post by maya
Hi D. Isler,

It is not a very good sign if you are indeed missing the
find.package() function, this is in the base package, and if functions
from base are missing, your entire version of R is likely corrupt.

If you just do not have some packages you want, and are having
dependency issues, make sure you have a connection to an up-to-date
CRAN mirror, R has write permissions to a library, and then try:

install.packages("package of interest", dependencies = TRUE)

Also, you should read the posting guide (see the footer of this
message as well as every other message ever on R-help) and report the
output of sessionInfo() to us.

Best regards,

Josh

On Sun, Mar 4, 2012 at 1:22 PM, maya <[hidden email]> wrote:

> Hello,
>
> I am a new R user, I have one R version in my Macbook and one in a ubuntu
> desktop.
> I was installing some packages from a secure private source to the R in
> ubuntu and it replaced some of the existing packages. While the version in
> my macbook works all ok, in the Ubuntu version of R, I am missing some basic
> functionalities like:
> find.package()
> and I can't install new packages which are throwing dependency errors.
>
>> install.packages("ggplot2")
> ..
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘ggplot2’ is not available
>
> Can you help me with what base packages I may be missing?
> Thanks in advance,
> D. Isler
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Which-packages-are-installed-with-the-default-R-installation-tp4444321p4444321.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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.



--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

______________________________________________
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Re: Which packages are installed with the default R installation?

Prof Brian Ripley
On 05/03/2012 04:56, Joshua Wiley wrote:
> Hi D. Isler,
>
> It is not a very good sign if you are indeed missing the
> find.package() function, this is in the base package, and if functions
> from base are missing, your entire version of R is likely corrupt.

Or old.  Which is why we ask for 'at a minimum' information in the
posting guide, and for you to update before posting. (find.package needs
R >= 2.13.0, AFAIR.)

> If you just do not have some packages you want, and are having
> dependency issues, make sure you have a connection to an up-to-date
> CRAN mirror, R has write permissions to a library, and then try:
>
> install.packages("package of interest", dependencies = TRUE)
>
> Also, you should read the posting guide (see the footer of this
> message as well as every other message ever on R-help) and report the
> output of sessionInfo() to us.
>
> Best regards,
>
> Josh
>
> On Sun, Mar 4, 2012 at 1:22 PM, maya<[hidden email]>  wrote:
>> Hello,
>>
>> I am a new R user, I have one R version in my Macbook and one in a ubuntu
>> desktop.
>> I was installing some packages from a secure private source to the R in
>> ubuntu and it replaced some of the existing packages. While the version in
>> my macbook works all ok, in the Ubuntu version of R, I am missing some basic
>> functionalities like:
>> find.package()
>> and I can't install new packages which are throwing dependency errors.

No, not-available errors.  Again, the message shows that the R used is
rather old ....

>>> install.packages("ggplot2")
>> ..
>> Warning message:
>> In getDependencies(pkgs, dependencies, available, lib) :
>>   package ‘ggplot2’ is not available
>>
>> Can you help me with what base packages I may be missing?
>> Thanks in advance,
>> D. Isler
>>
>>
>> --
>> View this message in context: http://r.789695.n4.nabble.com/Which-packages-are-installed-with-the-default-R-installation-tp4444321p4444321.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>


--
Brian D. Ripley,                  [hidden email]
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, UK                Fax:  +44 1865 272595

______________________________________________
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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.
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Re: Which packages are installed with the default R installation?

maya
Thank you all for your replies. It seems like now I have an older version of R

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

loaded via a namespace (and not attached):
[1] tools_2.10.1

> find.package()
Error: could not find function "find.package"
> find.package("ggplot2")
Error: could not find function "find.package"

and I can't install the new package ggplot2 while some other packages in CRAN db are still available with the same function

> install.package("ggplot2")
Error: could not find function "install.package"
> install.packages("ggplot2")
Warning in install.packages("ggplot2") :
  argument 'lib' is missing: using '/home/isler/R/x86_64-pc-linux-gnu-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘ggplot2’ is not available


> install.packages("package of interest", dependencies = TRUE)
Warning in install.packages("package of interest", dependencies = TRUE) :
  argument 'lib' is missing: using '/home/isler/R/x86_64-pc-linux-gnu-library/2.10'
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘package of interest’ is not available


Thank you,
D. Isler