[BioC] Assistance: mouse4302cdf installation

[Kasper Daniel Hansen]

There are ways around it if you install the package locally, but  
really the easiest way is to get help from your sysadmins to do the  
installation. Just tell them what li said (and you might think about  
installing a list of packages so you do not need to keep banging on  
their door).

Kasper

On Oct 24, 2006, at 9:45 PM, lidaof wrote:

> Hi,
> the error message told you have no privilege
> i recommend you logged as root when you need to install some  
> packages for R
> and the right method to install packages manually:
> "R CMD INSTALL mouse4302cdf_1.12.0.tar.gz" (you should have admin
> permissions)
>
> Good luck
>
> Li
>
>
> On 10/25/06, Melissa Paczkowski <mpaczkow at purdue.edu> wrote:
>>
>> We are using the newest version of Bioconductor (1.9) to perform  
>> an Affy
>> microarray analysis on some mouse chips.  When we start using the
>> "expresso"
>> command to normalize the signal intensity, we get the following error
>> statement:
>>
>> "mkdir: "/usr/local/R-2.4.0/lib/R/library/00LOCK": Permission denied
>> ERROR: failed to lock directory '/usr/local/R-2.4.0/lib/R/library'  
>> for
>> modifying
>>
>> The downloaded packages are in
>>        /tmp/Rtmpi41v2y/downloaded_packages
>> Error in getCdfInfo(object) : Could not obtain CDF environment,  
>> problems
>> encountered:
>> Specified environment does not contain Mouse430_2
>> Library - package mouse4302cdf not installed
>> Data for package affy did not contain mouse4302cdf
>> Library - package mouse4302cdf not installed
>> In addition: Warning messages:
>> 1: installation of package 'mouse4302cdf' had non-zero exit status  
>> in:
>> install.packages(cdfname, lib = lib, repos =  
>> Biobase:::biocReposList(),
>> 2: cannot create HTML package index in: tools:::unix.packages.html
>> (.Library)"
>>
>> We downloaded "mouse4302cdf_1.12.0.tar.gz", but we cannot install  
>> it.  We
>> tried
>> to use the following R commands to install this package:
>>
>> install.packages("mouse4302cdf")
>> install.packages2("mouse4302cdf")
>> attach(mouse4302cdf)
>> biocLite("mouse4302cdf")
>>
>> We also tried installing the "getBioC" package from the
>> www.bioconductor.org/download   .
>>
>> Thank you for your help.
>>
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>>
>
>
>
> -- 
> DaoFeng,Li
> Box A1053 China Agriculture University,
> No.2 Yuanmingyuan Rd.West Haidian District
> Beijing,100094
> P.R.China
> Tel:+86-10-62814726
> Cell:+8613121987798
>
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