[R-sig-Debian] Updating packages after install of r-base 2.6.2: cant update rgl

[Michael Friendly]

Thanks Johannes

See the tests below.

Johannes Ranke wrote:
> Hi Michael,
>
> * Michael Friendly <friendly at yorku.ca> [080409 22:00]:
>   
>> Hi
>>
>> I just upgraded my R from stabel/etch from 2.4.x to 2.6.2 via
>>
>> sudo apt-get install r-base
>> which worked fine, installing all dependencies
>>     
>
> I suppose you put some CRAN mirror into your /etc/apt/sources.list?
>   
 cat /etc/apt/sources.list
#deb file:///cdrom/ sarge main

deb http://debian.yorku.ca/debian/ stable main
deb-src http://debian.yorku.ca/debian/ stable main
deb http://debian.yorku.ca/debian-security stable/updates main
deb http://security.debian.org/ stable/updates main
# testing
deb http://debian.yorku.ca/debian/ testing main
# CRAN has newer stable than debian.yorku.ca
deb http://cran.R-project.org/bin/linux/debian stable/

>  
>   
>>  From R, as root, I did
>>
>> update.packages()
>>
>> but a number of packages packages failed to install, either for missing 
>> gfortran
>> or missing dependencies.
>>     
>
> Yes, you need to explicitly upgrade r-base-dev, too, if you want to
> install packages from CRAN.
>  
> ...
>   
>>  ...
>>
>> OK, I installed r-base-dev to get gfortran and other dependencies, then 
>> tried
>> update.packages() again.  This time only rgl failed, complaining about 
>> missing X11:
>>
>> trying URL 'http://probability.ca/cran/src/contrib/rgl_0.77.tar.gz'
>> Content type 'application/x-tar' length 803692 bytes (784 Kb)
>> opened URL
>> ==================================================
>> downloaded 784 Kb
>>
>> * Installing *source* package 'rgl' ...
>> checking for gcc... gcc -std=gnu99
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc -std=gnu99 accepts -g... yes
>> checking for gcc -std=gnu99 option to accept ANSI C... none needed
>> checking how to run the C preprocessor... gcc -std=gnu99 -E
>> checking for gcc... (cached) gcc -std=gnu99
>> checking whether we are using the GNU C compiler... (cached) yes
>> checking whether gcc -std=gnu99 accepts -g... (cached) yes
>> checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
>> checking for libpng-config... yes
>> configure: using libpng-config
>> configure: using libpng dynamic linkage
>> checking for X... no
>> configure: error: X11 not found but required, configure aborted.
>> ERROR: configuration failed for package 'rgl'
>> ** Removing '/usr/lib/R/site-library/rgl'
>> ** Restoring previous '/usr/lib/R/site-library/rgl'
>>     
>
>   

> Could you give us the output of
>
>     apt-cache policy xserver-xorg-core
>
> or just tell us if you have Xorg installed?
>
>   
Yes, I do:
 apt-cache policy xserver-xorg-core
xserver-xorg-core:
  Installed: 2:1.1.1-21
  Candidate: 2:1.1.1-21etch4
  Version table:
     2:1.3.0.0.dfsg-12 0
        200 http://debian.yorku.ca testing/main Packages
     2:1.1.1-21etch4 0
        900 http://debian.yorku.ca stable/main Packages
     2:1.1.1-21etch3 0
        900 http://debian.yorku.ca stable/updates/main Packages
        900 http://security.debian.org stable/updates/main Packages
 *** 2:1.1.1-21 0
        100 /var/lib/dpkg/status

>> Finally, I tried to install r-cran-rgl, but with no joy:
>>
>> euclid:~# apt-get install r-cran-rgl
>> Reading package lists... Done
>> Building dependency tree... Done
>> r-cran-rgl is already the newest version.
>> 0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded.
>>
>> Can anyone suggest what is wrong and how to fix it?
>>
>>     
>
>   


-- 
Michael Friendly     Email: friendly at yorku.ca 
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
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