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"gplots" packages does not work

8 messages · Fernando Pistón, Fernando Pistón Pistón, Steve Lianoglou +2 more

Original
Pascal Oettli
# 
Hi Fernando,

You have to reinstall package 'bitops' too.

Regards,
Pascal



----- Mail original -----
De?: Fernando Pist?n <fpiston at gmail.com>
??: r-help at r-project.org
Cc?: 
Envoy? le : Mardi 13 mars 2012 16h10
Objet?: [R] "gplots" packages does not work

I had installed de "gplots" package and then I loaded the library but the
package did not work.? I recieved a message like this:
Installing package(s) into
?/home/fpiston/R/x86_64-pc-linux-gnu-library/2.14?
(as ?lib? is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.es.r-project.org/src/contrib/gplots_2.10.1.tar.gz'
Content type 'application/x-gzip' length 226290 bytes (220 Kb)
opened URL
==================================================
downloaded 220 Kb

* installing *source* package ?gplots? ...
** package ?gplots? successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Error : package ?caTools? was built before R 2.10.0: please re-install it
ERROR: lazy loading failed for package ?gplots?
* removing ?/home/fpiston/R/x86_64-pc-linux-gnu-library/2.14/gplots?

The downloaded packages are in
?/tmp/Rtmp2ooBQr/downloaded_packages?
Warning message:
In install.packages("gplots", dependencies = TRUE) :
? installation of package ?gplots? had non-zero exit status
Installing package(s) into
?/home/fpiston/R/x86_64-pc-linux-gnu-library/2.14?
(as ?lib? is unspecified)
trying URL 'http://cran.es.r-project.org/src/contrib/caTools_1.12.tar.gz'
Content type 'application/x-gzip' length 61894 bytes (60 Kb)
opened URL
==================================================
downloaded 60 Kb

* installing *source* package ?caTools? ...
** Creating default NAMESPACE file
** libs
g++ -I/usr/share/R/include? ? ? -fpic? -O3 -pipe? -g -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/share/R/include? ? ? -fpic? -O3 -pipe? -g -c GifTools.cpp -o
GifTools.o
gcc -std=gnu99 -I/usr/share/R/include? ? ? -fpic? -O3 -pipe? -g -c
runfunc.c -o runfunc.o
g++ -shared -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib64/R/lib
-lR
installing to /home/fpiston/R/x86_64-pc-linux-gnu-library/2.14/caTools/libs
** R
** preparing package for lazy loading
Error : package ?bitops? was built before R 2.10.0: please re-install it
ERROR: lazy loading failed for package ?caTools?
* removing ?/home/fpiston/R/x86_64-pc-linux-gnu-library/2.14/caTools?

The downloaded packages are in
?/tmp/Rtmp2ooBQr/downloaded_packages?
Warning message:
In install.packages("caTools", dependencies = TRUE) :
? installation of package ?caTools? had non-zero exit status
Error: package ?caTools? was built before R 2.10.0: please re-install it
Loading required package: gtools
Loading required package: gdata

Attaching package: ?gdata?

The following object(s) are masked from ?package:stats?:

? ? nobs

The following object(s) are masked from ?package:utils?:

? ? object.size

Loading required package: caTools
Error: package ?caTools? was built before R 2.10.0: please re-install it
Steve Lianoglou
# 
Hi,

It does work -- it seems like that at some point you've upgraded your
R packages in an incorrect manner.

Specifically, it looks as if you've installed a new version of R and
just copied over libraries from a previous (pre R-2.10.x) version.

Look at this error message during the install:
On Tue, Mar 13, 2012 at 3:10 AM, Fernando Pist?n <fpiston at gmail.com> wrote:
[snip]
[snip]

Your gplots install immediately aborts after that.

In order to try automagically remedy the situation, you might try
something like:

R> update.packages(checkBuild=TRUE, ask=FALSE)

After that's done, try re-installing gplots.

HTH,
-steve
Steve Lianoglou
# 
Hi Fernando,

2012/3/13 Fernando Pist?n Pist?n <fpiston at ias.csic.es>:
I don't see Pascal's suggestion, so I guess I don't know what you did
(maybe just updated catTools by itself?)

In general, it is "good form" to not use packages built w/ older
version of R in your current R install. Whether or not you want to
follow that recommended practice, I'll leave up to you.

-steve
Pascal Oettli
# 
Hi Fernando,

To me, it is a good idea to regularly check the availability of update for installed packages, using 'update.packages()'.

Regards,
Pascal



----- Mail original -----
De?: Fernando Pist?n Pist?n <fpiston at ias.csic.es>
??: Steve Lianoglou <mailinglist.honeypot at gmail.com>
Cc?: r-help at r-project.org
Envoy? le : Mardi 13 mars 2012 17h06
Objet?: Re: [R] "gplots" packages does not work

Hi Steve,

The suggestion of Pacal worked ok, Do you think it is neccesary to
"update.packages"? Can I "update.packages" although the "gplots" work ok?


On Tue, Mar 13, 2012 at 8:38 AM, Steve Lianoglou <
mailinglist.honeypot at gmail.com> wrote:

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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On 13/03/2012 08:33, Pascal Oettli wrote:

            

      
      
      
    

        
Specifically, update.packages(checkBuilt=TRUE) to overcome the 
wrong-R-version issue (although the package installation could be so 
corrupted that this cannot find the version ...).

That is the default (these days) for the Windows GUI's menu.