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List:       r-sig-debian
Subject:    [R-sig-Debian] Problem with updating/reinstalling R under UBUNTU
From:       Lonjou Christine <chrislonjou () yahoo ! fr>
Date:       2009-08-20 15:18:36
Message-ID: 748882.54990.qm () web26004 ! mail ! ukl ! yahoo ! com
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Hello,

I am a new R user not at ease with installing and updating R package under Ubuntu \
(Hardy), so that I cannot run R anymore ...! I initially installed r version 2.6.2.2 \
(amd64) from Intrepid instead of Hardy (!), but it worked. I tried to update to \
version 2.9, but did not succeeded:  (1) I added to my /etc/apt/sources.list an entry \
:  deb http://cran-fr.r-project.org/bin/linux/ubuntu hardy

   and run the sudo apt-get update + install
   => but when I started R again it was always my version 2.6..2.2 
  
     (2) I loaded   R-2.9.1.tar.gz ; gunzip+tar 
           ./configure
           make     => error messages following:

------- make[4]: Entering directory `/data/prog/R-2.9.1/src/library/tools'
mkdir -p -- ../../../library/tools/R
mv: failed to preserve ownership for `all.R': Operation not permitted
mkdir -p -- ../../../library/tools/po
mkdir -p -- ../../../library/tools/man
mv: failed to preserve ownership for `../../../library/tools/man/tools.Rd': Operation \
not permitted make[4]: Leaving directory `/data/prog/R-2.9.1/src/library/tools'
make[4]: Entering directory `/data/prog/R-2.9.1/src/library/tools'
make[5]: Entering directory `/data/prog/R-2.9.1/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
gcc -std=gnu99 -I../../../../include   -I/usr/local/include     -fvisibility=hidden \
-fpic   -g -O2 -c text.c -o text.o gcc -std=gnu99 -I../../../../include   \
-I/usr/local/include     -fvisibility=hidden -fpic   -g -O2 -c init.c -o init.o gcc \
-std=gnu99 -I../../../../include   -I/usr/local/include     -fvisibility=hidden -fpic \
-g -O2 -c Rmd5.c -o Rmd5.o gcc -std=gnu99 -I../../../../include   \
-I/usr/local/include     -fvisibility=hidden -fpic   -g -O2 -c md5.c -o md5.o gcc \
-std=gnu99 -shared -L/usr/local/lib64 -o tools.so text.o init.o Rmd5.o md5.o make[6]: \
Entering directory `/data/prog/R-2.9.1/src/library/tools/src' make[6]: `Makedeps' is \
up to date. make[6]: Leaving directory `/data/prog/R-2.9.1/src/library/tools/src'
make[6]: Entering directory `/data/prog/R-2.9.1/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory `/data/prog/R-2.9.1/src/library/tools/src'
make[5]: Leaving directory `/data/prog/R-2.9.1/src/library/tools/src'
make[4]: Leaving directory `/data/prog/R-2.9.1/src/library/tools'
Error in namespaceExport(ns, exports) : 
   exportations non définies : checkDocFiles, checkDocStyle, checkFF, \
                checkReplaceFuns, checkS3methods, checkTnF, codoc, codocClasses, \
                codocData, undoc
Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
les méthodes S3 ‘print.checkDocFiles', ‘print.checkDocStyle', ‘print.checkFF', \
‘print.checkReplaceFuns', ‘print.checkS3methods', ‘print.checkTnF', \
‘print.codoc', ‘print.codocClasses', ‘print.codocData', ‘print.subdir_tests', \
‘print.undoc', ‘print.check_Rd_files_in_Rd_db', ‘print.check_Rd_xrefs', \
‘print.check_T_and_F', ‘print.check_code_usage_in_package', \
‘print.check_dotInternal', ‘print.check_make_vars', \
‘print.check_package_code_syntax', ‘print.check_package_depends', \
‘print.check_package_description', ‘print.check_package_description_encoding', \
‘print.check_package_license', ‘print.check_package_datasets', \
‘print.check_packages_used' sont déclarées dans NAMESPACE mais sont introuvables  \
Execution halted make[3]: *** [all] Error 1
make[3]: Leaving directory `/data/prog/R-2.9.1/src/library/tools'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/data/prog/R-2.9.1/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/data/prog/R-2.9.1/src'
make: *** [R] Error 1
root@Horus:/data/prog/R-2.9.1# 

-------

If I try to run R, I now get the following message:

$ R
/usr/local/bin/R: line 230: /usr/local/lib64/R/bin/exec/R: Permission denied
/usr/local/bin/R: line 230: exec: /usr/local/lib64/R/bin/exec/R: cannot execute: \
Success

Can anyone explain me how to simply desinstall all and reinstall it all?

Thank you in advance for your help

Christine





      
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