Lonjou Christine
2009-Aug-20 15:19 UTC
[R-sig-Debian] Problem with updating/reinstalling R under UBUNTU (Hardy)
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
[[alternative HTML version deleted]]
Vincent Goulet
2010-Mar-24 13:20 UTC
[R-sig-Debian] Problem with updating/reinstalling R under UBUNTU (Hardy)
Christine, It looks like your system is seriously FUBAR, on the R front at least. I recommend you deinstall everything R related. You may need to use a combination of apt-get, dpkg and good old rm (for the failed installation from sources). And please, don't try to build from source on Ubuntu unless you have very specific needs. We provide binary packages so that you don't have to do this. Once you system is clean, follow the instructions in the Ubuntu README on CRAN to get up and running again. HTH Vincent Le jeu. 20 ao?t ? 11:18, Lonjou Christine a ?crit :> > 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 d?finies : checkDocFiles, checkDocStyle, checkFF, checkReplaceFuns, checkS3methods, checkTnF, codoc, codocClasses, codocData, undoc > Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> > In addition: Warning message: > les m?thodes 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 d?clar?es 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 at 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 > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian