vbaabv
asked on
update R on Suse linux
I have R version 2.15.0 installed in /usr/local/bin, and this is the default; in other words when I type 'which R' this is the path I get.
I also have installed R into /usr/local/R-3.1.1/. I want to use this version R not just once but as the default, so that when I type 'which R', I get /usr/local/R-3.1.1
How do I do this ?
I also have installed R into /usr/local/R-3.1.1/. I want to use this version R not just once but as the default, so that when I type 'which R', I get /usr/local/R-3.1.1
How do I do this ?
rename /usr/local/bin executable and create a symlink in that same folder pointing to the executable in /usr/local/R-3.1.1
ASKER
Hi Seth,
Thank you very much for your answer.
I cd into '/usr/local/bin',
renamed 'R' to 'R-old_10-30-14',
then entered 'ln -s /usr/local/R-3.1.1/bin R'
But, now when I type 'which R', I get 'no R in ' followed by my PATH.
I seem to have made the link. When I 'ls -l', in the list is :
lrwxrwxrwx 1 mccormack users 22 2014-10-30 14:42 R -> /usr/local/R-3.1.1/bin
If I 'rm R', then 'ln -s /usr/local/R-3.1.1/bin/R R'
and then type 'R'
I get '/usr/local/bin/R: line 259: /usr/local/R-3.1.1/bin/exe c/R: No such file or directory
/usr/local/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe c/R: cannot execute: No such file or directory'
Thank you very much for your answer.
I cd into '/usr/local/bin',
renamed 'R' to 'R-old_10-30-14',
then entered 'ln -s /usr/local/R-3.1.1/bin R'
But, now when I type 'which R', I get 'no R in ' followed by my PATH.
I seem to have made the link. When I 'ls -l', in the list is :
lrwxrwxrwx 1 mccormack users 22 2014-10-30 14:42 R -> /usr/local/R-3.1.1/bin
If I 'rm R', then 'ln -s /usr/local/R-3.1.1/bin/R R'
and then type 'R'
I get '/usr/local/bin/R: line 259: /usr/local/R-3.1.1/bin/exe
/usr/local/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe
where does the 3.1.1 version of R reside?
in that bin folder or bin/exec ?
in that bin folder or bin/exec ?
ASKER
There is no bin/exec that I can find. The 3.1.1 version of R is in
/usr/local/R-3.1.1/bin
/usr/local/R-3.1.1/bin
your symlink is correct then pointing to bin/R
the errors show bin/R which is good though not sure where the bin/exec/R is coming from as i'm not a developer
what if you ran it directly /usr/local/R-3.1.1/bin/R ?
the errors show bin/R which is good though not sure where the bin/exec/R is coming from as i'm not a developer
what if you ran it directly /usr/local/R-3.1.1/bin/R ?
ASKER
I I run directly, '/usr/local/R-3.1.1/bin/R' , I get the same exact message:
/usr/local/R-3.1.1/bin/R: line 259: /usr/local/R-3.1.1/bin/exe c/R: No such file or directory
/usr/local/R-3.1.1/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe c/R: cannot execute: No such file or directory
/usr/local/R-3.1.1/bin/R: line 259: /usr/local/R-3.1.1/bin/exe
/usr/local/R-3.1.1/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe
how did you install this version?
ASKER
cd into /usr/local/R-3.1.1
'./configure'
then 'make',
but I do get some errors:
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/usr/local/R-3.1.1/src/ma in'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/usr/local/R-3.1.1/src/ma in'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/usr/local/R-3.1.1/src'
make: *** [R] Error 1
'./configure'
then 'make',
but I do get some errors:
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/usr/local/R-3.1.1/src/ma
make[2]: *** [R] Error 2
make[2]: Leaving directory `/usr/local/R-3.1.1/src/ma
make[1]: *** [R] Error 1
make[1]: Leaving directory `/usr/local/R-3.1.1/src'
make: *** [R] Error 1
That means you didn't create the R binary. You may be getting ahead of yourself. What messages did you get when you ran ./configure? You may be missing something that's needed for make to compile.
ASKER
There is a lot of output when I run ./configure and I have attached in a txt document all of the output resulting from running ./configure. I could not find anything that sticks out. Mostly 'yes' and when there was a 'no' it did not seem too important.
I have also included a text document of the output of running 'make'.
configure.txt
make.txt
I have also included a text document of the output of running 'make'.
configure.txt
make.txt
I don't see those errors you posted earlier in your recent make.txt file. Is it working now?
ASKER
No, it is still not working.
When I try to open R directly with '/usr/local/R-3.1.1/bin/R'
I get the following error messages:
/usr/local/R-3.1.1/bin/R: line 259: /usr/local/R-3.1.1/bin/exe c/R: No such file or directory
/usr/local/R-3.1.1/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe c/R: cannot execute: No such file or directory
If I cd into /usr/local/R-3.1.1/bin and type 'R',
I get -bash: R: command not found.
If I type ./R , then I get the same as above:
./R: line 259: /usr/local/R-3.1.1/bin/exe c/R: No such file or directory
./R: line 259: exec: /usr/local/R-3.1.1/bin/exe c/R: cannot execute: No such file or directory
When I try to open R directly with '/usr/local/R-3.1.1/bin/R'
I get the following error messages:
/usr/local/R-3.1.1/bin/R: line 259: /usr/local/R-3.1.1/bin/exe
/usr/local/R-3.1.1/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe
If I cd into /usr/local/R-3.1.1/bin and type 'R',
I get -bash: R: command not found.
If I type ./R , then I get the same as above:
./R: line 259: /usr/local/R-3.1.1/bin/exe
./R: line 259: exec: /usr/local/R-3.1.1/bin/exe
What do you get when you type the following?
ls -l /usr/local/R-3.1.1/bin/
How about when you try R.bin instead of just R? It looks like your makefile compiles it to R.bin.
ls -l /usr/local/R-3.1.1/bin/
How about when you try R.bin instead of just R? It looks like your makefile compiles it to R.bin.
ASKER
ls -l /usr/local/R-3.1.1
total 2450
drwxr-xr-x 2 oak users 640 2014-11-03 16:19 bin
-rw-r--r-- 1 oak users 0 2010-03-17 10:43 ChangeLog
-rw-r--r-- 1 oak users 442472 2014-10-31 15:08 config.log
-rw-r--r-- 1 oak users 10183 2014-06-04 18:15 config.site
-rwxr-xr-x 1 oak users 107187 2014-10-31 15:06 config.status
-rwxr-xr-x 1 oak users 1352905 2014-07-02 18:16 configure
-rw-r--r-- 1 oak users 90444 2014-06-13 18:15 configure.ac
-rw-r--r-- 1 oak users 33546 2014-10-31 14:02 configure.txt
-rw-r--r-- 1 oak users 18011 2010-03-17 10:43 COPYING
drwxr-xr-x 4 oak users 664 2014-10-31 15:06 doc
drwxr-xr-x 2 oak users 360 2014-10-31 15:06 etc
drwxr-xr-x 3 oak users 336 2014-10-31 15:07 include
-rw-r--r-- 1 oak users 1758 2013-07-17 18:05 INSTALL
drwxr-xr-x 2 oak users 120 2014-10-29 15:34 lib
-rwxr-xr-x 1 root root 275325 2014-10-31 15:07 libtool
drwxr-xr-x 2 oak users 552 2014-10-31 15:06 m4
-rw-r--r-- 1 root root 3922 2014-10-31 15:06 Makeconf
-rw-r--r-- 1 oak users 4156 2013-03-05 18:02 Makeconf.in
-rw-r--r-- 1 root root 7446 2014-10-31 15:06 Makefile
-rw-r--r-- 1 oak users 7446 2014-10-31 14:02 Makefile.bak
-rw-r--r-- 1 oak users 7204 2011-10-02 18:02 Makefile.fw
-rw-r--r-- 1 oak users 7593 2014-05-20 18:15 Makefile.in
-rw-r--r-- 1 oak users 142 2014-10-31 15:05 Makefrag.cc
-rw-r--r-- 1 oak users 59 2014-10-31 15:05 Makefrag.cc_lo
-rw-r--r-- 1 oak users 260 2014-10-31 15:05 Makefrag.cxx
-rw-r--r-- 1 oak users 60 2014-10-31 15:05 Makefrag.m
-rw-r--r-- 1 oak users 58083 2014-10-31 14:14 make.txt
drwxr-xr-x 2 oak users 208 2014-10-31 15:06 po
-rw-r--r-- 1 oak users 4131 2014-07-07 18:15 README
drwxr-xr-x 10 oak users 312 2014-10-31 15:06 share
drwxr-xr-x 12 oak users 344 2014-10-31 15:06 src
-rw-r--r-- 1 oak users 46 2014-07-10 03:01 SVN-REVISION
drwxr-xr-x 5 oak users 3416 2014-10-31 15:07 tests
drwxr-xr-x 2 oak users 752 2014-10-31 15:07 tools
-rw-r--r-- 1 oak users 6 2014-07-10 03:00 VERSION
-rw-r--r-- 1 oak users 14 2014-06-29 18:02 VERSION-NICK
When I try R.bin, then I get either a command not found or No such file or directory.
total 2450
drwxr-xr-x 2 oak users 640 2014-11-03 16:19 bin
-rw-r--r-- 1 oak users 0 2010-03-17 10:43 ChangeLog
-rw-r--r-- 1 oak users 442472 2014-10-31 15:08 config.log
-rw-r--r-- 1 oak users 10183 2014-06-04 18:15 config.site
-rwxr-xr-x 1 oak users 107187 2014-10-31 15:06 config.status
-rwxr-xr-x 1 oak users 1352905 2014-07-02 18:16 configure
-rw-r--r-- 1 oak users 90444 2014-06-13 18:15 configure.ac
-rw-r--r-- 1 oak users 33546 2014-10-31 14:02 configure.txt
-rw-r--r-- 1 oak users 18011 2010-03-17 10:43 COPYING
drwxr-xr-x 4 oak users 664 2014-10-31 15:06 doc
drwxr-xr-x 2 oak users 360 2014-10-31 15:06 etc
drwxr-xr-x 3 oak users 336 2014-10-31 15:07 include
-rw-r--r-- 1 oak users 1758 2013-07-17 18:05 INSTALL
drwxr-xr-x 2 oak users 120 2014-10-29 15:34 lib
-rwxr-xr-x 1 root root 275325 2014-10-31 15:07 libtool
drwxr-xr-x 2 oak users 552 2014-10-31 15:06 m4
-rw-r--r-- 1 root root 3922 2014-10-31 15:06 Makeconf
-rw-r--r-- 1 oak users 4156 2013-03-05 18:02 Makeconf.in
-rw-r--r-- 1 root root 7446 2014-10-31 15:06 Makefile
-rw-r--r-- 1 oak users 7446 2014-10-31 14:02 Makefile.bak
-rw-r--r-- 1 oak users 7204 2011-10-02 18:02 Makefile.fw
-rw-r--r-- 1 oak users 7593 2014-05-20 18:15 Makefile.in
-rw-r--r-- 1 oak users 142 2014-10-31 15:05 Makefrag.cc
-rw-r--r-- 1 oak users 59 2014-10-31 15:05 Makefrag.cc_lo
-rw-r--r-- 1 oak users 260 2014-10-31 15:05 Makefrag.cxx
-rw-r--r-- 1 oak users 60 2014-10-31 15:05 Makefrag.m
-rw-r--r-- 1 oak users 58083 2014-10-31 14:14 make.txt
drwxr-xr-x 2 oak users 208 2014-10-31 15:06 po
-rw-r--r-- 1 oak users 4131 2014-07-07 18:15 README
drwxr-xr-x 10 oak users 312 2014-10-31 15:06 share
drwxr-xr-x 12 oak users 344 2014-10-31 15:06 src
-rw-r--r-- 1 oak users 46 2014-07-10 03:01 SVN-REVISION
drwxr-xr-x 5 oak users 3416 2014-10-31 15:07 tests
drwxr-xr-x 2 oak users 752 2014-10-31 15:07 tools
-rw-r--r-- 1 oak users 6 2014-07-10 03:00 VERSION
-rw-r--r-- 1 oak users 14 2014-06-29 18:02 VERSION-NICK
When I try R.bin, then I get either a command not found or No such file or directory.
You've listed the wrong directory. I had asked for ls -l /usr/local/R-3.1.1/bin/, which is one level in. You listed ls -l /usr/local/R-3.1.1/. Your executable should be there.
You also have an INSTALL and a README file. Have you read them?
You can't run R.bin if it's not in your path. It might be in /usr/local/R-3.1.1/bin/
R.bin
You also have an INSTALL and a README file. Have you read them?
You can't run R.bin if it's not in your path. It might be in /usr/local/R-3.1.1/bin/
R.bin
ASKER
Sorry, here is /usr/local/R-3.1.1/bin
ls -l /usr/local/R-3.1.1/bin/
total 416
-rwxr-xr-x 1 oak users 1828 2014-09-16 21:49 BATCH
-rwxr-xr-x 1 oak users 317 2014-09-16 21:49 build
-rwxr-xr-x 1 oak users 317 2014-09-16 21:49 check
-rwxr-xr-x 1 oak users 2156 2014-09-16 21:49 COMPILE
-rwxr-xr-x 1 oak users 9459 2014-09-16 21:49 config
-rwxr-xr-x 1 root root 3606 2014-10-31 15:07 f77_f2c
-rwxr-xr-x 1 oak users 823 2014-09-16 21:49 INSTALL
-rwxr-xr-x 1 root root 14566 2014-10-31 15:07 javareconf
-rwxr-xr-x 1 root root 275325 2014-10-31 15:07 libtool
-rwxr-xr-x 1 oak users 1433 2014-09-16 21:49 LINK
-rwxr-xr-x 1 root root 3494 2014-10-31 15:07 mkinstalldirs
-rwxr-xr-x 1 root root 481 2014-10-31 15:07 pager
-rwxr-xr-x 1 root root 8642 2014-10-31 15:07 R
-rwxr-xr-x 1 root root 1373 2014-10-31 15:07 Rcmd
-rwxr-xr-x 1 oak users 312 2014-09-16 21:49 Rd2pdf
-rwxr-xr-x 1 oak users 359 2014-09-16 21:49 Rdconv
-rwxr-xr-x 1 oak users 258 2014-09-16 21:49 Rdiff
-rwxr-xr-x 1 oak users 158 2014-09-16 21:49 REMOVE
-rwxr-xr-x 1 oak users 310 2014-09-16 21:49 Rprof
-rwxr-xr-x 1 root root 21291 2014-10-31 15:08 Rscript
-rwxr-xr-x 1 root root 4121 2014-10-31 15:07 rtags
-rwxr-xr-x 1 oak users 155 2014-09-16 21:49 SHLIB
-rwxr-xr-x 1 oak users 318 2014-09-16 21:49 Stangle
-rwxr-xr-x 1 oak users 316 2014-09-16 21:49 Sweave
I have read the INSTALL which says a simple compilation by ./configure then make, and that is what I have done.
ls -l /usr/local/R-3.1.1/bin/
total 416
-rwxr-xr-x 1 oak users 1828 2014-09-16 21:49 BATCH
-rwxr-xr-x 1 oak users 317 2014-09-16 21:49 build
-rwxr-xr-x 1 oak users 317 2014-09-16 21:49 check
-rwxr-xr-x 1 oak users 2156 2014-09-16 21:49 COMPILE
-rwxr-xr-x 1 oak users 9459 2014-09-16 21:49 config
-rwxr-xr-x 1 root root 3606 2014-10-31 15:07 f77_f2c
-rwxr-xr-x 1 oak users 823 2014-09-16 21:49 INSTALL
-rwxr-xr-x 1 root root 14566 2014-10-31 15:07 javareconf
-rwxr-xr-x 1 root root 275325 2014-10-31 15:07 libtool
-rwxr-xr-x 1 oak users 1433 2014-09-16 21:49 LINK
-rwxr-xr-x 1 root root 3494 2014-10-31 15:07 mkinstalldirs
-rwxr-xr-x 1 root root 481 2014-10-31 15:07 pager
-rwxr-xr-x 1 root root 8642 2014-10-31 15:07 R
-rwxr-xr-x 1 root root 1373 2014-10-31 15:07 Rcmd
-rwxr-xr-x 1 oak users 312 2014-09-16 21:49 Rd2pdf
-rwxr-xr-x 1 oak users 359 2014-09-16 21:49 Rdconv
-rwxr-xr-x 1 oak users 258 2014-09-16 21:49 Rdiff
-rwxr-xr-x 1 oak users 158 2014-09-16 21:49 REMOVE
-rwxr-xr-x 1 oak users 310 2014-09-16 21:49 Rprof
-rwxr-xr-x 1 root root 21291 2014-10-31 15:08 Rscript
-rwxr-xr-x 1 root root 4121 2014-10-31 15:07 rtags
-rwxr-xr-x 1 oak users 155 2014-09-16 21:49 SHLIB
-rwxr-xr-x 1 oak users 318 2014-09-16 21:49 Stangle
-rwxr-xr-x 1 oak users 316 2014-09-16 21:49 Sweave
I have read the INSTALL which says a simple compilation by ./configure then make, and that is what I have done.
Does the following run? I see R in the Folder.
/usr/local/R-3.1.1/bin/R
If it does, then put a link to R in /usr/local/bin
ln /usr/local/R-3.1.1/bin/R /usr/local/bin/R
or if you prefer a symbolic link,
ln -s /usr/local/R-3.1.1/bin/R /usr/local/bin/R
/usr/local/R-3.1.1/bin/R
If it does, then put a link to R in /usr/local/bin
ln /usr/local/R-3.1.1/bin/R /usr/local/bin/R
or if you prefer a symbolic link,
ln -s /usr/local/R-3.1.1/bin/R /usr/local/bin/R
ASKER
/usr/local/R-3.1.1/bin/R
/usr/local/R-3.1.1/bin/R: line 259: /usr/local/R-3.1.1/bin/exe c/R: No such file or directory
/usr/local/R-3.1.1/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe c/R: cannot execute: No such file or directory
On the Internet I found a similar problem in which the solution was supposed to be '...a problem with a BLAS installation chosen by ./configure', but I have no idea of what BLAS is.
The problem was:
"I have just installed R-2.0.1 from R-2.0.1.tar.gz on SUSe 9.1 64bit. When
I am trying to launch R: R_HOME_DIR/bin/R; I am getting following message:
./R: line 151: /R_HOME_DIR/bin/exec/R: No such file or directory
./R: line 151: exec: /R_HOME_DIR/bin/exec/R: cannot execute: No such file"
I am on SUSE enteprise, SLSE.
/usr/local/R-3.1.1/bin/R: line 259: /usr/local/R-3.1.1/bin/exe
/usr/local/R-3.1.1/bin/R: line 259: exec: /usr/local/R-3.1.1/bin/exe
On the Internet I found a similar problem in which the solution was supposed to be '...a problem with a BLAS installation chosen by ./configure', but I have no idea of what BLAS is.
The problem was:
"I have just installed R-2.0.1 from R-2.0.1.tar.gz on SUSe 9.1 64bit. When
I am trying to launch R: R_HOME_DIR/bin/R; I am getting following message:
./R: line 151: /R_HOME_DIR/bin/exec/R: No such file or directory
./R: line 151: exec: /R_HOME_DIR/bin/exec/R: cannot execute: No such file"
I am on SUSE enteprise, SLSE.
It seems that the configure is doing the wrong thing and getting make to compile the wrong path into your binary.
It might be easier to follow the other instructions to install R. Add the repo and use zypper to install it.
http://cran.r-project.org/bin/linux/suse/README.html
It might be easier to follow the other instructions to install R. Add the repo and use zypper to install it.
http://cran.r-project.org/bin/linux/suse/README.html
you're running 9.1? that version is over 10 years old and was discontinued 8 years ago
there could be libraries that are not compatible because they are so old
there could be libraries that are not compatible because they are so old
I didn't catch that on my first pass. SUSE 14 is the latest.
ASKER
Sorry, my fault. I was not clear on my last post. The SUSE 9.1 was taken from an old thread I found with a google search. The person's problem seems very similar to mine and they were using SuSE. The error message they received seems pretty similar to the error message I am receiving, so I posted part of the question and answer as a possible clue to what might be my problem. The answer that person using SUSE 9.1 (it was an old post ) received had to do with BLAS. There were no more posts on the thread, so I thought the answer might have solved the problem, and may be helpful in solving my problem because I am using SLES. I will have to check the version I am using. It is probably abut 4 years old. However, I do not have a clue as to what BLAS is, so I have no idea if it would help me.
To find your SUSE version:
cat /etc/SuSE-release
cat /etc/SuSE-release
ASKER
Hi Seth and serialband,
Thanks again for your continued help.
Here is my SUSE version:
SUSE Linux Enterprise Server 11 (x86_64)
VERSION = 11
PATCHLEVEL = 1
Thanks for the link to BLAS on SuSE. I will read it over and see if I can figure anything as to why it would now be a problem.
Thanks again for your continued help.
Here is my SUSE version:
SUSE Linux Enterprise Server 11 (x86_64)
VERSION = 11
PATCHLEVEL = 1
Thanks for the link to BLAS on SuSE. I will read it over and see if I can figure anything as to why it would now be a problem.
Easiest way is to re-package opensuse source RPMs of R
rpmbuild -ba SPECS/R.spec
rpmbuild -ba SPECS/R.spec
ASKER
Thank you very much for your comment gheist. Unfortunately, your knowledge of this is way above mine and I don't quite understand.
To my limited understanding, it seems I should enter the command 'rpmbuild -ba SPECS/R.spec'. What directory should I be in when I do this ?
To my limited understanding, it seems I should enter the command 'rpmbuild -ba SPECS/R.spec'. What directory should I be in when I do this ?
You need to download source RPM with zypper source-download on normal openSUSE
Then build that source RPM into installable RPM on your SLES.
(zypper in fakeroot rpmbuild rpm2cpio)
Than just install resulting RPM.
Then build that source RPM into installable RPM on your SLES.
(zypper in fakeroot rpmbuild rpm2cpio)
Than just install resulting RPM.
If you upgrade to SUSE 11.3, you should be able to install it with yast2 or zypper.
zypper in R
Otherwise, go get the 1-Click Install from http://cran.r-project.org/bin/linux/suse/
You can get R for SUSE 11.1
http://software.opensuse.org/ymp/devel:languages:R:patched/openSUSE_11.1/R-patched.ymp
or the developer version for SUSE 11.1
http://software.opensuse.org/ymp/devel:languages:R:patched/openSUSE_11.1/R-patched-devel.ymp
zypper in R
Otherwise, go get the 1-Click Install from http://cran.r-project.org/bin/linux/suse/
You can get R for SUSE 11.1
http://software.opensuse.org/ymp/devel:languages:R:patched/openSUSE_11.1/R-patched.ymp
or the developer version for SUSE 11.1
http://software.opensuse.org/ymp/devel:languages:R:patched/openSUSE_11.1/R-patched-devel.ymp
ASKER
So, once I get the .ymp file. How do I use that ?
ASKER
We do hope to actually change from SLSE to CentOS or some other Linux distro, but that will be a big job because we have 14 TB of data that will have to be moved before that can be done and it will probably be a while before it can be done.
I just have a CLI to the server which is where I am trying to install the new version of R, so I am not using a desktop type environment where I can click on something. Can I still use the .ymp file ?
I just have a CLI to the server which is where I am trying to install the new version of R, so I am not using a desktop type environment where I can click on something. Can I still use the .ymp file ?
It's supposedly a One-Click install. Use a browser in Suse and click on those links.
https://en.opensuse.org/openSUSE:One_Click_Install_UserFAQ
https://en.opensuse.org/openSUSE:One_Click_Install
https://en.opensuse.org/openSUSE:One_Click_Install_UserFAQ
https://en.opensuse.org/openSUSE:One_Click_Install
He uses Suse Linux, not openSUSE
Dear Asker: please follow ymp links for your version of SuSE, not install openSUSE packages ever.
ymp is text file, if you read it you can construct zypper repo entries from the content.
Dear Asker: please follow ymp links for your version of SuSE, not install openSUSE packages ever.
ymp is text file, if you read it you can construct zypper repo entries from the content.
14TB could be shared via NFS to multiple machines, those can be centos, ubuntu, opensuse, gentoo or anything easily reproducable...
ASKER
Sorry for the delay in getting back to everyone.
Finding an R .ymp file for openSUSE is easy enough, but I can not seem to find a .ymp R file for SLES.
Our server administrator seemed to think that the problem was that I needed to specify to the R config file as to where readline 6 lib was located because it needs readline 6 for rl_sort_completion_matches and the config file was probably trying to use our systems base readline 5.2 instead. This is because part of the error command is:
-lreadline -lrt -ldl -lm
../unix/sys-std.o: In function `initialize_rlcompletion':
/usr/local/R-3.1.2/src/uni x/sys-std. c:689: undefined reference to
`rl_sort_completion_matche s'
collect2: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/usr/local/R-3.1.2/src/ma in'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/usr/local/R-3.1.2/src/ma in'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/usr/local/R-3.1.2/src'
make: *** [R] Error 1
He didn't go beyond that in terms of instruction or explanation. After searching through the R config file and make file, I could not find anywhere that I could change a path where it looks for readline.
Beginning to think that this is an unsolvable problem.
Finding an R .ymp file for openSUSE is easy enough, but I can not seem to find a .ymp R file for SLES.
Our server administrator seemed to think that the problem was that I needed to specify to the R config file as to where readline 6 lib was located because it needs readline 6 for rl_sort_completion_matches
-lreadline -lrt -ldl -lm
../unix/sys-std.o: In function `initialize_rlcompletion':
/usr/local/R-3.1.2/src/uni
`rl_sort_completion_matche
collect2: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/usr/local/R-3.1.2/src/ma
make[2]: *** [R] Error 2
make[2]: Leaving directory `/usr/local/R-3.1.2/src/ma
make[1]: *** [R] Error 1
make[1]: Leaving directory `/usr/local/R-3.1.2/src'
make: *** [R] Error 1
He didn't go beyond that in terms of instruction or explanation. After searching through the R config file and make file, I could not find anywhere that I could change a path where it looks for readline.
Beginning to think that this is an unsolvable problem.
This page you saw before:
http://cran.r-project.org/bin/linux/suse/
It has links for R for *ALL* suse and opensuse versions.
http://cran.r-project.org/bin/linux/suse/
It has links for R for *ALL* suse and opensuse versions.
ASKER
Thanks. I saw the OpenSuse written everywhere, I did not realize the SLE was for SLES.
So, I downloaded R-patched-devel.ymp for SLE 11 SP1. Transferred it to our server in the /user/local folder, changed permissions to 755 and then typed:
./R-patched-devel.ymp
Which returned the following:
./R-patched-devel.ymp: line 1: syntax error near unexpected token `newline'
./R-patched-devel.ymp: line 1: `<metapackage xmlns:os="http://opensuse.org/Standards/One_Click_Install" xmlns="http://opensuse.org/Standards/One_Click_Install">'
So, I downloaded R-patched-devel.ymp for SLE 11 SP1. Transferred it to our server in the /user/local folder, changed permissions to 755 and then typed:
./R-patched-devel.ymp
Which returned the following:
./R-patched-devel.ymp: line 1: syntax error near unexpected token `newline'
./R-patched-devel.ymp: line 1: `<metapackage xmlns:os="http://opensuse.org/Standards/One_Click_Install" xmlns="http://opensuse.org/Standards/One_Click_Install">'
There's several SUSE 11 links on that page that I first linked that gheist relinked. Click on the version that matches your SUSE version. Use a browser from your SUSE system.
Otherwise, scroll down and follow the instructions to add it to your repo, then run zypper.
Otherwise, scroll down and follow the instructions to add it to your repo, then run zypper.
Installing using the command line
As superuser do
VERSION=$(grep VERSION /etc/SuSE-release | sed -e 's/VERSION = //')
zypper addrepo -f \
http://download.opensuse.org/repositories/devel\:languages\:R\:patched/openSUSE_$VERSION/ \
R-patched
which automatically determines your installed version of openSUSE. After that
zypper install R-patched R-patched-devel
will install R and all dependencies. This only works for supported versions of openSUSE.
ASKER
When I try to install with zypper, I get the following:
sudo zypper install R-patched-devel
Error building the cache:
[|] Repository type can't be determined.
Warning: Disabling repository 'dell-omsa-hw' because of the above error.
Loading repository data...
Reading installed packages...
'R-patched-devel' not found.
Resolving package dependencies...
Nothing to do.
sudo zypper install R-patched-devel
Error building the cache:
[|] Repository type can't be determined.
Warning: Disabling repository 'dell-omsa-hw' because of the above error.
Loading repository data...
Reading installed packages...
'R-patched-devel' not found.
Resolving package dependencies...
Nothing to do.
You have problems with dell repositories.
Please fix them before installing anything else.
At least make sure 'zypper ref' exits cleanly before adding extra repositories.
Please fix them before installing anything else.
At least make sure 'zypper ref' exits cleanly before adding extra repositories.
ASKER
I have removed dell-omsa-hw.repo from /etc/zypp/repos.d/.
Now when I type:
I get: If only one argument is used, it must be a URI pointing to a .repo file.
addrepo (ar) [options] <URI> <alias>
addrepo (ar) [options] <file.repo>
Add a repository to the sytem. The repository can be specified by its URI or can be read from specified .repo file (even remote). (with a list of Command options.)
Now when I type:
sudo VERSION=$(grep VERSION /etc/SuSE-release | sed -e 's/VERSION = //') zypper addrepo -f http://download.opensuse.org/repositories/devel\:languages\:R\:patched/openSUSE_$VERSION
/R-patched
I get: If only one argument is used, it must be a URI pointing to a .repo file.
addrepo (ar) [options] <URI> <alias>
addrepo (ar) [options] <file.repo>
Add a repository to the sytem. The repository can be specified by its URI or can be read from specified .repo file (even remote). (with a list of Command options.)
ASKER
This did work:
Adding repository 'R-base (SLE_11_SP1)' [done]
Repository 'R-base (SLE_11_SP1)' successfully added
Enabled: Yes
Autorefresh: Yes
URI: http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_11_SP1/
sudo VERSION=$(grep VERSION /etc/SuSE-release | sed -e 's/VERSION = //') zypper addrepo -f http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_11_SP1/devel:languages:R:base.repo
Adding repository 'R-base (SLE_11_SP1)' [done]
Repository 'R-base (SLE_11_SP1)' successfully added
Enabled: Yes
Autorefresh: Yes
URI: http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_11_SP1/
ASKER
However, there were problems with installing R-base:
sudo zypper install R-base
Loading repository data...
Reading installed packages...
Resolving package dependencies...
The following NEW packages are going to be installed:
R-base R-base-devel xdg-utils
The following packages are not supported by their vendor:
R-base R-base-devel
3 new packages to install.
Overall download size: 46.3 MiB. After the operation, additional 67.0 MiB will be used.
Continue? [y/n/?] (y): y
Retrieving package xdg-utils-1.0.2-36.18.noar ch (1/3), 49.0 KiB (183.0 KiB unpacked)
Failed to mount cd:///?devices=/dev/sr0 on /var/adm/mount/AP_0x000000 05: Mounting media failed (mount: no medium found on /dev/sr0)
Please insert medium [SUSE-Linux-Enterprise-Ser ver-11-SP1 11.1.1-1.152] #1 and type 'y' to continue or 'n' to cancel the operation. [yes/no] (no):
sudo zypper install R-base
Loading repository data...
Reading installed packages...
Resolving package dependencies...
The following NEW packages are going to be installed:
R-base R-base-devel xdg-utils
The following packages are not supported by their vendor:
R-base R-base-devel
3 new packages to install.
Overall download size: 46.3 MiB. After the operation, additional 67.0 MiB will be used.
Continue? [y/n/?] (y): y
Retrieving package xdg-utils-1.0.2-36.18.noar
Failed to mount cd:///?devices=/dev/sr0 on /var/adm/mount/AP_0x000000
Please insert medium [SUSE-Linux-Enterprise-Ser
you might wish to install libR* and R-devel too...
ASKER
When installing libR*, I get a screen message that I can not do because I do not have the SUSE cd.
Please insert medium [SUSE-Linux-Enterprise-Ser ver-11-SP1 11.1.1-1.152] #1 and type 'y' to continue or 'n' to cancel the operation. [yes/no] (no): n
Failed to provide Package termcap-2.0.8-981.18. Do you want to retry retrieval?
Please insert medium [SUSE-Linux-Enterprise-Ser
Failed to provide Package termcap-2.0.8-981.18. Do you want to retry retrieval?
You need to rename that repo too and use online ubscription
I think it is in yast / Software/ Configure repositories and Configure subscription.
I think it is in yast / Software/ Configure repositories and Configure subscription.
ASKER
I tried 'whereis YaST' and found two locations: /sbin/YaST and /lib/YaST, but there is no Software or Configure repositories and/ Configure subscription.
I found a SuSEconfig.functions file in /lib/YaST, but its 100 lines and I do not see anything familiar in it.
If I try 'whereis termcap-2.0.8-981.18', I just get 'termcap-2.0.8-981.18: '.
I appreciate all the help, but I think the only solution is going to be to re-install a new OS,
I found a SuSEconfig.functions file in /lib/YaST, but its 100 lines and I do not see anything familiar in it.
If I try 'whereis termcap-2.0.8-981.18', I just get 'termcap-2.0.8-981.18: '.
I appreciate all the help, but I think the only solution is going to be to re-install a new OS,
you can run commad "sudo yast"
ASKER
The 'sudo yast' command, when entered on this machine anyway, results in :
'sudo: yast: command not found'
'sudo: yast: command not found'
It is not about R, simply your package manager is in bad disorder.
Can you run a yast or YaST when logged in as root and FIX SOFTWARE REPOSITORIES?
Can you run a yast or YaST when logged in as root and FIX SOFTWARE REPOSITORIES?
ASKER
Can I fix the software repos without having to use the command 'yast'. I always get the 'sudo: yast: command not found'.
ASKER CERTIFIED SOLUTION
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ASKER
Wow ! I did't know there was anything like this on the server. But, I am having some difficulty moving around. There are commands in brackets. How do I use them; with the mouse, typing ?
TAB is auto-complete character. I wrote it as [tab]
For software completeness get hold of OpenSUSE 13.1 , later adding evergreen it will last for another 3 years and run R 3.1.2. Also 13.x series do not stick with CD as repository.
For software completeness get hold of OpenSUSE 13.1 , later adding evergreen it will last for another 3 years and run R 3.1.2. Also 13.x series do not stick with CD as repository.
ASKER
After sudo -s and then Yast, how do I get out of this to back to the regular > prompt ?
How did you register system first time?
Press Alt and the highlighted key
Press Alt and the highlighted key
You cannot add new SLES 10 systems after 31 Jul 2013
Or SLES9U1 19 Jan 2005
Please acquire reasonably fresh system as ones you mentioned are between year and 10 EOL.
Or SLES9U1 19 Jan 2005
Please acquire reasonably fresh system as ones you mentioned are between year and 10 EOL.
ASKER
Thanks for your patience.