How to set up R to run from a directory with no bin or root access?
I need to run the latest version of R on our server. We have an older version in the bin directory, so that simply typing R in the command line brings this up. It is set up such that:
>which R
/bin/R
Our administrators will not upgrade R at this time and I need to use the latest version. In the past, I've been able to run programs without any bin or root access by simply putting them in my directory. I can then call those programs by typing out the whole path, instead of just typing "R".
I am unable to find a method for installing R that does not involve installing it in the bin through an installer such as apt-get. Is there a way for me to install R in my own directory, as I have done for other programs, without placing it in the /bin/ folder of system-wide executables, and without admin privileges?
We are on CentOS Linux release 7.2.1511
Update:
When I attempt the following, as recommended:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
I get the following error because I don't have access to the /data/ directory it default to.
checking build system type... mkdir: cannot create directory
'/data/cg55281-32717': Permission denied mkdir: cannot create
directory '/data/cg-55281': Permission denied config.guess: cannot
create a temporary directory in /data configure: error: cannot guess
build type; you must specify one
r linux unix installation centos
asked Nov 22 '18 at 2:07
nagleminaglemi
85
add a comment |
I need to run the latest version of R on our server. We have an older version in the bin directory, so that simply typing R in the command line brings this up. It is set up such that:
>which R
/bin/R
Our administrators will not upgrade R at this time and I need to use the latest version. In the past, I've been able to run programs without any bin or root access by simply putting them in my directory. I can then call those programs by typing out the whole path, instead of just typing "R".
I am unable to find a method for installing R that does not involve installing it in the bin through an installer such as apt-get. Is there a way for me to install R in my own directory, as I have done for other programs, without placing it in the /bin/ folder of system-wide executables, and without admin privileges?
We are on CentOS Linux release 7.2.1511
Update:
When I attempt the following, as recommended:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
I get the following error because I don't have access to the /data/ directory it default to.
checking build system type... mkdir: cannot create directory
'/data/cg55281-32717': Permission denied mkdir: cannot create
directory '/data/cg-55281': Permission denied config.guess: cannot
create a temporary directory in /data configure: error: cannot guess
build type; you must specify one
r linux unix installation centos
asked Nov 22 '18 at 2:07
nagleminaglemi
85
How about installing R locally through anaconda? Also perhaps worth taking a look at: How to install R 3.2.2 using a conda environment on CentOS
– Maurits Evers
Nov 22 '18 at 2:28
add a comment |
I need to run the latest version of R on our server. We have an older version in the bin directory, so that simply typing R in the command line brings this up. It is set up such that:
>which R
/bin/R
Our administrators will not upgrade R at this time and I need to use the latest version. In the past, I've been able to run programs without any bin or root access by simply putting them in my directory. I can then call those programs by typing out the whole path, instead of just typing "R".
I am unable to find a method for installing R that does not involve installing it in the bin through an installer such as apt-get. Is there a way for me to install R in my own directory, as I have done for other programs, without placing it in the /bin/ folder of system-wide executables, and without admin privileges?
We are on CentOS Linux release 7.2.1511
Update:
When I attempt the following, as recommended:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
I get the following error because I don't have access to the /data/ directory it default to.
checking build system type... mkdir: cannot create directory
'/data/cg55281-32717': Permission denied mkdir: cannot create
directory '/data/cg-55281': Permission denied config.guess: cannot
create a temporary directory in /data configure: error: cannot guess
build type; you must specify one
r linux unix installation centos
asked Nov 22 '18 at 2:07
nagleminaglemi
85
I need to run the latest version of R on our server. We have an older version in the bin directory, so that simply typing R in the command line brings this up. It is set up such that:
>which R
/bin/R
Our administrators will not upgrade R at this time and I need to use the latest version. In the past, I've been able to run programs without any bin or root access by simply putting them in my directory. I can then call those programs by typing out the whole path, instead of just typing "R".
I am unable to find a method for installing R that does not involve installing it in the bin through an installer such as apt-get. Is there a way for me to install R in my own directory, as I have done for other programs, without placing it in the /bin/ folder of system-wide executables, and without admin privileges?
We are on CentOS Linux release 7.2.1511
Update:
When I attempt the following, as recommended:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
I get the following error because I don't have access to the /data/ directory it default to.
checking build system type... mkdir: cannot create directory
'/data/cg55281-32717': Permission denied mkdir: cannot create
directory '/data/cg-55281': Permission denied config.guess: cannot
create a temporary directory in /data configure: error: cannot guess
build type; you must specify one
r linux unix installation centos
r linux unix installation centos
asked Nov 22 '18 at 2:07
nagleminaglemi
85
asked Nov 22 '18 at 2:07
nagleminaglemi
85
edited Nov 23 '18 at 1:00
naglemi
asked Nov 22 '18 at 2:07
nagleminaglemi
85
asked Nov 22 '18 at 2:07
nagleminaglemi
85
asked Nov 22 '18 at 2:07
nagleminaglemi
85
85
How about installing R locally through anaconda? Also perhaps worth taking a look at: How to install R 3.2.2 using a conda environment on CentOS
– Maurits Evers
Nov 22 '18 at 2:28
add a comment |
How about installing R locally through anaconda? Also perhaps worth taking a look at: How to install R 3.2.2 using a conda environment on CentOS
– Maurits Evers
Nov 22 '18 at 2:28
How about installing R locally through anaconda? Also perhaps worth taking a look at: How to install R 3.2.2 using a conda environment on CentOS
– Maurits Evers
Nov 22 '18 at 2:28
How about installing R locally through anaconda? Also perhaps worth taking a look at: How to install R 3.2.2 using a conda environment on CentOS
– Maurits Evers
Nov 22 '18 at 2:28
add a comment |
1 Answer
1
active
oldest
votes
Yes, This can be easily done as follows:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
# build R
make
# install
make install
Once you build your own version of R, set environment variables:
export PATH=/path/to/your/local/dir/install/bin:$PATH
export R_HOME=/path/to/your/local/dir/install/lib64/R
These variables need to be set every time you want to use your own version of R.
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once atconfiguretime, and once again atmake installtime viamake DESTDIR=/path/to/your/local/dir/install install.
– Dirk Eddelbuettel
Nov 23 '18 at 1:06
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer/path/to/your/local/dir/must be a directory which you created.
– Katia
Nov 23 '18 at 15:56
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
|
show 2 more comments
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Yes, This can be easily done as follows:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
# build R
make
# install
make install
Once you build your own version of R, set environment variables:
export PATH=/path/to/your/local/dir/install/bin:$PATH
export R_HOME=/path/to/your/local/dir/install/lib64/R
These variables need to be set every time you want to use your own version of R.
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once atconfiguretime, and once again atmake installtime viamake DESTDIR=/path/to/your/local/dir/install install.
– Dirk Eddelbuettel
Nov 23 '18 at 1:06
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer/path/to/your/local/dir/must be a directory which you created.
– Katia
Nov 23 '18 at 15:56
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
|
show 2 more comments
Yes, This can be easily done as follows:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
# build R
make
# install
make install
Once you build your own version of R, set environment variables:
export PATH=/path/to/your/local/dir/install/bin:$PATH
export R_HOME=/path/to/your/local/dir/install/lib64/R
These variables need to be set every time you want to use your own version of R.
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once atconfiguretime, and once again atmake installtime viamake DESTDIR=/path/to/your/local/dir/install install.
– Dirk Eddelbuettel
Nov 23 '18 at 1:06
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer/path/to/your/local/dir/must be a directory which you created.
– Katia
Nov 23 '18 at 15:56
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
|
show 2 more comments
Yes, This can be easily done as follows:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
# build R
make
# install
make install
Once you build your own version of R, set environment variables:
export PATH=/path/to/your/local/dir/install/bin:$PATH
export R_HOME=/path/to/your/local/dir/install/lib64/R
These variables need to be set every time you want to use your own version of R.
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
Yes, This can be easily done as follows:
wget http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
# untar the sources
tar xzvf R-3.5.1.tar.gz
cd R-3.5.1
# configure
./configure --prefix=/path/to/your/local/dir/install --enable-R-shlib --enable-memory-profiling --enable-R-profiling --with-valgrind-instrumentation=2
# build R
make
# install
make install
Once you build your own version of R, set environment variables:
export PATH=/path/to/your/local/dir/install/bin:$PATH
export R_HOME=/path/to/your/local/dir/install/lib64/R
These variables need to be set every time you want to use your own version of R.
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
answered Nov 22 '18 at 4:37
KatiaKatia
2,4891718
2,4891718
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once atconfiguretime, and once again atmake installtime viamake DESTDIR=/path/to/your/local/dir/install install.
– Dirk Eddelbuettel
Nov 23 '18 at 1:06
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer/path/to/your/local/dir/must be a directory which you created.
– Katia
Nov 23 '18 at 15:56
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
|
show 2 more comments
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once atconfiguretime, and once again atmake installtime viamake DESTDIR=/path/to/your/local/dir/install install.
– Dirk Eddelbuettel
Nov 23 '18 at 1:06
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer/path/to/your/local/dir/must be a directory which you created.
– Katia
Nov 23 '18 at 15:56
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 '18 at 1:01
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once at
configure time, and once again at make install time via make DESTDIR=/path/to/your/local/dir/install install.– Dirk Eddelbuettel
Nov 23 '18 at 1:06
Essentially every GNU program works this way and the answer is entirely correct. But to be safe you could also set the prefix twice: once at
configure time, and once again at make install time via make DESTDIR=/path/to/your/local/dir/install install.– Dirk Eddelbuettel
Nov 23 '18 at 1:06
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer
/path/to/your/local/dir/ must be a directory which you created.– Katia
Nov 23 '18 at 15:56
@naglemi In addition to what Dirk suggested above I would also recommend to check the permissions for the directory where you are trying to install R. It looks like you are trying to install R into a directory where you do not have permissions to write. In my answer
/path/to/your/local/dir/ must be a directory which you created.– Katia
Nov 23 '18 at 15:56
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
I have read, write and execute priveledges for the local directory I am trying to install to, and I created this directory. However, I'm still getting this error because it's trying to write something to this /data/ folder which I do not have access to and did not tell it to install anything into. I don't know why it's trying to do this. I grepped the "configure" script for "/data/" and it's not in there, or in the command to call the script.
– naglemi
Nov 23 '18 at 21:25
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
@naglemi It looks like your latest error says that configure cannot determine build type. This is a separate error. See some suggestions here: stackoverflow.com/questions/4810996/…
– Katia
Nov 23 '18 at 21:45
|
show 2 more comments
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How about installing R locally through anaconda? Also perhaps worth taking a look at: How to install R 3.2.2 using a conda environment on CentOS
– Maurits Evers
Nov 22 '18 at 2:28