How to set up R to run from a directory with no bin or root access?
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0
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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
add a comment |
up vote
0
down vote
favorite
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
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 at 2:28
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
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
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
edited Nov 23 at 1:00
asked Nov 22 at 2:07
naglemi
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 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 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 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 at 2:28
add a comment |
1 Answer
1
active
oldest
votes
up vote
0
down vote
accepted
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.
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 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 atconfigure
time, and once again atmake install
time viamake DESTDIR=/path/to/your/local/dir/install install
.
– Dirk Eddelbuettel
Nov 23 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 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 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 at 21:45
|
show 2 more comments
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
accepted
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.
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 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 atconfigure
time, and once again atmake install
time viamake DESTDIR=/path/to/your/local/dir/install install
.
– Dirk Eddelbuettel
Nov 23 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 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 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 at 21:45
|
show 2 more comments
up vote
0
down vote
accepted
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.
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 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 atconfigure
time, and once again atmake install
time viamake DESTDIR=/path/to/your/local/dir/install install
.
– Dirk Eddelbuettel
Nov 23 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 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 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 at 21:45
|
show 2 more comments
up vote
0
down vote
accepted
up vote
0
down vote
accepted
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.
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 at 4:37
Katia
2,4441718
2,4441718
I've updated my original post to show an error I'm getting on the third step of this.
– naglemi
Nov 23 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 atconfigure
time, and once again atmake install
time viamake DESTDIR=/path/to/your/local/dir/install install
.
– Dirk Eddelbuettel
Nov 23 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 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 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 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 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 atconfigure
time, and once again atmake install
time viamake DESTDIR=/path/to/your/local/dir/install install
.
– Dirk Eddelbuettel
Nov 23 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 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 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 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 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 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 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 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 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 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 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 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 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 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 at 2:28