I'm trying to have a way to download R for multiple clients with no internet access. Is there a way to download the .tar.gz files for all of R and its dependencies, so you don't need to download with internet connection? If there is a way to do that will R still show up with the "whereis R" command on linux? I'm trying to find a way in which I can give someone the downloaded files already within a package and they just run a .sh script that will download everything and R's dependencies for them with no real user intervention.
You may follow the manual on the topic "installing R under Unix-alike". Briefly: download the source and make it.
Download R and untar it
You can download the source from:
https://cran.r-project.org/sources.html
Then, use "tar" to extract the source and build it. Let's suppose that you want to install R 4.2:
tar -xf R-4.2.0.tar.gz
Make
Go to a directory where you will install R. Note that the path shouldn't contain spaces.
./configure
make
make check
If you want to install all the R tree (binaries, manuals, libraries...) use:
make install
Installing packages from source
To install packages in R, you can use the function install.packages() with the name of the file ('...tar.gz') to be installed and the argument "repos" set as "NULL"
You can also install the packages from a shell:
R CMD INSTALL -l /path/to/library packagename
Check the manual for additional information
You may also be interested in looking at this information:
https://cran.r-project.org/bin/linux/redhat/
https://cran.r-project.org/sources.html
The R manual describes how to install R from source in:
R-admin > Obtaining R > Getting and unpacking the sources
R-admin > Installing R under Unix-alikes
Related
I have been trying to install R packages directly from the terminal but I am struggling much more than setting up the libraries I want in Windows. Sometimes it works if I install every single dependency for more complex packages by downloading them from CRAN and placing them in the R folder.
I appreciate this is not efficient but the recurrent error if I run R within the terminal while installing some of the packages is the following:
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
* removing ‘/anaconda3/lib/R/library/<package name>’
[...]
In install.packages("<package name>") :
installation of package ‘fpc’ had non-zero exit status
I have been looking across many forums but the only solution I found so far is to install single dependencies manually by downloading them and dropping them in the master R folder. It is taking way longer than expected.
Any suggestion will be appreciated. Thanks
in my case (centos 7):
/home/xilab/miniconda3/lib/R/etc/Makeconf is a empty file!
find ~ -name Makeconf
/home/xilab/miniconda3/pkgs/r-base-3.6.1-hce969dd_0/lib/R/etc/Makeconf
/home/xilab/miniconda3/pkgs/r-base-3.6.1-h8900bf8_2/lib/R/etc/Makeconf
/home/xilab/miniconda3/envs/python2.7/lib/R/etc/Makeconf
/home/xilab/miniconda3/lib/R/etc/Makeconf
/home/xilab/miniconda3/pkgs/r-base-3.6.1-hce969dd_0/lib/R/etc/Makeconf is not empty,so:
mv /home/xilab/miniconda3/lib/R/etc/Makeconf /home/xilab/miniconda3/lib/R/etc/Makeconf.backup
cp /home/xilab/miniconda3/pkgs/r-base-3.6.1-hce969dd_0/lib/R/etc/Makeconf /home/xilab/miniconda3/lib/R/etc/Makeconf
problem solved!
I have seen this problem in conda version of R where /yours/anaconda/environment/lib/R/etc/ has a file Makeconf.mro.original together with an empty Makeconf file. This should not be intended.
During installation of some packages R checks what is within this Makeconf file, one such check is for SHLIB_LIBADD.
I just backed up the empty (or whatever) Makeconf file. Then copied Makeconf.mro.original to Makeconf.
This solved my case.
EDIT:
Recently I saw in centos-machine that Makeconf.mro.original file is not made after install.packages("name of library") failed. There is no easy solution for this.
In my case R installation was inside a conda environment. So, I created a new conda environment with R installation. The fresh installation has a Makeconf file in etc directory. So, I copied the Makeconf file from fresh R to my previously working R's etc directory.
It may be better to keep a backup copy of Makeconf from etc to a Makeconf.bak for future problems, in your working R etc directory.
I hope this helps for some cases.
I had this problem when trying to run install.packages("RPostgres") in a conda-installed version of R . The solution was to use conda as the package manager instead of R's install.packages function. That meant running these commands at a normal system command prompt (not in R):
conda search -c conda-forge RPostgres
# shows various versions of r-rpostgres
conda install -c conda-forge r-rpostgres
For reasons that are too long to explain here, I must use R.2.8.1 (unfortunately). I need to have the xlsx package installed on it. Since I am on R 2.8.1, about ten years old, I can't use the latest version of xlsx but an older version, for instance xlsx_0.1.3 from 2010 seems a good choice. However the previous releases per R-CRAN policy are only available in tar.gz.
This is very unfortunate to me because I have to use RGui on windows which only accepts .Zip packages in installation. Therefore I tried the following stuff, in vain:
1-I tried to use Rcmd but I get the following error message:
C:\Program Files (x86)\R\R-2.8.1\bin>Rcmd INSTALL C:\Users\username\Downloads\xlsx_0.1.3.tar.gz
Can't use 'defined(#array)' (Maybe you should just omit the defined()?) at C:\PROGRA~2\R\R-28~1.1/bin/INSTALL line 42.
so I give up on this one.
2-Then I think that the best solution is to convert the package xlsx_0.1.3.tar.gz into a compatible xlsx_0.1.3.zip package by building it using R.2.8.1 but I can't make it. Here is one of the things I have tried so far.
I have unziped xlsx_0.1.3.tar.gz and I organized it in the following way, which brought me the furthest:
Documents\xlsx
Documents\xlsx\activate.bat
Documents\xlsx\build_xlsx.bat
Documents\xlsx\R
Documents\xlsx\R\inst
Documents\xlsx\R\man
Documents\xlsx\R\other
Documents\xlsx\R\R
Documents\xlsx\R\DESCRIPTION
Documents\xlsx\R\NAMESPACE
Documents\xlsx\R\NEWS
Documents\xlsx\R\WISHLIST
inside activate.bat, I wrote:
SET TMP=C:\Users\username\Documents\TOTO\xlsx\tmp
SET TEMP=%TMP%
SET RTOOLSPATH=C:\DEV_307\toto\Rtools
SET RPATH=C:\DEV\toto\R\R-2.8.1
SET PATH=%RTOOLSPATH%\bin;%RTOOLSPATH%\MinGW\bin;%RPATH%\bin;%PATH%
inside build_xlsx.bat, I wrote:
R CMD BUILD R
R CMD check --no-examples --no-tests R
R CMD build --docs=normal --binary R
Then I still get:
C:\Users\username\Documents\TOTO\xlsx>R CMD BUILD R
* checking for file 'R/DESCRIPTION' ... OK
* preparing 'R':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
Can't use 'defined(#array)' (Maybe you should just omit the defined()?) at C:\DEV\toto\R\R-2.8.1/bin/INSTALL line 42.
ERROR
Installation failed.
Removing 'C:/Users/username/Documents/Rinst1210839349'
Thank you for your help
I can't include structured content in comments. This is really a comment.
The structure of source packages (which is what you have with xlsx_0.1.3.tar.gz if you pulled it from the CRAN archives) hasn't changed (much) since 2.8.1.
You'll also need to grab rJava_0.8-3.tar.gz and xlsxjars_0.2.0.tar.gz from the archive as xlsxjars + xlsx rely on rJava.
Extract each (since Windows R 2.8.1 seems to not grok gz files). They should make rJava, xlsxjars and xlsx directories each.
Move to the parent directory of both.
Run:
R CMD javareconf
R CMD build rJava
R CMD INSTALL rJava_0.8-3.zip # I believe this will be the name
R CMD build xlsxjars
R CMD INSTALL xlsxjars_0.2.0.zip
R CMD build xlsx
R CMD INSTALL xlsx_0.1.3.zip
and you should be gtg.
I was trying to install the package RINDSEL but I am unable to install it and I keep getting the following error:
Error in install.packages : cannot open the connection
I downloaded the package from:
rindsel_1.0_2.zip | Integrated Breeding Platform
and loaded it from the directory. Other packages from the directory can be installed but just not this one.
Is the package corrupt or could there be any other error?
I would really be grateful for any help. Thanks in advance
Rename the zip file RinSel Software into Rindsel. That's the name specified in the discription file.
Then, you can install the package in R with the command
install.packages("C:/path/to/Rindsel.zip",repos=NULL,type="win.binary")
That works fine... at first (!!!).
Problem with the Rindsel package is. It is quite old. It was build with R 2.13.1. Therefore, if you want to load the library which would be the next step to use the package in R you will get the error:
Problems building package (Error: "package has been build before R-3.0.0")
My suggestion: Contact the authors of the package and ask them if they can either provide the source file that you can build the package by yourself or if they can bundle the Rindsel package with a newer R version.
(Or you could try to hunt down an old R version and see if you can get the thing running with an old R... However, I would not seriously suggest to do that. It would probably result in conflicting dependencies with the other required packages...)
EDIT 15-02-2018: OP asked if one can build an R package with sources that are presumeably the Rindsel source files.
Yes, basically, you could do that. You would have to make a your own description and namespace file and put the source file in the R folder than invoke the command in R to build it....
But it's not neccessary with the script files provided by the link the OP posted.
OP, just run the scripts in R! It's quite easy.
Download the zip-file and extract it on your machine.
Go to that directory. The R command would be
setwd('path/to/your/directory')
Than run the R script, e.g, the KNIndex.r. It's simple:
source('KNIndex.r')
Then the script will run and produce some output / prompts.
For future readers,
I was able to fix the error by running RStudio with administrative privileges to get the command to work.
If that does not fix it, you might wish to try
Installing "r tools" if that is not installed already. That can be downloaded from
https://cran.r-project.org/bin/windows/Rtools/
Download a relevant package that you are trying to install (e.g., tidyverse_1.3.0.zip) from https://cran.rstudio.com/
and install that from local path
It can also be installed directly from the web using install.packages("https://cran.rstudio.com/bin/windows/contrib/4.0/tidyverse_1.3.0.zip")
I had the same problem. R was not able to extract and compile the package files to the default installation directory for some system-specific reasons (not R related).
I was able to fix this by specifying the installation directory of the package lib using:
install.packages("your package", lib = 'path/to your/required/installation/directory')
You can then load the package by specifying the lib.loc option while loading it:
library('your package', lib.loc='path/to your/required/installation/directory')
A better solution:
Create a new environment variable (if you are using windows) R_LIBS_USER with the following directory path/to your/required/installation/directory.
This will change the default installation directory of the packages and make it easier to load and install them without specifying the location everytime.
This question already has answers here:
How do I install an R package from source?
(7 answers)
Closed 6 years ago.
I would like to install the plyr package from a .tar.gz file, into my library of R packages on a linux machine. How would I go about doing this? Do I just place it in the library directory? What if I do not have write permissions?
In the command line:
R CMD INSTALL <package-name>.tar.gz
Or in R:
install.packages(<pathtopackage>, repos = NULL, type="source")
From the command line,
R CMD INSTALL plyr_x.y.z.tar.gz
If you don't have permission to write to the standard library directory and can't use sudo to override, you can install it somewhere else via
R CMD INSTALL -l <user_lib> plyr_x.y.z.tar.gz
where <user_lib> is a directory you can write to. You may need to specify lib.loc when subsequently loading the package, if <user_lib> is not in .libPaths (see #DWin's answer).
See http://cran.r-project.org/doc/manuals/R-admin.html for more information; R CMD INSTALL --help may also be useful, albeit terse.
If you do not have permissions to the default installed library you can add to the search path that R uses with .libPaths which "gets/sets the library trees within which packages are looked for."
.libPaths() # will display all current libraries
?.libPaths
The second argument to install.packages (after the name of your plyr.version.tar.gz file) could be a user-controlled library directory.
?install.packages
I was a bit puzzled by first asking about installing from CRAN and then asking about installing a tar.gz file from which I formed the impression that you had already downloaded the file and were hoping to install it.
This question already has answers here:
How do I install an R package from source?
(7 answers)
Closed 6 years ago.
I would like to install the plyr package from a .tar.gz file, into my library of R packages on a linux machine. How would I go about doing this? Do I just place it in the library directory? What if I do not have write permissions?
In the command line:
R CMD INSTALL <package-name>.tar.gz
Or in R:
install.packages(<pathtopackage>, repos = NULL, type="source")
From the command line,
R CMD INSTALL plyr_x.y.z.tar.gz
If you don't have permission to write to the standard library directory and can't use sudo to override, you can install it somewhere else via
R CMD INSTALL -l <user_lib> plyr_x.y.z.tar.gz
where <user_lib> is a directory you can write to. You may need to specify lib.loc when subsequently loading the package, if <user_lib> is not in .libPaths (see #DWin's answer).
See http://cran.r-project.org/doc/manuals/R-admin.html for more information; R CMD INSTALL --help may also be useful, albeit terse.
If you do not have permissions to the default installed library you can add to the search path that R uses with .libPaths which "gets/sets the library trees within which packages are looked for."
.libPaths() # will display all current libraries
?.libPaths
The second argument to install.packages (after the name of your plyr.version.tar.gz file) could be a user-controlled library directory.
?install.packages
I was a bit puzzled by first asking about installing from CRAN and then asking about installing a tar.gz file from which I formed the impression that you had already downloaded the file and were hoping to install it.