I have recently, set up an AWS accountand am in the process of uploading R packages I require
The process runs smoothly with CRAN packages using the command e.g.
sudo su c "R e \"install.packages('ggplot2', repos='http://cran.rstudio.com/')\""
For non-CRAN packages, I got some help from this source
https://github.com/hadley/devtools/issues/414 and tried
Rscript -e 'library(devtools); library(methods); install_github(commandArgs(TRUE))' "ramnathv/rCharts"
The zipped package (and others on github ) download but then I get the error
'lib="/usr/local/lib/R/site-library"' is not writable .
although that is where the R packages were written to
Has anyone successfully achieved this process and could give me the solution
Tx
It looks like you just need sudo to install to that directory. You could try
sudo Rscript -e 'library(devtools); library(methods); install_github(commandArgs(TRUE))' "ramnathv/rCharts"
or
git clone https://github.com/ramnathv/rCharts.git
sudo R CMD INSTALL rCharts
Related
I am building a docker image using rocker/tidyverse.
My Dockerfile:
FROM rocker/tidyverse:4.0.4
COPY train.R /train.R
COPY install.R /install.R
COPY entrypoint.sh /entrypoint.sh
# pre install the packages during build
RUN Rscript install.R
Here's the install.r script from above:
install.packages('pacman')
pacman::p_load(lubridate, Metrics, foreach)
Also tried a variation of this with just install.packages(<packagename>) for each of the packages in the install.r script.
When I attempt to build I get an error message:
docker-compose build rtrain
Step 5/5 : RUN Rscript install.R
---> Running in 3ebf7ab0c227
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
Warning: unable to access index for repository https://packagemanager.rstudio.com/cran/__linux__/focal/2021-03-30/src/contrib:
cannot open URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2021-03-30/src/contrib/PACKAGES'
Warning message:
package 'pacman' is not available for this version of R
If I remove RUN Rscript install.r from build but instead run the image and then exec into it, I am able to run it with just Rsctipt install.r. It's only during build that this happens.
On the page on the first url I linked to above there's a mention of script install2.r but I could not find any mention of this anywhere. The full blurb:
NOTES
do not use apt-get install r-cran-* to install R packages on this stack . The requested R version and all R packages are installed from source in the version-stable stack. Installing R packages from apt (e.g. the r-cran-* packages) will install the version of R and versions of the packages that were built for the stable debian release (e.g. debian:stretch ), giving you a second version of R and different packages. Please install R packages from source using the install.packages() R function (or the install2.r script), and use apt only to install necessary system libraries (e.g. libxml2 ). If you would prefer to install only the latest verions of packages from pre-built binaries using apt-get , consider using the r-base stack instead.
Underlining I did try modifying install.r to just be repeated rows of install.packages("lubridate") install.packages("Metrics") and install.packages("foreach") but the same error happens.
How can I install packages during build using this image?
Changing my version to 4.0.1 solved my problem:
FROM rocker/tidyverse:4.0.1
Then everything else the same, worked.
I have to perform a remote R installation on an Ubuntu 16.10 system. As part of this, I have to install specific packages on that host. I want to install these packages Rcmdr,list,ggplot2,afex,lsmeans. Since I am doing this remotely, I cannot use
sudo -i R
to first enter the R CLI and then install with install.packages(). Instead I must somehow install the packages from the Ubuntu CLI.
I found these links:
multiple R package installation with
install.packages()
R CMD INSTALL -l usage syntax to install multiple packages in
section
6.3
Use of repos parameter inside
install.packages()
However, some packages have dependencies:
The list package depends on utils and sandwich.
The Rcmdr package depends on grDevices, utils, splines, RcmdrMisc, car.
The ggplot2 package also has dependencies.
I would like to install only the packages Rcmdr,list,ggplot2 with all their dependencies. Normally, I would do it this way:
install.packages(c('Rcmdr','list','ggplot2'), dependencies=TRUE)
QUESTIONS
How do I specify the dependencies option in R CMD for one package
only? Is this the way to install them
R CMD INSTALL -l Rcmdr dependencies=TRUE, list dependencies=TRUE, \
ggplot2 dependencies=TRUE, afex, lsmeans
or this incorrect?
Also, how to I specify the repos parameter inside R CMD INSTALL -l?
EDIT
As per the first comment below, sudo is not needed above.i.e. sudo -i R can be replaced by R.
Regarding your questions:
Question 1
This may not be the best approach. Consider instead Rscript -e 'install.packages(...)' which is what R CMD INSTALL ... calls anyway. You have better control over options here. And read on...
Question 2
On all Ubuntu machines at work and home I do this via /etc/R/Rprofile.site via something like
## Example of Rprofile.site
local({
r <- getOption("repos")
r["CRAN"] <- "https://cloud.r-project.org"
r["ghrr"] <- "https://ghrr.github.io/drat"
options(repos = r)
})
where we usually add a third and network-local repo. You may just want CRAN here -- it uses the 'always-close to you' CDN administered by RStudio for the R Project and R Consortium. The ghrr drat is a helper repo I set up.
Question 3
sudo is not needed per something I add to the official Debian/Ubuntu package for R -- but you need to be a member of the group that owns /usr/local/lib/R/site-library.
Now, if I may, two more suggestions:
Littler
The r executable is available to you via sudo apt-get install r-cran-littler. I use it on the command-line; and you probably want to look into the basic install.r script and the extended install2.r. I tend to create a softlink from /usr/local/bin to the package directory for these and other (such as update.r). I have been running many (Ubuntu and Debian) machines like that for many years.
Michael Rutter repos, and Docker
We actually have about 3000 CRAN packages as binaries for Ubuntu so you could just do sudo apt-get install ... and all dependendies would get resolved. Look eg in this script of mine (which uses them on Travis) or some of the Docker files I maintain such as this one.
I am working on an off-line Ubuntu server and I would like to write an IPython notebook with only R code. I understand that for this to work I need to install the IRkernel. This shouldn't be a problem if the server was on-line, but unfortunately this is not the case. Any suggestions how to install the IRkernel off-line are greatly appreciated.
Oliver
(I have installed Anaconda3-2.2.0-x86-64 and R 3.0.2 on the Ubuntu server)
You can use Cube to download the required Ubuntu packages (I think just zmq3) on an online computer and then install it on your offline server.
You would then need to download the needed R packages (rzmq,repr,IRkernel,IRdisplay - in tar.gz form)
To load those into your server you can use the following commands to install the R packages from source.
R CMD INSTALL package_ 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> package_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 this manual for more information; R CMD INSTALL --help may also be useful
It's a less than ideal solution but it should work assuming there aren't any dependancies I've missed.
A friend sent me along this great tutorial on webscraping The New York Times with R. I would really love to try it. However, the first step is to install a package called [RJSONIO][2] from source.
I know R reasonably well, but I have no idea how to install a package from source.
I'm running macOS (OS X).
If you have the file locally, then use install.packages() and set the repos=NULL:
install.packages(path_to_file, repos = NULL, type="source")
Where path_to_file would represent the full path and file name:
On Windows it will look something like this: "C:\\RJSONIO_0.2-3.tar.gz".
On UNIX it will look like this: "/home/blah/RJSONIO_0.2-3.tar.gz".
Download the source package, open Terminal.app, navigate to the directory where you currently have the file, and then execute:
R CMD INSTALL RJSONIO_0.2-3.tar.gz
Do note that this will only succeed when either: a) the package does not need compilation or b) the needed system tools for compilation are present. See: R for Mac OS X
You can install directly from the repository (note the type="source"):
install.packages("RJSONIO", repos = "http://www.omegahat.org/R", type="source")
A supplementarily handy (but trivial) tip for installing older version of packages from source.
First, if you call "install.packages", it always installs the latest package from repo. If you want to install the older version of packages, say for compatibility, you can call install.packages("url_to_source", repo=NULL, type="source"). For example:
install.packages("http://cran.r-project.org/src/contrib/Archive/RNetLogo/RNetLogo_0.9-6.tar.gz", repo=NULL, type="source")
Without manually downloading packages to the local disk and switching to the command line or installing from local disk, I found it is very convenient and simplify the call (one-step).
Plus: you can use this trick with devtools library's dev_mode, in order to manage different versions of packages:
Reference: doc devtools
From CRAN, you can install directly from a GitHub repository address. So if you want the package at https://github.com/twitter/AnomalyDetection, using
library(devtools)
install_github("twitter/AnomalyDetection")
does the trick.
In addition, you can build the binary package using the --binary option.
R CMD build --binary RJSONIO_0.2-3.tar.gz
If you have source code you wrote yourself, downloaded (cloned) from GitHub, or otherwise copied or moved to your computer from some other source, a nice simple way to install the package/library is:
In R
It's as simple as:
# install.packages("devtools")
devtools::install('path/to/package')
From terminal
From here, you can clone a GitHub repo and install it with:
git clone https://github.com/user/repo.git
R -e "install.packages('devtools');devtools::install('path/to/package')"
Or if you already have devtools installed, you can skip that first bit and just clone the repo and run:
R -e "devtools::install('path/to/package')"
Note that if you're on ubuntu, install these system libraries before installing devtools (or devtools won't install properly).
apt-get update
apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y
A friend sent me along this great tutorial on webscraping The New York Times with R. I would really love to try it. However, the first step is to install a package called [RJSONIO][2] from source.
I know R reasonably well, but I have no idea how to install a package from source.
I'm running macOS (OS X).
If you have the file locally, then use install.packages() and set the repos=NULL:
install.packages(path_to_file, repos = NULL, type="source")
Where path_to_file would represent the full path and file name:
On Windows it will look something like this: "C:\\RJSONIO_0.2-3.tar.gz".
On UNIX it will look like this: "/home/blah/RJSONIO_0.2-3.tar.gz".
Download the source package, open Terminal.app, navigate to the directory where you currently have the file, and then execute:
R CMD INSTALL RJSONIO_0.2-3.tar.gz
Do note that this will only succeed when either: a) the package does not need compilation or b) the needed system tools for compilation are present. See: R for Mac OS X
You can install directly from the repository (note the type="source"):
install.packages("RJSONIO", repos = "http://www.omegahat.org/R", type="source")
A supplementarily handy (but trivial) tip for installing older version of packages from source.
First, if you call "install.packages", it always installs the latest package from repo. If you want to install the older version of packages, say for compatibility, you can call install.packages("url_to_source", repo=NULL, type="source"). For example:
install.packages("http://cran.r-project.org/src/contrib/Archive/RNetLogo/RNetLogo_0.9-6.tar.gz", repo=NULL, type="source")
Without manually downloading packages to the local disk and switching to the command line or installing from local disk, I found it is very convenient and simplify the call (one-step).
Plus: you can use this trick with devtools library's dev_mode, in order to manage different versions of packages:
Reference: doc devtools
From CRAN, you can install directly from a GitHub repository address. So if you want the package at https://github.com/twitter/AnomalyDetection, using
library(devtools)
install_github("twitter/AnomalyDetection")
does the trick.
In addition, you can build the binary package using the --binary option.
R CMD build --binary RJSONIO_0.2-3.tar.gz
If you have source code you wrote yourself, downloaded (cloned) from GitHub, or otherwise copied or moved to your computer from some other source, a nice simple way to install the package/library is:
In R
It's as simple as:
# install.packages("devtools")
devtools::install('path/to/package')
From terminal
From here, you can clone a GitHub repo and install it with:
git clone https://github.com/user/repo.git
R -e "install.packages('devtools');devtools::install('path/to/package')"
Or if you already have devtools installed, you can skip that first bit and just clone the repo and run:
R -e "devtools::install('path/to/package')"
Note that if you're on ubuntu, install these system libraries before installing devtools (or devtools won't install properly).
apt-get update
apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y