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.
Related
I'm facing difficulties downloading the r package rsvg. I created first an environment with conda for the latest R version 4.0.2 following these instructions. I was able to download many other R packages & bioconductor packages without problem, however, this one produces huge pile of lines while configuring it and ends with errors downloadind its dependencies (systemfonts, stringi, stringr, gdtools, magick, svglite, knitr). My exact command is install.packages("rsvg", dependencies =T). Trying to download each of those packages produced also a tree of required dependencies (with configuration fail at the end of each).
Among the lines I noticed this error /user/include/freetype2/freetype/config/ftheader.h:3:12: fatal error x86_64-linux-gnu/freetype2/config/fthreader.h no such file or directory which make me suspect that my R installation is incopmlete or corrupted. I tested it with other R versions (e.g. R 3.6.0) yet the same error appear. Installing it on windows (Rstudio 3.6.2) also didn't work, and now I'm wondering if this package needs to be installed differently or it is system related problem? Any help would be highly appreciated
You need to create a new environment and then you can install R 4.+ in Anaconda. Follow these steps.
conda create --name r4-base
After activating r4-base run these commands
conda install -c conda-forge r-base
conda install -c conda-forge/label/gcc7 r-base
Finally, you will notice r-basa version 4 will be installed.
Thereafter, you can install any supported packages. But with this only, you won't have the ability to use it in the Jupyter notebook. You need to install install.packages('IRkernel') and Jupyter notebook as well if you want to use it. Otherwise you are good to go with R-Studio.
For Jupyter Installation and RKernel.
conda install jupyter
Then open the R console. Write in R console
install.packages('IRkernel')
IRkernel::installspec()
Congrats! You can use Notebook for Python and R.
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
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
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