i am trying to install r package in ubuntu to deploy the app in shiny-server with required version i have tried the below code but it was throwing an error
Error: unexpected '/' in "install.packages(http:/"
Execution halted
Code:
sudo su - -c "R -e \"install.packages("http://cran.r-project.org/src/contrib/Archive/shinydashboard/shinydashboard_0.6.1.tar.gz", repos=NULL)\""
Is there any other way to install this packages in ubuntu
Try:
sudo su - \
-c "R -e \"install.packages('http://cran.r-project.org/src/contrib/Archive/shinydashboard/shinydashboard_0.6.1.tar.gz',
repos=NULL, type ='source')\""
Related
I am attempting to do a fresh build of a Shiny server, using CentOS 8. I have been using the instructions on the Shiny server download site.
I have been successful up to the point of installing the Shiny R packages. Using the code on the website
sudo su -
-c "R -e "install.packages('shiny', repos='https://cran.rstudio.com/')"">
I am getting the following error/response: <[root#CP-Shiny]# sudo su - \ -c "R -e "install.packages('shiny', repos='https://cran.rstudio.com/')""
su: user -c does not exist
Does this work?
sudo su - -c "R -e \"install.packages('shiny', repos='https://cran.rstudio.com/')\""
It escapes the quotes inside quotes using \
I am trying to create a dockerfile that builds an image from Rocker/tidyverse and include Spark from sparklyr. Previously, on this post: Unable to install spark with sparklyr in Dockerfile, I was trying to figure out why spark wouldn't download from my dockerfile. After playing with it for the past 5 days I think I have found the reason but have no idea how to fix it.
Here is my Dockerfile:
# start with the most up-to-date tidyverse image as the base image
FROM rocker/tidyverse:latest
# install openjdk 8 (Java)
RUN apt-get update \
&& apt-get install -y openjdk-8-jdk
# Install devtools
RUN Rscript -e 'install.packages("devtools")'
# Install sparklyr
RUN Rscript -e 'devtools::install_version("sparklyr", version = "1.5.2", dependencies = TRUE)'
# Install spark
RUN Rscript -e 'sparklyr::spark_install(version = "3.0.0", hadoop_version = "3.2")'
RUN mv /root/spark /opt/ && \
chown -R rstudio:rstudio /opt/spark/ && \
ln -s /opt/spark/ /home/rstudio/
RUN apt-get install unixodbc unixodbc-dev --install-suggests
RUN apt-get install odbc-postgresql
RUN install2.r --error --deps TRUE DBI
RUN install2.r --error --deps TRUE RPostgres
RUN install2.r --error --deps TRUE dbplyr
It has no problem downloading everything up until this line:
RUN Rscript -e 'sparklyr::spark_install(version = "3.0.0", hadoop_version = "3.2")'
Which then gives me the error:
Step 5/11 : RUN Rscript -e 'sparklyr::spark_install(version = "3.0.0", hadoop_version = "3.2")'
---> Running in 739775db8f12
Error in download.file(installInfo$packageRemotePath, destfile = installInfo$packageLocalPath, :
download from 'https://archive.apache.org/dist/spark/spark-3.0.0/spark-3.0.0-bin-hadoop3.2.tgz' failed
Calls: <Anonymous>
Execution halted
ERROR: Service 'rocker_sparklyr' failed to build : The command '/bin/sh -c Rscript -e 'sparklyr::spark_install(version = "3.0.0", hadoop_version = "3.2")'' returned a non-zero code: 1
After doing some research I thought that it was a timeout error, in which case I ran beforehand:
RUN Rscript -e 'options(timeout=600)'
This did not increase the time it took to error out again. I installed everything onto my personal machine through Rstudio and it installed with no problems. I think the problem is specific to docker in that it isn't able to download from https://archive.apache.org/dist/spark/spark-3.0.0/spark-3.0.0-bin-hadoop3.2.tgz
I have found very little documentation on this problem and am relying heavily on this post to figure it out. Thank you in advance to anyone with this knowledge for reaching out.
download the version yourself and then use this function to install
sparklyr::spark_install_tar(tarfile ="~/spark/spark-3.0.1-bin-hadoop3.2.tgz")
I am using a continuumio/miniconda3:latest base container and activating a Conda environment.
This all works fine.
When I run:
RUN R -e "install.packages('devtools',repos = 'http://cran.us.r-project.org')"
I get an error:
configure: Package dependency requirement 'libgit2 >= 0.26.0' could not be satisfied.
-----------------------------------------------------------------------
Unable to find the libgit2 library on this system. Building 'git2r'
using the bundled source of the libgit2 library.
To build git2r with a system installation of libgit2, please install:
libgit2-dev (package on e.g. Debian and Ubuntu)
libgit2-devel (package on e.g. Fedora, CentOS and RHEL)
libgit2 (Homebrew package on OS X)
and try again.
If the libgit2 library is installed on your system but the git2r
configuration is unable to find it, you can specify the include and
lib path to libgit2 with:
given you downloaded a tar-gz archive:
R CMD INSTALL git2r-.tar.gz --configure-vars='INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib'
or cloned the GitHub git2r repository into a directory:
R CMD INSTALL git2r/ --configure-vars='INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib'
or download and install git2r in R using
install.packages('git2r', type='source', configure.vars='LIB_DIR=-L/path/to/libs INCLUDE_DIR=-I/path/to/headers')
On macOS, another possibility is to let the configuration
automatically download the libgit2 library from the Homebrew
package manager with:
R CMD INSTALL git2r-.tar.gz --configure-vars='autobrew=yes'
or
R CMD INSTALL git2r/ --configure-vars='autobrew=yes'
or
install.packages('git2r', type='source', configure.vars='autobrew=yes')
-----------------------------------------------------------------------
configure: Attempting configuration of bundled libgit2
checking size of void*... 8
checking for library containing inflate... no
configure: error: in `/tmp/Rtmpbkmfhr/R.INSTALL8c407eb001/git2r':
configure: error:
---------------------------------------------
The zlib library that is required to build
git2r was not found.
Please install:
zlib1g-dev (package on e.g. Debian and Ubuntu)
zlib-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the zlib library is installed on your
system but the git2r configuration is
unable to find it, you can specify the
include and lib path to zlib with:
R CMD INSTALL git2r --configure-vars='LIBS=-L/path/to/libs CPPFLAGS=-I/path/to/headers'
---------------------------------------------
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/opt/conda/envs/r-app/lib/R/library/git2r’
I have libgit2-dev installed at the start of my Dockerfile using apt-get install libgit2-dev and it installs libgit2 version 0.27.7.
Now the odd part about this is if I start the container and access it, I can run the "install.packages('devtools',repos = 'http://cran.us.r-project.org')" just fine and it works.
Dockerfile:
FROM continuumio/miniconda3:latest
RUN apt-get update -y; apt-get upgrade -y; \
apt-get install -y vim ssh libgit2-dev zlib1g-dev \
build-essential gcc gfortran g++
RUN conda update -n base -c defaults conda
COPY environment.yml environment.yml
RUN conda env create -f environment.yml
RUN echo "source activate r-env" >> ~/.bashrc
ENV PATH /opt/conda/envs/r-env/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
RUN R -e "install.packages('devtools',repos = 'http://cran.us.r-project.org')"
environment.yml:
name: r-env
channels:
- conda-forge
- defaults
dependencies:
- python=3.7
- r-essentials
- r-base
Replace the last line of your Dockerfile with:
RUN Rscript -e "install.packages('devtools',repos = 'http://cran.us.r-project.org')"
I managed to install the following package on my local RStudio session:
install.packages("devtools")
devtools::install_github("tidyverse/googlesheets4")
I am now trying to install it directly in the Dockerfile of my RStudio session on my server.
For that, below the line:
RUN R -e "install.packages(c('DT', 'shiny', 'DBI', 'devtools'))"
I have added:
RUN R -e "devtools::install_version('tidyverse/googlesheets4')"
But when I launch the docker-compose up -d command I get this error:
Error in package_find_repo(package, repos) : couldn't find package
'tidyverse/googlesheets4' Calls: ... ->
download_version_url -> package_find_repo Execution halted ERROR:
Service 'rstudio' failed to build: The command '/bin/sh -c R -e
"devtools::install_version('tidyverse/googlesheets4')"' returned a
non-zero code: 1
Do you know what could be the issue?
Thanks a lot.
After install.packages("Rmpfr") I'm getting this error
configure: error: Header file mpfr.h not found; maybe use
--with-mpfr-include=INCLUDE_PATH
ERROR: configuration failed for package ‘Rmpfr’
I typed the suggestion --with-mpfr-include=INCLUDE_PATH into the terminal w/o success.
Look here: https://github.com/cran/Rmpfr
You first have to install the dependend libraries.
sudo apt-get install libmpfr-dev
sudo su - -c "R -e \"install.packages('Rmpfr', repos='http://cran.rstudio.com/')\""
It is also a better solution to install the R-Packages from the console, not inside R, since every user on the machine will have access to the package then. Otherwise it will just be in your personal library.