I am installing R. I am getting this error when runing ./configure :
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not available
Any hint,
Thanks
Use the following command will solve this problem
./configure --with-readline=no --with-x=no
--with-x=no turns off the X Windows System . It is the GUI for the Linux and Unix-like OS. My computer has no X Windows installed, so I turn off.
But I highly recommand to install readline library before R installtion with '--with-readline=yes', as the command operation style is quitely unfriendly with '--with-readline=no' . See more libreadline installation in linux for more details
you can use the following command for more install configuration details
./configure --help
on I found problem on compiling R 3.1.1 so as a part of solution , i recommend to install the below libraries first before you compile this R and use
sudo apt-get install build-essential
sudo apt-get install fort77
sudo apt-get install xorg-dev
sudo apt-get install liblzma-dev libblas-dev gfortran
sudo apt-get install gcc-multilib
sudo apt-get install gobjc++
sudo apt-get install aptitude
sudo aptitude install libreadline-dev
Thank you other people who posted and kept the knowledge going..
I think you need the GNU readline package. You can install it with apt-get, aptitude, or the appropiate tool for your distribution. In Ubuntu:
aptitude install libreadline-dev
On Linux version 2.6.18-371.3.1.el5 (centos) the following worked for me
yum install readline-devel
and use --with-x=no in configure option as mentioned by others
I added this in the file taken here:
http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/2012/08/installing-the-development-version-of-r-on-ubuntu-alongside-the-current-version-of-r.html
CXXFLAGS="-ggdb -pipe -Wall -pedantic -I/usr/include/readline5" \
CPPFLAGS="-I/usr/include/readline5" \
LDFLAGS="-L/usr/lib64/readline5" \
On Centos 7, building R-3.5.0, If you want to install in /data/R-3.0.5.
wget https://www.stats.bris.ac.uk/R/src/base/R-3/R-3.5.0.tar.gz
tar -zxvf R-3.5.0.tar.gz
cd R-3.5.0.tar.gz
mkdir -p /data/R-3.0.5
yum group install "Development tools" -y
yum install readline-devel -y
yum install xorg-x11-server-devel libX11-devel libXt-devel -y
yum yum install libbz2-devel -y
yum install lzma -y
yum install xz xz-devel -y
yum install pcre pcre-devel -y
yum install libcurl-devel -y
yum install texinfo -y
yum install texinfo-tex -y
yum install texlive -y
yum install texlive-fonts-extra -y
yum install levien-inconsolata-fonts -y
yum install java-1.8.0-openjdk -y
./configure --prefix=/data/R-3.0.5 '--with-cairo' \
'--with-jpeglib' '--with-readline' '--with-tcltk' \
'--with-blas' '--with-lapack' '--enable-R-profiling' \
'--enable-R-shlib' \
'--enable-memory-profiling'
make
make install
The error means your system cannot find the required package. On Ubuntu, you can refer to this document to install all missing dependencies. It works for R 4.0
https://github.com/Jiefei-Wang/Painless-R-compilation-and-installation-on-Ubuntu
Related
I need to install this specific python version, to prepare a developer environment, because I'm maintaining a system with multiple libraries based on python 3.6.9.
I recently installed Ubuntu 22.04 on my laptop, but I had no success trying to install this python version.
I tried to install with apt-get after adding the deadsneak repository, but this python version is not available.
I tried installing from source by compiling, but it did not work. Running sudo make altinstall exited with this error:
Segmentation fault (core dumped)
make: *** [Makefile:1112: altinstall] Erro 139
I have faced the same problems and could make it work by adding some additional flags when running ./configure
Here are my steps:
Step 1 – Prerequsities
sudo apt-get install -y make build-essential libssl-dev zlib1g-dev \
libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev \
libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev \
libgdbm-dev libnss3-dev libedit-dev libc6-dev
Step 2 – Download Python 3.6
wget https://www.python.org/ftp/python/3.6.15/Python-3.6.15.tgz
tar -xzf Python-3.6.15.tgz
Step 3 – Compile Python Source
cd Python-3.6.15
./configure --enable-optimizations -with-lto --with-pydebug
make -j 8 # adjust for number of your CPU cores
sudo make altinstall
Step 4 – Check the Python Version
python3.6 -V
If you need it to install with pyenv, you could try this one:
$ sudo apt install clang -y
$ CC=clang pyenv install 3.6.9
I'm trying to build docker image for my R shiny app. Below is theDockerfile.
# Install R version 3.6
FROM r-base:3.6.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
xtail \
wget \
libudunits2-dev \
libgdal-dev
# Install R packages that are required
RUN R -e "install.packages(c('remotes', 'tidyr', 'dplyr', 'ggplot2', 'stringr','shiny', 'shinydashboard','shinyWidgets','shinyjs', 'rlang','scales','DT','lubridate', 'plotly', 'leaflet', 'leafpop', 'visNetwork', 'wordcloud2', 'arules'), repos='http://cran.rstudio.com/')"
RUN R -e "remotes::install_github('nik01010/dashboardthemes')"
# Download and install ShinyServer (latest version)
RUN wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
# Copy configuration files into the Docker image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
# Make the ShinyApp available at port 80
EXPOSE 80
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
CMD ["/usr/bin/shiny-server.sh"]
However, my image building failed quite early. Below is all the logs. It seems like some Ubuntu package issue which I do not quite understand.
I'm new to docker. I have not clue what to do with those error messages. Appreciate if anyone can help find out what needs to be done. Thanks.
Sending build context to Docker daemon 113.4MB
Step 1/10 : FROM r-base:3.6.0
---> 876f4d7b60e9
Step 2/10 : RUN apt-get update && apt-get install -y sudo gdebi-core pandoc pandoc-citeproc libcurl4-gnutls-dev libcairo2-dev libxt-dev xtail wget libudunits2-dev libgdal-dev
---> Running in 825a69c5a05f
Get:2 http://deb.debian.org/debian testing InRelease [116 kB]
Get:1 http://cdn-fastly.deb.debian.org/debian sid InRelease [146 kB]
Get:3 http://deb.debian.org/debian testing/main amd64 Packages [7,690 kB]
Get:4 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages [8,225 kB]
Fetched 16.2 MB in 6s (2,724 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
libc6-dev : Breaks: libgcc-8-dev (< 8.4.0-2~) but 8.3.0-7 is to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.
The command '/bin/sh -c apt-get update && apt-get install -y sudo gdebi-core pandoc pandoc-citeproc libcurl4-gnutls-dev libcairo2-dev libxt-dev xtail wget libudunits2-dev libgdal-dev' returned a non-zero code: 100
The error message you are receiving is not Docker specific, but rather concerns your package manager apt.
Although you are updating the package list using apt-get update, you do not install newer versions of packages. What happens now is that you are trying to install a newer version of an already installed package which leads to the error message.
If you use apt-get upgrade, apt will install the newer versions of your installed packages.
Changing the 5th line as shown below will fix that issue:
RUN apt-get update && apt-get upgrade -y && apt-get install -y \
I'm trying to build a Docker container that runs R with the package RJava. I have tried the following code:
# Install R version 3.6.3
FROM rocker/tidyverse:3.6.3
# Make ~/.R
RUN mkdir -p $HOME/.R
# Install Ubuntu packages && then R packages
RUN install2.r --error \
lubridate magrittr RPostgres DBI broom rlang rJava
However I get the following: installation of package ‘rJava’ had non-zero exit status.
Can anyone help me with this. I'm thinking that maybe it is because Java is not installed. Does anyone know how to install Java on this docker container?
I've tried adding the following to my dockerfile as per another post I found however I get the error saying 'The repository 'http://ppa.launchpad.net/webupd8team/java/ubuntu focal Release' does not have a Release file:
# Install "software-properties-common" (for the "add-apt-repository")
RUN apt-get update && apt-get install -y \
software-properties-common
# Add the "JAVA" ppa
RUN add-apt-repository -y \
ppa:webupd8team/java
# Install OpenJDK-8
RUN apt-get update && \
apt-get install -y openjdk-8-jdk && \
apt-get install -y ant && \
apt-get clean;
# Fix certificate issues
RUN apt-get update && \
apt-get install ca-certificates-java && \
apt-get clean && \
update-ca-certificates -f;
# Setup JAVA_HOME -- useful for docker commandline
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64/
RUN export JAVA_HOME
I'm new to docker and any help with this would be much appreciated.
The rocker images are based on debian, not ubuntu. Specifically it is Debian GNU/Linux 10 (buster). With that version, you can install java by installing the package openjdk-11-jdk via apt and you don't need to add any repositories for openjdk-8-jdk.
So a working dockerfile that installs rJava:
FROM rocker/tidyverse:3.6.3
RUN apt-get update && \
apt-get install -y openjdk-11-jdk && \
apt-get install -y liblzma-dev && \
apt-get install -y libbz2-dev
RUN Rscript -e "install.packages('rJava')"
Note: liblzma-dev and libbz2-dev are additional system dependencies for compiling rJava.
Simply my Question is How to Install Swoole in Ubuntu 14.04 LTS
I have tried
sudo pecl install swoole
am getting handfull of errors, already posted here
Is there any alternate way to install the same...
Swoole Installation alternate ways
1.Install from source
sudo apt-get install php7-dev
git clone https://github.com/swoole/swoole-src.git
cd swoole-src
phpize
./configure
make && make install
2.Example for static compile
git clone -b PHP-7.2 --depth 1 https://github.com/php/php-src.git
cd php-src/
git clone -b master --depth 1 https://github.com/swoole/swoole-src.git ext/swoole
./buildconf --force
./configure --prefix=/usr/local/php7 --disable-all --enable-cli --disable-cgi --disable-fpm --disable-phpdbg --enable-bcmath --enable-hash --enable-json --enable-mbstring --enable-mbregex --enable-mbregex-backtrack --enable-sockets --enable-pdo --with-sodium --with-password-argon2 --with-sqlite3 --with-pdo-sqlite --with-pcre-regex --with-zlib --with-openssl-dir --enable-swoole-static --enable-openssl --with-swoole
time make -j `cat /proc/cpuinfo | grep processor | wc -l`
sudo make install
Some Linux distributions do not include the PHP-XML extension in their PHP package and will need to be enabled before using PECL. You can install using apt-get install php-xml and you may need to install PHPize to compile Swoole, you can install it using apt-get install php7.*-dev or whatever PHP version you are using.
Then try again with sudo pecl install swoole
For those who installed PHP from ondrej/php PPA (quite common way to install PHP in Ubuntu) it's quite easy now:
sudo apt install php-swoole
Or for specific version:
sudo apt install php7.4-swoole
Tip. This is how you usually install ondrej/php PPA:
sudo apt install software-properties-common
sudo add-apt-repository ppa:ondrej/php
sudo apt-get update
Install swoole for version specific should work for example if you have php 7.3 use
sudo apt install php7.3-swoole
replace the version to your local php env
I am trying to install RStudio on Centos 6.4 with an already installed R version.
I got the following error:
error: Failed dependencies:
libcrypto.so.6()(64bit) is needed by rstudio-server-0.97.336-x86_64
libgfortran.so.1()(64bit) is needed by rstudio-server-0.97.336-x86_64
libssl.so.6()(64bit) is needed by rstudio-server-0.97.336-x86_64
Any hint will be highly appreciated.
I fixed this error following this link:
http://jermdemo.blogspot.com.es/2011/08/installing-rstudio-server-on-scientific.html
You have to install some dependencies:
yum install libcrypto.so.6 -y
yum install libgfortran.so.1 -y
yum install libssl.so.6 -y
yum install openssl098e-0.9.8e -y
yum install gcc41-libgfortran-4.1.2 -y
yum install pango-1.28.1 -y
and the tricky one:
wget ftp.scientificlinux.org/linux/scientific/6.0/x86_64/os/Packages/compat-
libgfortran-41-4.1.2-39.el6.x86_64.rpm
rpm -Uvh compat-libgfortran-41-4.1.2-39.el6.x86_64.rpm
and install Rstudio with no-deps flag:
rpm -Uvh --nodeps rstudio-server-0.97.336-x86_64.rpm
rstudio-server verify-installation