RStudio in KDE Neon - r

How can I install RSudio in KDE Neon I have downloaded rstudio-1.4.1106-amd64.deb and I ran sudo dpkg -i rstudio-1.4.1106-amd64.deb in terminal, I got following:
dpkg: dependency problems prevent configuration of rstudio: rstudio depends on libclang-dev; however: Package libclang-dev is not installed. rstudio depends on libpq5; however: Package libpq5 is not installed.
dpkg: error processing package rstudio (--install): dependency problems - leaving unconfigured Processing triggers for desktop-file-utils (0.24-1ubuntu3) ... Processing triggers for mime-support (3.64ubuntu1) ... Processing triggers for hicolor-icon-theme (0.17-2) ... Processing triggers for shared-mime-info (1.15-1) ... Errors were encountered while processing:rstudio

There are some packages required that are not installed by default. Please try the following, which worked for me on Kubuntu 20.04 recently:
URL='https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.4.1106-amd64.deb'; FILE=`mktemp`; wget "$URL" -qO $FILE && sudo dpkg -i $FILE; rm $FILE
sudo apt --fix-broken install

First I had to find and fix broken packages:
apt --fix-broken install
Then the package installed correctly for me:
sudo dpkg -i rstudio-2022.02.3-492-amd64.deb

Related

not able to install GCC on Solaris 11.4

I installed Solaris 11.4 x86 in VirtualBox. I need to install the GCC compiler so that I can run c code in Solaris. But each time I try to install the package this error occurs:
Errors were encountered while attempting to retrieve package or file data for the
requested operation. Details follow:
http protocol error: Unknown error code: 500 reason: Internal Server Error
URL: 'http://pkg.oracle.com/solaris/release/solaris/file/1/53eb07cd6fade116a6fdea7397c6839929ec0925'
publisher information:
I have used the following commands:
sudo pkg install developer/gcc/gcc-c-7
also tried -nv option
sudo pkg install -nv gcc
sudo pkg install -nv gcc-7
sudo pkg install -nv developer/gcc-7
see the output of the following command:
kashif#OS:~$ pkg list | grep GCC
output:
system/library/gcc/gcc-c++-runtime 7.3.0-11.4.0.0.1.14.0 i--
system/library/gcc/gcc-c++-runtime-7 7.3.0-11.4.0.0.1.14.0 i--
system/library/gcc/gcc-c-runtime 7.3.0-11.4.0.0.1.14.0 i--
system/library/gcc/gcc-c-runtime-7 7.3.0-11.4.0.0.1.14.0 i--
image below shows gcc package information from repostiry
I am trying to solve this problem for 2 days. I have read documentation from
https://docs.oracle.com/cd/E37838_01/html/E60979/publisher-config.html
I also tried to install developerstudio 12.6 but it didn't work.
overall picture of error and command:
I have googled for errors tried to find information about errors and searched for how to install GCC on Oracle Solaris 11. I couldn't find any solution to this problem.
Try "wget http://pkg.oracle.com/solaris/release/p5i/0/developer%2Fgcc.p5i" or your preferred gcc package and manually install it with pkg install. You can try:
pkg install -v
after downloading.

Unable to install R library of facebook prophet on CentOS7

I am trying to install R library for Facebook's prophet on centOS 7. For easy reproducibility, I am providing a dockerfile and commands.
FROM centos:7
RUN yum -y install epel-release
RUN yum -y groupinstall "Development Tools"
RUN yum -y install proj
RUN yum -y install udunits2-devel
RUN yum -y install openssl-devel
RUN yum -y install libjpeg-turbo-devel
RUN yum -y install libcurl-devel
RUN yum -y install v8-devel
RUN yum -y install R
To build the dockerfile, use following command.
docker build -t test_prophet_installation .
Once it is built, I run the container using this next command.
docker run -it --entrypoint=/bin/bash test_prophet_installation
Now, I am inside my container. I tried to install prophet using below command.
su - -c "R -e \"install.packages('prophet', repos='http://cran.rstudio.com/')\""
The above command said, one of the dependencies of prophet i.e rstan failed to install. So I tried to install 'rstan' using the following command.
su - -c "R -e \"install.packages('rstan', repos='http://cran.rstudio.com/')\""
After running the above command, I got the following error.
Error in .shlib_internal(args) :
C++14 standard requested but CXX14 is not defined
* removing '/usr/lib64/R/library/rstan'
The downloaded source packages are in
'/tmp/RtmpsPDQ9G/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("rstan", repos = "http://cran.rstudio.com/") :
installation of package 'rstan' had non-zero exit status
2: In file.create(f.tg) :
cannot create file '/usr/share/doc/R-3.6.0/html/packages.html', reason 'No such file or directory'
3: In make.packages.html(.Library) : cannot update HTML package index
I tried almost all the troubleshooting from Google to solve above error still no luck. I think, I am not setting some environment variable correctly.
The problem here is that when using the yum groupinstall "Development Tools", the installed gcc is 4.8.5 and therefore does not support C++14 (as you can see here).
In order to solve this you need to add the following:
RUN yum -y install centos-release-scl
RUN yum -y install devtoolset-8-gcc*
RUN scl enable devtoolset-8 sh
on top of this, you have to define the Makevars for rstan. You can find an explanation here: https://github.com/stan-dev/rstan/issues/569
I created this Makevars:
CXX14 = g++ -std=c++1y -Wno-unused-variable -Wno-unused-function -fPIC
and added a COPY in my Dockerfile:
COPY Makevars /root/.R/Makevars
I'm using the following command to download the packages:
install.packages('rstan', repos='http://cran.rstudio.com/', dependencies = TRUE)
Some things are still not working as expected but it's a step forward.
EDIT:
this approach does not work since the system keeps using the old g++. I ended up using the docker image centos/devtoolset-7-toolchain-centos7:latest.

How to install Rmpfr on Ubuntu 18.04?

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.

how can i install the packages in r properly and correctly using Rstudio app?

I tried to install "xlsx" package using Rstudio, and i couldn't install it.
I am trying to install my packages using install.packages("xlsxjars"). I already tried doing that from Tools window in Rstudio app, and I tried using the console.
I am using Linux (Gnome 17.04). I get this error:
input
install.packages("xlsxjars")
output
Installing package into ‘/home/aim/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/xlsxjars_0.6.1.tar.gz'
Error in install.packages : error reading from connection
if you get some Errors while installing r packages kind of somthing.so is miising or some packages are missing depending on the version of R, you should try this commands because, i had this kind of errors with R 3.0.x in Ubuntu 14.04
so i upgrade my R version to fix it with the following commands :
sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" »
gpg —keyserver keyserver.ubuntu.com —recv-key E084DAB9
gpg -a —export E084DAB9 | sudo apt-key add -
sudo apt-get —purge remove r-base-core
sudo apt-get update
sudo apt-get -y install r-base
sudo apt-get update
now i can install all packages without errors
I totally agree with the answer of #kissi salim yahia
Just want to add . When you tape in R
install.packages("your_package")
you got some dependencies below.
these one may have troubles sometimes. So just need to install them manually from the SHELL like:
sudo apt-get install r-cran-your_dependencie
I spent a while struggling with that too. Eventually I just gave up as the java in that package was out of date and I would have needed to load older Java up to get it to run. I would suggest readxl instead.
A simple intro to the package can be found here: https://www.datacamp.com/community/tutorials/r-tutorial-read-excel-into-r#readxl

Installing Rmpi on Ubuntu 16.04 VirtualBox

I created a new ubuntu-16.04.2-desktop-amd64 machine on VM VirtualBox and I want to be able to use the R environment with Rmpi.
Both of the below approaches gives a similar error.
Updated simplified pre-build binary approach:
When Ubuntu had installed I opened a terminal and executed the following commands:
~$ sudo apt-get update
~$ sudo apt-get install openmpi-bin
~$ sudo apt-get install r-base
~$ sudo apt-get install r-cran-rmpi
~$ R
This opened the R terminal and I invoking the follow function which resulted in an error:
> library(Rmpi)
libmpi.so: cannot open shared object file: No such file or directory
Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
call: fun(libname, pkgname)
error: Cannot start MPI_Init(). Exit
Error: package or namespace load failed for ‘Rmpi’
Alternative approaches that I have attempted include using a local OpenMPI installation and using the R function install.packages to install the Rmpi package (see below). These all resulted in the same error.
I have also tried using MPICH by substituting ~$ sudo apt-get install mpich as the second command in the above procedure (including using the R function for installing the package) which results in an even more onerous runtime error.
Does anyone know what I have done wrong or what I can do to resolve this installation error?
Or alternatively, have anyone been able to successfully install a VirtualBox machine with Rmpi using any Linux distro or an image with pre-installed components?
Original local installation approach:
I have followed the instructions on this blog to download OpenMPI version 2.1.0, compile and install it. However when I try to install the package in R with:
> install.packages("Rmpi", configure.args =
c("--with-Rmpi-include=/home/jormunr/openmpi/include",
"--with-Rmpi-libpath=/home/jormunr/openmpi/lib",
"--with-Rmpi-type=OPENMPI",
"--with-mpi=/home/jormunr/openmpi/"))
it gives the following error
Error: .onLoad failed in loadNamespace() for 'Rmpi', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/jormunr/R/x86_64-pc-linux-gnu-library/3.2/Rmpi/libs/Rmpi.so':
libmpi.so.20: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
I can see that the 'libmpi.so.20' file is in the /home/jormunr/openmpi/lib that I provided as one of the parameter to the installation.
[Disclaimer: I am not a Linux expert and merely have user level skills. Any contributions or corrections from an expert will be greatly appreciated.]
Pre-build Binary Approach
Although trying various ways to install the prebuilt binaries I did not manage to get this option to work. This involved executing in the terminal the command 'sudo apt-get install r-cran-rmpi' to install the r-cran-rmpi prebuilt packages which also automatically installs the libopenmpi1.10 package that is a listed prerequisite. However, it appears that the file 'libmpi.so' is not included in the libopenmpi1.10 package but expected by the Rmpi library which causes an error in the R environment that it cannot find this file.
Local Installation Approach
The local installation did eventually succeed with a few amendments. I created a new ubuntu-16.04.2-desktop-amd64 VirtualBox image with default settings, except for 2048MB of memory and 32GB of hard drive space. When installed I opened a terminal and executed the commands from the Jovinge Lab website with the inclusion of the penultimate command which amends the run-time link editor's path and enables the install.package() function of R to find the 'libmpi.so' file. (also changed the version to 1.10.6 as this is the latest version release of version 1 – see below for version 2)
~$ cd /home/jormunr
~$ wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz
~$ tar -zxvf openmpi-1.10.6.tar.gz
~$ cd openmpi-1.10.2
~$ ./configure --prefix=/home/jormunr
~$ make
~$ make install
~$ sudo apt-get install r-base
~$ export LD_LIBRARY_PATH=/home/jormunr/lib:$LD_LIBRARY_PATH
~$ R
This opens an R terminal and I invoked the function:
> install.packages("Rmpi", configure.args =
+ c("--with-Rmpi-include=/home/jormunr/include/",
+ "--with-Rmpi-libpath=/home/jormunr/lib/",
+ "--with-Rmpi-type=OPENMPI",
+ "--with-mpi=/home/jormunr/"))
This now executed without errors and I could test it with the following R statements:
> library("Rmpi")
> mpi.spawn.Rslaves()
master (rank 0, comm. 1) of size 2 is running on: Valhalla
slave1 (rank 1, comm. 1) of size 2 is running on: Valhalla
> mpi.close.Rslaves()
[1] 1
> mpi.quit()
When I tried this process with the OpenMPI Version 2.1.0 the installation completed successfully but the above test had issues; the mpi.spawn.Rslaves() function completed but mpi.close.Rslaves() did not complete – it never returned and the terminal was left hanging.
I experienced similar challenges. I landed on this solution where libopenmpi-dev was the secret.
sudo apt-get install openmpi-common openmpi-bin libopenmpi-dev r-base
sudo apt-get install r-cran-rmpi
sudo su
R
install.packages("doMPI", dependencies=TRUE)

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