I have installed R that in turns installs openblas - but not to /usr/local :
==> openblas
openblas is keg-only, which means it was not symlinked into /usr/local,
because macOS provides BLAS and LAPACK in the Accelerate framework.
For compilers to find openblas you may need to set:
export LDFLAGS="-L/usr/local/opt/openblas/lib"
export CPPFLAGS="-I/usr/local/opt/openblas/include"
For pkg-config to find openblas you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/openblas/lib/pkgconfig"
My primary use case for openblas is with R and scipy. The latter _no longer supports the Macos Accelerate package`: so there's no problem with redirecting to brew. The former will be using the brew anyways: so I see no harm in doing this. But how to do it?
Two steps made this work:
Uninstall openblas via brew:
brew uninstall --ignore-dependencies openblas
Reinstall R
brew install R
Manually create symbolic link to /usr/local :
sudo ln -s /usr/local/opt/openblas /usr/local
Now we have R !
$R
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin18.6.0 (64-bit)
..
>
Related
I'm having trouble installing R from a homebrew formula on our Intel garbage can mac pro at work. I was having trouble installing tidyverse from source code so I removed and have been attempting to reinstalling R, as I thought it might have been a version mismatch somewhere.
I used
brew install R
and after a bunch of output where it's downloading other packages, I get back the following
==> Installing dependencies for r: libpng, freetype, fontconfig, gettext, libffi, pcre, glib, pkg-config, libpthread-stubs, xorgproto, libxau, libxdmcp, libxcb, libx11, libxext, libxrender, lzo, pixman, cairo, gmp, isl, mpfr, libmpc, lz4, xz, zstd, gcc, jpeg-turbo, openblas, pcre2, readline, ca-certificates, openssl#1.1 and tcl-tk
==> Installing r dependency: libpng
Unknown option: -C
usage: git [--version] [--help] [-c name=value]
[--exec-path[=<path>]] [--html-path] [--man-path] [--info-path]
[-p|--paginate|--no-pager] [--no-replace-objects] [--bare]
[--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>]
<command> [<args>]
Error: Command failed with exit 129: git
Is this in fact a git error? What is the -C command?
Things I've tried:
removing and reinstalling command line tools
removing and reinstalling Homebrew
My machine:
Mac Pro (Late 2013)
2.7 GHz 12-Core Xeon E5
Thanks!
Sam
I think it tries to use an old version of git at /usr/bin/git, but you need to run brew install git to install a newer version of git to /usr/local/bin/git.
If /usr/local/bin/ isn't on your PATH before /usr/bin/, then you can add a line like this to ~/.bash_profile:
export PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
However /usr/local/bin is included in /etc/paths by default, so it should be added to PATH by programs that run path_helper (like Terminal and iTerm 2 but not Script Editor or Emacs.app).
I am sure this is a trivial question, but I am trying to install multiple R versions in Linux. I am not using R studio server pro and am instead using the free R studio server. I followed this documentation to install R but got errors when I attempted to locate it. However, when I run a command to see what version of R is installed, there is no error.
R is installed!
(base) noah#noah-VirtualBox:/opt/R/4.1.3$ /opt/R/4.1.3/bin/R --version
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
Attempts
(base) noah#noah-VirtualBox:/opt/R/4.1.3$ R
Command 'R' not found, but can be installed with:
sudo apt install r-base-core
(base) noah#noah-VirtualBox:/opt/R/4.1.3$ which R
(base) noah#noah-VirtualBox:/opt/R/4.1.3$
Steps to reproduce
export R_VERSION=4.1.3
curl -O https://cran.rstudio.com/src/base/R-4/R-${R_VERSION}.tar.gz
tar -xzvf R-${R_VERSION}.tar.gz
cd R-${R_VERSION}
# Build and install R
./configure \
--prefix=/opt/R/${R_VERSION} \
--enable-memory-profiling \
--enable-R-shlib \
--with-blas \
--with-lapack
make
sudo make install
# Verify R installation
/opt/R/${R_VERSION}/bin/R --version
# Create a symlink to R
sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
sudo ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
# Export path so Rstudio can find it
export RSTUDIO_WHICH_R='/opt/R/4.1.3/bin'
You are overcomplicating it. Just install in, say,
/opt/R/4.2.0/
/opt/R/4.1.2/
/opt/R/4.0.5/
and then either set the $PATH to the bin/ directory in the version you want, or call R directly. It is what pretty much exactly what many of us have done with two versions of R (i.e. R-release and R-devel):
$ R --version | head -1
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
$
$ /usr/lib/R/bin/R --version | head -1
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
$
$ /usr/local/lib/R-devel/bin/R --version | head -1
R Under development (unstable) (2022-05-24 r82398) -- "Unsuffered Consequences"
$
The first two are the same as that is my 'default' version. The third is my one alternate. And that is all there is to it.
If you add /usr/local/bin to your $PATH variable you would have been able to launch R, if it was not already present.
You could add it to .bashrc in your home directory
echo "export path=\"${PATH}:/usr/local/bin\"" |tee -a ~/.bashrc
Links for installing R from package, Ubuntu / Debian, RHEL 9, RHEL 8, RHEL/CentOS7
https://docs.posit.co/resources/install-r/
Also see
(Optional) Install multiple versions of R, on the same page.
I am trying to set up Rstudio on an Ubuntu cloud server (gcloud). I currently have version R-3.4.4 on RStudio, but would like to upgrade. The issue is, I am unable to.
I am running the following version of Ubuntu.
name#sc1:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.5 LTS
Release: 18.04
Codename: bionic
I installed the RStudio server for Ubuntu 18 as suggested here: https://www.rstudio.com/products/rstudio/download-server/debian-ubuntu/
So essentially running to install the server:
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.4.1717-amd64.deb
sudo gdebi rstudio-server-1.4.1717-amd64.deb
Checking the version of R Studio I have:
sudo -i R
Output:
name#sc1:~$ sudo -i R
R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
However, this is what pops up in my RStudio.
Anyone have ideas for what I'm doing wrong? How can I upgrade my package?
Furthermore, in my /home/user/R/x86_64-pc-linux-gnu-library directory, I have an R-3.4 folder, which is confusing…
Turns out that after I installed R 4.0, I had to restarted the VM and that seemed to work. Unclear why this is, but at least it worked!
I'm trying to install gifski which is a dependency for gganimate.
I get this error.
------------------ RUST COMPILER NOT FOUND --------------------
Cargo was not found on the PATH. Please install cargo / rustc:
- yum install cargo (Fedora/CentOS)
- apt-get install cargo (Debian/Ubuntu)
- brew install rustc (MacOS)
Alternatively install Rust from: <https://www.rust-lang.org>
---------------------------------------------------------------
The yum install cargo command didn't work, so I installed Rust with
curl https://sh.rustup.rs -sSf | sh
The installation prompt said I needed to add $HOME/.cargo/bin to my path environment variable, so I tried this.
$ source $HOME/.cargo/env
$ export PATH=$PATH:$HOME/.cargo/bin
$ export PATH=$PATH:/.cargo/bin
$ export PATH=$HOME/.cargo/bin
I reset my machine and I continue to receive the same error.
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Amazon Linux AMI 2018.03
I would like to know if there is a way i can use Intel MKL library instead of OpenBlas. I have installed MKL. Below is the version info
Julia Version 0.6.0
Commit 903644385b (2017-06-19 13:05 UTC)
Platform Info:
OS: macOS (x86_64-apple-darwin13.4.0)
CPU: Intel(R) Core(TM) i7-4770HQ CPU # 2.20GHz
WORD_SIZE: 64
BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
LAPACK: libopenblas64_
LIBM: libopenlibm
LLVM: libLLVM-3.9.1 (ORCJIT, haswell)
Kindly let me know if this can be done
This is the procedure I have used to install Julia (0.6.0) with Intel MKL (compiling from source) in macOS Sierra. Remember to uninstall previous versions of Julia first.
Install Xcode.
Launch a Terminal and update the command line tools:
$ xcode-select --install
Install Homebrew.
Use Homebrew to install gfortran:
$ brew install gfortran
Take advantage of Homebrew and install also wget:
$ brew install wget
Go to the Intel Performance Libraries webpage, register yourself and download these free libraries for OS X and install them (as with a regular DMG package):
Intel Threading Building Blocks (TBB)
Intel Math Kernel Library (MKL)
Download the Julia source (Tarball with dependencies):
$ wget https://github.com/JuliaLang/julia/releases/download/v0.6.0/julia-0.6.0-full.tar.gz
Uncompress the file and move the folder to your $HOME directory.
Launch a Terminal and change to the Julia source directory:
$ cd ~/julia-0.6.0
With your preferred tool, edit the file Make.inc and enable the use of Intel MKL and Intel MKL FFT. Save and close the file. Use the picture as a guide:
Set up the Intel MKL environment, for Intel64 architecture with 8 bytes integer support (ILP64):
$ source /opt/intel/mkl/bin/mklvars.sh intel64 ilp64
Compile Julia:
$ make
If there is a problem compiling Julia, create a symbolic link in the Julia's lib folder to the Intel MKL library and run make again:
$ ln -s /opt/intel/mkl/lib/libmkl_rt.dylib usr/lib/libmkl_rt.dylib
$ make
I did not try to run make install because I do not have Administrator privileges in my Mac, but you are free to do it. Anyway, you can run Julia from this folder:
$ ./julia
Next time you open a Terminal probably your Intel MKL variables would have gone. Just add these lines to your ~/.bash_profile:
# Intel MKL
source /opt/intel/mkl/bin/mklvars.sh intel64 ilp64
Yes this is possible but much easier to do if you are happy to re-install a clean version of julia.
You will need to edit the Make.user file as described here: https://github.com/JuliaLang/julia#intel-compilers-and-math-kernel-library-mkl