I'm getting a little bit crazy with this issue. I'm trying to install an R package using conda in my environment (python 2.7) in my home on a cluster (i.e. without root permissions). I firstly installed R in my env using:
conda install -c r r=3.4
Then:
conda install -c conda-forge python-igraph
(because igraph is required by my library of interest)
and finally:
conda install -c conda-forge r-diffusionmap
Unfortunately when I launch R the following message appears:
Error: package or namespace load failed for 'RevoUtilsMath': .onLoad
failed in loadNamespace() for 'RevoUtilsMath', details: call: NULL
error: Remove Microsoft R and then re-install. Be sure to select MKL
libraries as an install option.
During startup - Warning message:
package 'RevoUtils' was built under R version 3.4.3
What does it mean? How can I solve this?
Thank you in advance
I had this same issue after I installed some libraries (Rcpp included) in my root R, but not my conda environment (which screwed up conda). This would cause kernel death anytime a jupyter notebook running R was even opened.
The fix for me was:
Uninstall Anaconda3
Reinstall Anaconda3
Reinstall all the libraries I needed (mostly just Bioconductor in R)
A few other issues popped up, like package inconsistencies, but I dealt with those as described here.
All R packages on conda-forge (or Bioconda) are compiled against one single version or R for each new release branch (usually starting from patch 1, so 3.x.1, except for 3.4.3). This is due to ABI incompatibility problems.
Also note that defaults and conda-forge channels are (where) not binary compatible (although now they should be). And that since 2018 the default anaconda channel is distributing Microsoft R Open as default R, whether all packages from conda-forge should be preferably used with R from conda-forge.
You should be able to solve this issue by installing R using conda install -c conda-forge r-base.
the same error information for me when I open R for run code in ubuntu platform(18.4), and there is no other useful methods to solve it.My R version is 3.4.3.enter image description here
Related
I did put R on path using the .bashrc file. And yet, I do not have access to R through the command line. I have nevertheless no issues with RStudio. When I check for the R location with which R, I get /home/myself/anaconda3/bin/R. I have Ubuntu 20.04. The error message that I get is /home/myself/anaconda3/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory. I have version R version 4.1.3 which I have installed recently. Working in JupyterLab in anaconda, I installed again R in a conda environement. Unfortunately, I get inside the conda environment the same error message.
When I try to install the missing package, I get the message:libreadline6 : PreDepends: multiarch-support but it is not installable.
I also tried to install libreadline with conda, conda install -c conda-forge m2-libreadline (as suggested on the anaconda site) as well as conda install -n base -c conda-forge libreadline.so.6. The message I get is: `PackagesNotFoundError: The following packages are not available from current channels:
libreadline.so.6
m2-libreadline`
I will highly appreciate your help. Thanks.
My goal is to use this package (https://github.com/tiagodc/TreeLS) but it was deprecated from CRAN (https://cran.r-project.org/web/packages/TreeLS/index.html). It requires an older version of R yet its dependencies such as the raster package require R 3.5 or up. I considered two approaches.
using R studio and changing the global options to an older version of R, but I frequently use many geospatial packages and since this package has older dependencies I didn't want to install older versions of packages I use all the time.
Create a virtual environment in Mini Conda 3 dedicated to use for this package. I choose this option because it would be self contained.
Here is the workflow so far.
conda search -c r r
conda create -n newR351 -c conda-forge r-base=3.5.1 -y
conda install -c r rtools -y
Successfully creates a conda environment called newR351 and installs r tools to that environment folder within mini conda 3.
Location of conda environment with R 3.5.1 install
C:\Users\me\Miniconda3\envs\newR351
When I try to install devtools so I can remote install TreeLS from github I get a warning with zero exit status. The devtools package installs, but it installed to my appdata folder and not my mini conda environment.
conda install -c r devtools -y
The downloaded source packages are in
'C:\Users\me\AppData\Local\Temp\RtmpYByvp8\downloaded_packages'
How can I access devtools on my conda environment newR351? Do I need to build a cran skeleton? When I activate R in this environment and try to load the devtools library I get this.
(newR351) C:\Users\me>R
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
...
>library(devtools)
Error in library(devtools) : there is no package called 'devtools'
What are best practices for creating an environment specific for an older R package? Anyone else use TreeLS?
First, the devtools isn't showing up because R packages in Conda repositories are conventionally prefixed with "r-", so installing conda install r-devtools should do the trick. However, I don't think Conda is the best strategy here.
Below R version 3.6, the Conda package coverage for R packages is rather poor. Also, installing non-Conda packages that require compilation into a Conda R environment is a pain and generally doesn't work out-of-the-box in my experience. Plus, not only does the TreeLS require compilation, but it has dependencies that are not Conda packages which require compilation. I would avoid this.
Option 1 is feasible. R allows multiple installations, and with manipulating environment variables (I think RSTUDIO_WHICH_R, R_LIBS are the pertinent ones) one can switch between them.
However, were this my situation, I'd spin up a docker container, probably rocker/rstudio:3.5 and use that for this project. Since the underlying image is Linux, it'll take awhile to compile, but you can version it at that point and then always have that available to spin up. This avoids having to muck around with any system settings and should be mostly straight-forward installing.
I used to work in R 3.4.0 version. Hovewer, this version doesn't support such packages as keras and tensorflow.
I was adviced to upgrade my R version to the newest one.
I downloaded the most recent R version 4.0.2 from the official site, then ran the following code:
install.packages("keras")
library(keras)
install_keras()
And got the following error:
Error in install_keras() :
You should call install_keras() only in a fresh R session that has not yet initialized Keras and TensorFlow (this is to avoid DLL in use errors during installation)
After this, when I tried to quit R session by q() , I faced the following error:
Error: option error has NULL value
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error: option error has NULL value
I've never faced such an error before. When I used old R version, I typed q() and then had to choose between y and n. No errors appeared.
I'm asking you to help to to solve this problem.
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 activate r4-base
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.
Find the location of R.exe on your computer. In my computer, this executable is at
C:\Program Files\R\R-3.4.3\bin
Open another Anaconda Prompt as Administrator and change directories to wherever R.exe is on your computer with cd file path. On my computer, it’s cd C:\Program Files\R\R-3.4.3\bin, but it might be different for you.
Then run R from within Anaconda Prompt in Admin mode with R.exe
You’ll notice that you’re in an R session. From here, run the following three commands into the terminal.
install.packages("devtools")
devtools::install_github("IRkernel/IRkernel")
IRkernel::installspec()
In order, they (1) install the devtools package which gets you the install_github() function, (2) install the IR Kernel from GitHub, and (3) tell Jupyter where to find the IR Kernel.
Open Jupyter notebook and enjoy your new R kernel!
Get more information here
#Rheatey Bash works perfectly. but i was facing python.exe this program cant start because api-ms-win-core-path-l1-1-0.dll python system error. this is a problem running on windows 7 but i resolved this issue by installing the kernel following https://richpauloo.github.io/2018-05-16-Installing-the-R-kernel-in-Jupyter-Lab/ and it works fine
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.
I am trying to install two packages in R (3.3.2): devtools and git2r. They are depending on the existence of zlib. This comes with macOS Sierra (10.12.3) and it's version 1.2.8 by default.
When I'm trying to install these packages I get the error below.
I've been trying a lot of things.
directly installing via CRAN in RStudio: no effect.
trying to locate zlib on macOS: can't find zlib.
installing via R CMD INSTALL git2r: no effect.
I notice someone has a similar issue posted on GitHub: https://github.com/ropensci/git2r/issues. There is no solution yet.
Does anyone here have an idea?
Thanks!
Sander
ERROR MESSAGE BELOW
configure error in "/private/tmp/RtmpP6HZFx/R.INSTALLe73412909267/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 --configure-args='--with-zlib-include=INCLUDE_PATH --with-zlib-lib=LIB_PATH' git2r"
See "config.log" for more details
ERROR: configuration failed for package "git2r"
*removing "/usr/local/lib/R/3.3/site-library/git2r"
UPDATE: the same issue persists on macOS X 10.12.5 in combination with R 3.4.0 - the latter I need for DESeq2.
Solution...Mmm. Not really. I simply uninstalled R and all the packages, and than I reinstalled everything again. I installed R and RStudio via homebrew, following the instructions here: https://rud.is/b/2015/10/22/installing-r-on-os-x-100-homebrew-edition/.
Oddly enough: all issues disappeared.
UPDATE #1: this solution does not - obviously - work for the combination R 3.4.0 and macOS X 10.12.5. We need a solution for this issue.
UPDATE #2: I have discovered what I believe was the issue: a wrong path to the xcode command line tools.
sudo xcode-select --reset did the trick and now xcode-select -p points to /Library/Developer/CommandLineTools. And which xcode-select points to /usr/bin/xcode-select. Googling I discovered that it is not needed to install Xcode through the App Store as it states on http://railsapps.github.io/xcode-command-line-tools.html:
"On earlier versions of macOS, it was more difficult to install Xcode Command Line Tools. It required a huge download of the full Xcode package from the Mac App Store or registration as an Apple developer for a smaller Command Line Tools package. Mac OS X Mavericks made installation of Xcode Command Line Tools much simpler.".
i was having the same problem. i have a note 8(samsung). just go to GitHub and install zlib from there.