I currently have a conda environment created as "r_env" and is trying to install the "tensorflow" package into R on terminal. However, in R I keep having the same error, regardless if I am install "tensorflow" or "png" package directly from terminal after loading R.
I currently have the following packages installed in the conda env:
It appears to me that the installer is trying to look for the library files in ./conda/envs/r_env/lib/R/library whilst it is already installed in ./conda/envs/r_env. How may I rectify this issue? (Note: I do not have sudo privileges, but any solutions at this point is helpful!)
Use this code to install tensorFlow:
library(keras)
install_keras()
devtools::install_github("rstudio/keras")
install_tensorflow(package_url = "https://pypi.python.org/packages/b8/d6/af3d52dd52150ec4a6ceb7788bfeb2f62ecb6aa2d1172211c4db39b349a2/tensorflow-1.3.0rc0-cp27-cp27mu-manylinux1_x86_64.whl#md5=1cf77a2360ae2e38dd3578618eacc03b")
library(tensorflow)
After that try installing png:
install.packages("png")
library(png)
Finally check png:
capabilities()["png"]
Output:
png
TRUE
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.
Got the errors
Error : package ‘stringr’ was installed before R 4.0.0: please re-install it and BiocManager Installation path not writeable, unable to update packages:
and further down the road rstudio gave me
/usr/local/lib/R/lib/libR.so not found
I had a similar problem when upgrading from R 3.6 to 4.0 in my Linux box.
I am also answering this because this question is one of the first results google gives when looking for this problem.
It turns out that, even by removing R (apt purge) there is a folder that remains in the system creating a lot of problems for the future installation.
I want to link the GREAT answer that was given here and saved me:
https://askubuntu.com/questions/1219737/installing-ggplot2-for-r-3-6-on-ubuntu-18-04
In Linux systems you should look in:
$ ls /usr/local/lib/R/site-library
If the folder has a list of directories you should remove everything with:
sudo rm -Rf /usr/local/lib/R/site-library
Then reinstall R and all the libraries.
This is a long answer to how to fix these errors but I assume necessary and also tips and tricks included (e.g. don't install R 4.0.2 right now (Jul 25, 2020)). It caused me a lot of pain because there were many more errors that I ran into on the way.
Error : package ‘stringr’ was installed before R 4.0.0: please re-install it and BiocManager Installation path not writeable, unable to update packages:
I removed .RData in my home folder (invisible, use ls -la) This fixed my problem for the installed before R 4.0.0 error, but did not fix my bioconductor problems. I assume it might work if you only had the re-install error.
After many attempts at trying to get my packages to load but only getting these errors, I opted to reinstall R. In R, I ran .libpaths and deleted all the files in each of the directories. I then reinstalled R by downloading R from https://www.r-project.org/ and ran the general compile commands in the downloaded folder ./configure --enable-R-shlib --with-blas --with-lapack make sudo make install. The --enable-R-shlib is needed for rstudio to be able to use R, but the others aren't.
On Jul 25, 2020 I tried to install from apt on ubuntu, but rstudio was not able to find libR.so (error of /usr/local/lib/R/lib/libR.so not found). I tried to compile from source R 4.0.2 with the ./configure --enable-R-shlib which should make the libR.so but this returned an error.
I assume this to be an underlying problem as running ./configure --enable-R-shlib compile from source with R 4.0.0, I got the files and Rstudio opened up (please fix R 4.0.2 and subsequently apt).
I then ran the general
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.11")
to install biocmanager and it finally worked.
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 using Windows, and am unable to install any package in R. I tried it with R 3.53 and 3.62. Both give an error.
I get the following type of error in the end:
Error in install.packages : cannot open file 'C:/Users/Arti Agarwal/Documents/R/win-library/3.5/file3a2065f64427/BH/include/boost/geometry/util/readme.txt': Permission denied
I also get this type of an error in between:
There is a binary version available but the source version is later:
binary source needs_compilation
yaml 2.2.0 2.2.1 TRUE
I don't know how to troubleshoot this further. Any suggestions?
I think I fixed it. Posting the answer for the benefit for anyone else having the same problem.
1) I fixed the file permission error by running R as admin.
2) The packages don't work with R 3.6.2 or R 3.5.3 but strangely enough they work with R 3.6.1
It gives a warning that the package was built with R 3.6.2 but it doesnt work with it when you install it. Hence the confusion.
thanks for all of your help.
Install conda for windows
# if you have 64 bit computer:
https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe
# if 32 bit computer:
https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86.exe
Run the exe.
Create a new environment for your R:
# create new virtual environment for R with name 'newR'
conda create --name newR
# enter this created environment
conda activate newR # or: source activate newR
# install there now newest R
conda install -c conda-forge r-base
# you can also install rstudio
conda install -c conda-forge rstudio
# and also more difficult to install R packages
# search for them by googling: 'conda install <packagename>'
# mostly in anaconda site you see command for install.
# next time you want to start R do:
# enter environment
conda activate newR # if that doesn't work: source activate newR
# start R
R
Learn basic conda commands investing only 11 minutes:
https://www.youtube.com/watch?v=YJC6ldI3hWk
If you want to become a serious developer/programmer - sooner or later anyway you have to learn conda.
I am trying to run R code in Jupyter and the R Kernel was added. Most of the time, packages can be installed successfully. However, some of the packages, such as RCurl and ggmap, would got error while installing.
Example:
install.packages("RCurl")
Warning message in install.packages("RCurl"):
“installation of package ‘RCurl’ had non-zero exit status”Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
What should I do?
Try to specify CRAN as repository in your install.packages statement when installing RCurl and ggmap. For example:
install.packages("RCurl", repos='http://cran.us.r-project.org')
This Stack Overflow post on installing R packages through Anaconda/Jupyter beyond those included in R essential provides more detail.
(Side note: I had encountered the same issue when trying to install R packages on computer clusters. This solution worked for me.)
use conda comment:
conda install r-RCurl
I kept getting the non-zero exit status when trying to install packages with Jupyter notebook with R kernel and was failing because of multiple dependencies when wanting to install a package. I am not an expert in any of these so please forgive me if I make an error in explaining or if it is a non-issue for you but please feel free to comment to clear things out. I just want to share my success story so hopefully it can help someone else: I am working on a MacBook Pro. Here are the information I get when I run R.version() on my jupyter notebook with R kernel:
$platform 'x86_64-conda_cos6-linux-gnu'
$arch 'x86_64'
$os 'linux-gnu'
$system 'x86_64, linux-gnu'
$language 'R'
$version.string 'R version 3.6.1 (2019-07-05)'
These are the steps to take to fix the issue:
Go to https://anaconda.org/
Search the package name that you are trying to install
Copy the one line that is given to install the package, it should be something like:
Conda install -c r r-caret #conda install -c r r-package_name
NOTE: sometimes during installing packages, you’re asked whether or not you want to continue, so add --y at the end of the above statement to continue, so something like this
Conda install -c r r-caret --y
(I will always add it just to be on the safe side)
Click on the new launcher (+ icon) to create a new notebook with PySpark (once opened it has .ipynp extension)
On the first cell paste the copied line from step 2 and run
Once done, restart the kernel on the current notebook
Restart the kernel on your other notebook with R kernel
Run library(package_name) on your notebook with R kernel (e.x. library(caret))
install.packages("Hmisc", .libPaths(), repos='http://cran.us.r-project.org')
This command will install the packagae in the conda
"/home/user/anaconda3/lib/R/library" and use the cran r repository as source.
Add path in Anaconda
As per this answer,
one can also add additional paths in anaconda to load libraries from (for eg., the location where R studio saves the user-installed packages) with
.libPaths( c( .libPaths(), "~/userLibrary") )
For example, the following worked for me:
In Anaconda :
.libPaths( c( .libPaths(), "C:\Users\name\Documents\R\win-library\3.5") )
When I tried to add anaconda's library path to RStudio, it resulted in errors (The procedure entry point MARK_NOT_MUTABLE could not be located in the dynamic link library << arose 4 times in succession) after installation of a package, though the package seemed to load.
Replace name with your local user folder name
Add/change path in RStudio
A useful link to make changes in default user-installed library paths :
https://www.accelebrate.com/library/how-to-articles/r-rstudio-library
To find out where a package has been installed:
find.package('package_name')
The directions nobody else supplied worked for me, but I found this guide, and it worked. Spent way too much time trying all these when I just needed a few simple commands. https://developers.refinitiv.com/en/article-catalog/article/setup-jupyter-notebook-r
I already had R and python installed, so I skipped to step 3. The only seems to mention windows, but it worked for me on mac as well. After following them I was able to install the packages using install.packages("dplyr", repos = "http://cran.us.r-project.org") in a cell in jupyter.
You have to create a directory in which your package will be and do for eg:
install.packages('ggplot2',loc='your directory')
First Step: You can install the IRkernel packages by running the following command in an R console:install.packages('IRkernel')
Second Step: You will have to make Jupyter see the newly installed R kernel by installing a kernel spec. To install system-wide, set user to False in the installspec command IRkernel::installspec(user = FALSE)
Setup Jupyter Notebook for R