I am having the same problem as this and this.
I have installed R and rstudio through a conda environment which included r-rgl. I am now trying to install a package within R that requires rgl. However, calling library(rgl) gives the error
Error: package or namespace load failed for ‘rgl’:
package ‘rgl’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
I have tried to install rgl from within R, but then I get this message:
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/path/to/miniconda3/envs/my_conda_env/lib/R/library/rgl’
* restoring previous ‘/path/to/miniconda3/envs/my_conda_env/lib/R/library/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/vh/.../downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
The solution to the last error seems to be installing XQuartz in Mac, but I had it installed before. So I tried specifying install.packages("rgl", INSTALL_opts = "--with-libpng-prefix=/usr/X11/") but I still get the error above. Any suggestions? I'm quite lost now...
TL;DR: how do I connect my XQuartz installation with each conda environment that I create?
Related
I am having trouble installing packages, I was not able to install any. I got the following error in my r console:
ERROR: dependency 'cachem' is not available for package 'memoise'
* removing 'C:/Users/VasquezV/Documents/R/win-library/3.4/memoise'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\VasquezV\Documents\R\win-library\3.4" C:\Users\VasquezV\AppData\Local\Temp\1\RtmpuiYtO1/downloaded_packages/memoise_2.0.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘memoise’ had non-zero exit status
The major issue with this problem is that the cli package might not be updated as it often shows 3.1.1 installed but 3.3.0 required. Hence you have two solutions:
install.packages(cli) - there are chances that even this step
might fail as the error message is displayed: "Error in unpacking packages."
Uninstall Cran R and R studio and reinstall it or install the package for replacing the existing one to solve the issue.
This will definitely work as I have solved the issue through this way itself.
I'm currently operating in macOS with the R version of 3.6.3.
When I tried to install the package ggm, a warning occurred as follows.
Warning in install.packages :
dependency ‘graph’ is not available
also installing the dependency ‘igraph’
Then when it completed installing, it seemed not to work either:
ERROR: compilation failed for package ‘igraph’
* removing ‘/usr/local/lib/R/3.6/site-library/igraph’
ERROR: dependencies ‘igraph’, ‘graph’ are not available for package ‘ggm’
* removing ‘/usr/local/lib/R/3.6/site-library/ggm’
What is happening? I have searched for this error and didn't find anything that helps. Please help me. I'll be much appreciated!
I had the same problem.
To install the package graph you need to install the latest version of Bioconductor (i.e. package called BioManager).
Then you install the package graph and then simply run the installation for the ggm package.
install.packages("BiocManager")
BiocManager::install("graph")
install.packages("ggm")
library(ggm)
The package is then loaded into your R enviroment.
I am trying to install R2jags an r package in HPC linux environment, but doesn't work. This does work in windows, but not in HPC linux. I tried several options like:
install.packages("https://cran.r-project.org/src/contrib/R2jags_0.5-7.tar.gz", repos=NULL
but ends up with error:
ERROR: dependency 'rjags' is not available for package 'R2jags'
* removing '/ddn/home/grpl22/R/x86_64-pc-linux-gnu-library/3.6/R2jags'
Warning message:
In install.packages("https://cran.r-project.org/src/contrib/R2jags_0.5-7.tar.gz", :
installation of package '/tmp/Rtmprf6lN0/downloaded_packages/R2jags_0.5-7.tar.gz' had non-zero exit status
any sugeestion please how i can install this?
I am getting this errors trying to install caret package:
ERROR: compilation failed for package ‘ddalpha’
* removing ‘/home/rspark/R/x86_64-redhat-linux-gnu-library/3.3/ddalpha’
Warning in install.packages :
installation of package ‘ddalpha’ had non-zero exit status
ERROR: dependency ‘ddalpha’ is not available for package ‘recipes’
* removing ‘/home/rspark/R/x86_64-redhat-linux-gnu-library/3.3/recipes’
Warning in install.packages :
installation of package ‘recipes’ had non-zero exit status
ERROR: dependency ‘recipes’ is not available for package ‘caret’
* removing ‘/home/rspark/R/x86_64-redhat-linux-gnu-library/3.3/caret’
Warning in install.packages :
installation of package ‘caret’ had non-zero exit status
Any ideas?
install.packages("ddalpha")
It gives the same error:
/usr/lib64/R/library/BH/include/boost/exception/exception.hpp:137: error: expected declaration before end of line
make: *** [AlphaProcedure.o] Error 1
ERROR: compilation failed for package ‘ddalpha’
* removing ‘/home/rspark/R/x86_64-redhat-linux-gnu-library/3.3/ddalpha’
I have found a solution.
I had the same problem. After installing caret with all its dependencies, ddalpha was not installed. Then I tried installing the package ddalpha alone. I got the message:
" There is a binary version available but the source version is later:
binary source needs_compilation
ddalpha 1.2.1 1.3.1 TRUE
Do you want to install from sources the package which needs compilation?
y/n: n"
Well, if I anwser yes, it doesn't work. But when I answer no, it does work. It looks like the new version has some problem, but the previous one works fine.
As Roman indicated in the comments, ddalpha and recipes are dependencies that aren't installed yet. You can manually install them as follows:
install.packages(c('ddalpha', 'recipes'))
Alternatively, you can tell the install.packages() command to grab the necessary packages during the install process.
install.packages('caret', dependencies=TRUE)
Or list them explicitly:
install.packages('caret', dependencies=c('ddalpha', 'recipes'))
Or, if you use an IDE such as RStudio, the package manager that's included will automatically handle these dependencies for you.
If these suggestions don't solve the problem, you may try updating your instance of R to the latest (3.4.1 as I write this). Also, ddalpha is dependent on the Rcpp package version 0.11.0 or greater, so you may update that package.
update.packages('Rcpp')
I was facing the same issues, and I had tried almost all the methods mentioned here. But the only one that worked for me was updating my IDE and that sorted it out.
I had the same issue, running
install.packages('caret', dependencies=TRUE)
from console solved it. I don't know why at the packages window install with "install dependencies" checked didn't work..
R studio: 2022.07.1
R: 3.6.3
On one computer running R 2.15.2 I have installed packages from a .zip file (these packages happened to be ggplot2 and data.table, but I don't think the specific package is my issue.) Everything works fine. I took these packages to a computer without an internet connection and installed them. This other computer is running R 3.0.1. The packages seemed to install without a problem (using R's "install package(s) from local zip file" option). When I call the packages with the library(), I get the following error:
Error: package '<insert name of newly installed package here>' was build before 3.0.0: please-re-install it
Can anyone explain potential causes for this error to be thrown? Are there particular directories that the .zip packages must be in for a proper install? If R is installed on a separate partition from where the .zip packages were loaded, could this cause the error?
I'm at a loss, any pointers are greatly appreciated. This is a difficult one to reproduce; if you need any other version/system parameters to understand the problem, please don't hesitate to ask.
I found this solution while look at GitHub ggplot2 issue #796
update.packages(checkBuilt = TRUE, ask = FALSE)
It will update all the packages that need to be reinstalled.
Running install.packages("codetools") can fix this issue for R 3.0.2, if you have the same problem like me:
installing to /home/user/R/x86_64-pc-linux-gnu-library/3.0/Rcpp/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘**codetools**’ was built before R 3.0.0: please re-install it
Error : unable to load R code in package ‘Rcpp’
ERROR: lazy loading failed for package ‘Rcpp’
I installed shiny according https://github.com/rstudio/shiny-server/wiki/Ubuntu-step-by-step-install-instructions
and got the same error at the step
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
Warning messages:
1: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘Rcpp’ had non-zero exit status
2: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘httpuv’ had non-zero exit status
3: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘shiny’ had non-zero exit status
I tried the answer by Richard Lee by starting R
R
and got the error
Warning in install.packages("shiny") :
'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to use a personal library instead? (y/n) n
Error in install.packages("shiny") : unable to install packages
obviously no write permission, so
sudo R
Now I tried again
install.packages("shiny")
and got a number of errors
Error : package ‘codetools’ was built before R 3.0.0: please re-install it
Error : package ‘RJSONIO’ was built before R 3.0.0: please re-install it
Error : package ‘caTools’ was built before R 3.0.0: please re-install it
Error : package ‘bitops’ was built before R 3.0.0: please re-install it
Error : package ‘digest’ was built before R 3.0.0: please re-install it
Error : package ‘xtable’ was built before R 3.0.0: please re-install it
Each time I got an error, I re-installed the requested package
install.packages("codetools")
install.packages("RJSONIO")
etc.
and eventually, I was able to install Rccp, httpuv, and even shiny.
Now it works!!
Also see
Shiny package installation on R version 3.0.2 "Frisbee Sailing"
I am using rkward on precise
I had a similar error using rkward. Specifically this one:
'lib = "/usr/local/lib/R/site-library"' is not writable
I temporarily changed the permissions for this directory so that rkward could run this from its console:
update.packages(checkBuilt = TRUE, ask = FALSE)
all to fix this:
Error: package '' was build before 3.0.0: please-re-install it
so that (sigh...) I could fix 'default' configuration for audio on precise. I couldn't use play() etc. in rkward.
That just needed phonon-backend-gtstreamer
I tried to install swirl on R(v3.1.0) on ubuntu 12.04LTS:
sudo R
install.packages("swirl")
But faced a similar error:
Error : package ‘codetools’ was built before R 3.0.0: please re-install it
Error : unable to load R code in package ‘httr’
ERROR: lazy loading failed for package ‘httr’
* removing ‘/usr/local/lib/R/site-library/httr’
ERROR: dependencies ‘testthat’, ‘httr’ are not available for package ‘swirl’
* removing ‘/usr/local/lib/R/site-library/swirl’
Doing following helped me:
install.packages('codetools')
install.packages("swirl")
library("swirl")
swirl()
| Welcome to swirl! Please sign in. If you've been here before, use the same
| name as you did then. If you are new, call yourself something unique.
What shall I call you?
I hope the same may help fix your installation issue.
Here is the work-around that I used:
I installed the latest version of R on an internet-capable computer. I then loaded the my required packages (Packages->install packages->select mirror->select package...
After R is finished installing, it displays a message of where the temporary .zip package is located. I navigated to this location, grabbed the temp package, and burnt it to a cd.
In this way, I could get the newer package build onto a computer without internet access. I would still be interested to know if there is an easy way to rebuild a package downloaded on an early R version to make it compatible with the latest version (without needed an internet connection).
Thanks for pointing me in the right direction #JoshuaUlrich