I am attempting (repeatedly) to load BiodiversityR, which automatically loads Rcmdr. BiodiversityR loads fine, according to my Rstudio window, but when it attempts to load Rcmdr, it gives me the following error message:
Loading required package: Rcmdr
Error : .onAttach failed in attachNamespace() for 'Rcmdr', details:
call: data(dune)
error: object 'dune' not found
Error: package 'Rcmdr' could not be loaded
I am working on a MacBook, using OSX 10.6.8. I have tried uninstalling and re-installing Rcmdr and RcmdrMisc, loading a bunch of Rcmdr plug-ins, and updating all installed packages that BiodiversityR and Rcmdr rely on (including vegan), to no avail. I've also restarted R, tried using R instead of Rstudio, etc. Any help on this is much appreciated.
Cecilia Hennessy LaBonte
Purdue University
I was facing the same problem, and here's how I finally managed to install Rcmdr on my mac (R 3.5.1):
1 -
install.packages("data.table", type = "source",
repos = "http://Rdatatable.github.io/data.table")
library('data.table')
install.packages('car')
library('car')
2 - Install: https://www.xquartz.org/ (XQuartz-2.7.11.dmg)
3 - Logout & login again. (or restart your Mac), and:
install.packages('Rcmdr')
4 - Confirm installation of the missing packages that will be asked to install.
5 - Launch it:
library('Rcmdr')
I hope it can help!
Related
I've successfully installed rstan, but when I try to attach it with library(rstan) I get a pop-up window with the title "RGui (64-bit): Rgui.exe - Entry Point Not Found" and the message content
The procedure entry point EXTPTR_PTR could not be located in the dynamic link library C:\Users\MyName\Documents\R\win-library\4.0\Rcpp\libs\x64\Rcpp.dll.
In the R console itself I get
> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
Error: package or namespace load failed for ‘rstan’ in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'C:/Users/Daniel/Documents/R/win-library/4.0/Rcpp/libs/x64/Rcpp.dll':
LoadLibrary failure: The specified procedure could not be found.
I'm running 4.0.0 (2020-04-24) 'Arbor Day', on a 64 bit Windows machine with Windows 10.
I thought this might have been an issue with Rtools (Rtools 4.0 not found during package installation), but having reinstalled rtools40 and properly added it to my path - and then reinstalling all of my packages to make sure there were no dependency issues - the problem with rstan persists. Any idea what might be going wrong here, and how I can get rstan working?
Quick ones:
Did you build it yourself from source, or did you install binaries?
You should probably upgrade to R 4.0.2 as there were known issues with 4.0.0 and 4.0.1.
There is no issue with Rcpp per se; it builds on Windows as it should (see CRAN check pages).
But we did have numerous reports on the issue in 2. So please upgrade R to 4.0.2 and try that.
We need to updata R. In your script does the following:
First install the package
install.packages("installr")
Then:
library(installr)
updateR()
After that we install the last R update.
This help me to fix the error of Can't load the library in Windows - EXTPTR_PTR could not be located in the dynamic library
I needed to install the R package quadprog, which only works for R with version 3.6.0. So I installed R (3.6.0 version), and open it with RStudio. But now I failed to load any libraries, even after I installed the packages successfully using install.packages("package_name"). Specifically, the libraries I need to load are caret, forecast and ggplot2. I tried re-installing R but it still does not work. The error message I get is
Error: package or namespace load failed for ‘forecast’ in
dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so,
6): Symbol not found: ___cxa_uncaught_exceptions Referenced from:
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
Expected in: /usr/lib/libc++abi.dylib in
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
After installing Rcpp package successfully with install.packages("Rcpp") , I still got the message above when I tried library(Rcpp). So I am completely stumbled here...(before upgrades, everything works fine except I cannot install quadprog, so cannot install forecast package as well). Can anyone please help me fix this issue?
Please see below the images showing that the packages are stored in the same directory path of the R.
I read that you need to recompile your old packages after upgrading to newer version of R. Run the following line in your R terminal
update.packages(ask=FALSE,
checkBuilt=TRUE,
repos="https://cloud.r-project.org")
Then
install.packages(c("Rcpp", "caret", "forecast", "ggplot2", "quadprog"),
dependencies=TRUE,
repos="https://cloud.r-project.org")
Had similar issue, restart R session and install Rcpp from source
install.packages("Rcpp", type="source")
then load the library
library(Rcpp)
if still getting the error, restart R session and try loading library again.
I ended up by getting and then google searching the exact error code :). I fixed it by installing the latest version of R from CRAN along with the latest version of Rstudio. What I think happened was that when I updated some packages R and Rstudio were out of sync.
I am trying to install the forecast package which depends on uroot, which apparently have been written to require a GPU?
install.packages("uroot") yields the following error. Has anyone found this issue and may suggest a work around? I am using ubuntu 16.04.
I have the file in question located here: /usr/local/cuda-8.0/ and I added to my path export PATH=/usr/local/cuda-8.0/:$PATH
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/rstudio2/R/x86_64-pc-linux-gnu-library/3.2/uroot/libs/uroot.so':
libcudart.so.8.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/rstudio2/R/x86_64-pc-linux-gnu-library/3.2/uroot’
Warning in install.packages :
installation of package ‘uroot’ had non-zero exit status
Just in case this is useful for someone, I stumbled with the same problem trying to install "imputeTS" with R version 3.5.1 on Fedora 27 with CUDA 10.0 correctly installed an setted in PATH.
for me it just happened that I was running install.package("imputeTS") (which depends on forecast) in a R console as root, installing the packages to the user home solved the problem. It's seems that the libraries are searched in different places according to the user running the script, it's important to note that.
I just migrated to Linux. On an Ubuntu 18.04 setup, using install.packages with dependencies set to TRUE succeeded with no complaints. (No GPU on mu box.)
install.packages("forecast", dep=TRUE)
# there are quite a few dependencies and you happened to be missing one
packageDescription()
#-----------includes this line----------
Imports: colorspace, fracdiff, ggplot2 (>= 2.2.1), graphics, lmtest,
magrittr, nnet, parallel, Rcpp (>= 0.11.0), stats,
timeDate, tseries, urca, uroot, zoo
You can try to modify file "/etc/rstudio/rserver.conf", add "LD_LIBRARY_PATH" env, like:
rsession-ld-library-path=/usr/local/cuda/lib64
Actually, When you open session of "RStudio Server" from browser, the session does't get env from the ".bashrc".
I am running OSX 10.10, R-Studio Version 0.99.484, and R version 3.2.2.
I just made a fresh install of R and R-Studio using the installers from their respective websites. I use install.packages to install "mosaic" and then I try loading it using library, but it gives me the following error:
library("mosaic", lib.loc="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
Error : object ‘dendro_data.hclust’ is not exported by 'namespace:ggdendro'
Error: package or namespace load failed for ‘mosaic’
I tried reinstalling ggdendro but nothing. Does anyone have any advice on how to deal with this issue?
I encountered this same error and seem to have somewhere along the way resolved it. Steps taken include:
cleaned out my libraries (local and System)
used Disk Utility to repair any odd permissions
reinstalled R
opened RStudio and imported package with dependencies from the repository:
> install.packages("mosaic", lib="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
console prompted me to choose the older precompiled package or the newer, I chose older
Do you want to install from sources the package which needs compilation?
y/n: n
mosaic loaded happily
> library("mosaic", lib.loc="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
I am trying to install the package "rjags" in R but am running into the following error:
Loading required package: rjags
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so, 10): Symbol not found: __ZN5RangeC1ERKSt6vectorIiSaIiEES4_
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so
Expected in: /usr/local/lib/libjags.3.dylib
in /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so
Error: package ‘rjags’ could not be loaded
I've installed JAGS on my Mac (running Mavericks), and I am running R-3.1.2. I've tried installing from the url using the devtools package, as recommended by this site:
install_url("http://sourceforge.net/projects/mcmc-jags/files/rjags/3/rjags_3-2.tar.gz",
args="--configure-args='--with-jags-include=/Users/casallas/homebrew/opt/jags/include/JAGS
--with-jags-lib=/Users/casallas/homebrew/opt/jags/lib'
"
)
I've also gone through the instructions on this other site , trying the different versions of JAGS and receive the same error. I'm at a loss for what to try next and am sure the solution is simple. Does anyone have any insights? Thanks so much!
I found that while I was unable to install rjags from the url, if I installed the package from source on my computer I was successful. I did this by downloading the appropriate package from here (which for me was rjags_3-14.tgz) and ran the following command:
install.packages(path_to_file, repos = NULL, type="source")
The error:
Symbol not found: __ZN5RangeC1ERKSt6vectorIiSaIiEES4_
Is (nearly) always caused by a mismatch between standard libraries between the Mavericks build of R (actually rjags) and Snow Leopard build of JAGS (or vice versa). For more info see the instructions at https://sourceforge.net/projects/mcmc-jags/files/JAGS/3.x/Mac%20OS%20X/
I'm guessing that compiling the package yourself from source worked because it matched the version of the standard library that JAGS is using, but this will no longer match the version that R is using (although I'm not sure if this is a major problem, it is not recommended). You would be better to match the builds of R and JAGS and use the pre-built rjags library from CRAN.
It is interesting that you say you have tried both builds of JAGS but I suggest trying again along these lines:
1) Use .Platform$pkgType in R to confirm if it you are using mac.binary (SL) or mac.binary.mavericks (Mavericks) - or failing that re-install the Mavericks binary of R from CRAN
2) Exit R
3) Re-install the appropriate version of JAGS
4) Re-open R and re-install the rjags library from CRAN
5) Try library(rjags)
If this doesn't work can you provide more information so I can try and track down a possible problem with the JAGS builds?
Thanks,
Matt