Trying to install rgdal package in R 3.3.0 on Ubuntu 16.04 using install.packages("rgdal") and getting the following error:
In file included from
/usr/local/lib/R/site-library/sp/include/sp.h:13:0,
from rgdal.h:15,
from OGR_write.cpp:11: /usr/share/R/include/S.h:41:3: error: #error S.h can not be used from C++ code: use R.h instead #
error S.h can not be used from C++ code: use R.h instead
anyone else seen this and know how to fix it? Or do we need to wait for a fix to the rgdal package itself?
Wild guess: you could try to reinstall sp before, just to have any dependency up-to-date.
Related
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 updated R 3.4.4 to R 3.5.0 today. And my package cannot pass R CMD check anymore. It fails at checking whether package can be installed ... ERROR.
In another hand my package works, I can install it and use it as long as I don't check it.
The error is the following:
Error: package or namespace load failed for ‘sp’:
package ‘lattice’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Error : package ‘sp’ could not be loaded
I tried to reinstall lattice these ways:
sudo apt-get --reinstall install r-cran-lattice
or
remove.packages("lattice", lib="~/R/x86_64-pc-linux-gnu-library/3.5")
install.package("lattice")
The package lattice is installed correctly in both cases. But it does not solve my problem. Also I ensured to have a single version of lattice removing either the r-cran one or the self compiled version. Nothing works.
Edit By the way I can do library(sp) or library(lattice) it works. But not with R CMD check
The error message tells you that the binary you are attempting to install comes from an insufficient / incompatible R version.
Two fixes:
Install from source as you did. After that check with AP <- available.packages() that you really only have one.
Use the correct binarie: read this README at CRAN and switch to Michael's 'R 3.5' repos. Many of us have been doing that for weeks.
Lastly, the r-sig-debian list is a friendly place for these questions and more. Subscribe first so that you can post.
I am fairly new to R. I have tried to google my question, and tried a few things, to no avail.
I am working on a MAC * High Sierra version 10.13.5
I am working with R * R version 3.5.0 (2018-04-23) -- "Joy in Playing"
I am unable to install the package "gtools", and I don't know what to do to make it work??
install.packages("gtools", type="source")
Warning: unable to access index for repository https://mirrors.sorengard.com/cran/src/contrib:
cannot open URL 'https://mirrors.sorengard.com/cran/src/contrib/PACKAGES'
Warning message:
package ‘gtools’ is not available (for R version 3.5.0)
I have also tried to install from a file saved on my computer, but this did not work either
library(gtools)
Error: package or namespace load failed for ‘gtools’:
package ‘gtools’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
You could try specifying a specific repository, for example:
install.packages("gtools", repos="https://cran.rstudio.com/")
Why are you using install from source? typically to install a package u only need to use the command
install.packages("gtools")
Then it will automatically ask u for a mirror to download from. It seems like "gtools" is available for R 3.5, so try to download it from another mirror and it should work.
I am currently running R 3.4.4 through Rstudio on a windows system. I have a code that I ran successfully several months ago, but now it seems my gdalUtils is unable to connect with my rgdal install. Any function I call receives the following error:
Probably broken install of `gdal` at 'C:/PROGRA~2/GDAL/'
Error in as.Date.default(unlist(versions)) :
do not know how to convert `unlist(versions)` to class “`Date`”
I've tried searching for the gdal install within the rgdal package and get the same error. I've also tried uninstalling and reinstalling everything to no avail. Any advice would be appreciated!
A
I am trying to install the packages on R v3.2.4 from GitHub, and even after installing Rcpp I keep getting an error:
install_github("marmap","ericpante")
Skipping install of 'marmap' from a github remote, the SHA1 (3e62fc8d) has not changed since last install.
Use 'force = TRUE' to force installation
Warning message:
Username parameter is deprecated. Please use ericpante/marmap
Any idea of what the possible problem might be? Should I downgrade R to run it or there is a better option?
PS. running on OSX 10.12.1 (Sierra)
library(marmap)
Attaching package: 'marmap'
The following object is masked from 'package:grDevices':
as.raster