I have spent hours trying to think of a ways to install some packages in R that just refuse to load. I have tried uninstalling and installing again, downloading from URL etc etc. but nothing seems to work. Please help me before I give up on teach entirely
{
library(psych)
Error: package or namespace load failed for ‘psych’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/alan/Library/R/3.5/library/lattice/libs/lattice.so':
dlopen(/Users/alan/Library/R/3.5/library/lattice/libs/lattice.so, 6): Library not loaded: #rpath/R/lib/libR.dylib
Referenced from: /Users/alan/Library/R/3.5/library/lattice/libs/lattice.so
Reason: Incompatible library version: lattice.so requires version 3.5.0 or later, but libR.dylib provides version 3.1.0
I had a previous version of R installed so found the directory a directory full of libraries that must have been clashing. I just deleted the whole folder and went from scratch
Related
I've been having some issues getting R to run properly on the shared cluster at my institution , where i don't have root access. Some things will work but it gets tricky when i need to install packages etc. The current issue i'm trying to trouble shoot is the following error when trying to load the caret package:
Loading required package: lattice
Loading required package: ggplot2
Error: package or namespace load failed for ‘ggplot2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/cifs/hariri-long/Scripts/Tools/R/packages/rlang/libs/rlang.so':
/cifs/hariri-long/Scripts/Tools/R/packages/rlang/libs/rlang.so: undefined symbol: R_removeVarFromFrame
Error: package ‘ggplot2’ could not be loaded
Execution halted
I found this page suggesting i install rlang as follows:
> install.packages("rlang",type="source")
Installing package into ‘/cifs/hariri-long/Scripts/Tools/R/packages’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/usr/share/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.13/library ./tcl8.5.13/library
but i get the above tcl error. since i've seen this in other threads:
> capabilities("tcltk")
tcltk
TRUE
it looks like tcl on my system is 8.6, but i don't know how to tell R to look for that version.
$ whereis tcl
tcl: /usr/lib64/tcl8.6 /usr/include/tcl.h /usr/share/tcl8.6
$ which R
/opt/apps/rhel7/R-3.6.0/bin/R
Any ideas? The OS is CentOS 8. Thanks!
I ended up deciding to try using a more recent R version (4.1.1) to solve this issue. I was hesitant to do this at first because I have run into issues with availability / compatibility of packages I need in more recent R versions, but I wasn't getting anywhere troubleshooting this issue otherwise. I figured that since TCL 8.6 is what was installed on the system, a newer version of R might be able to work with it, and seems i was right, since I got past the first error I was having when I switched.
I did get a new error regarding an issue loading the shared library Libtk8.6.so. So I downloaded the .so file from here and unpacked it to my home directory using rpm2cpio (i don't have root access so i can't just use yum install etc). After that i just had to re-install all my packages for the new R version and it worked!
I am installing emojifont package. The package installs properly however when I try to call it through the library function I get the following error
Error: package or namespace load failed for ‘emojifont’:
.onLoad failed in loadNamespace() for 'sysfonts', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so, 6): Library not loaded: /opt/X11/lib/libfreetype.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so
Reason: image not found
What ended up working for me was installing XQuartz. I had this problem with both emojifont and sysfonts until I installed XQuartz and then both loaded without problems. I can't tell you much about what XQuartz is doing but it seems to be needed for the compatibility between MacOS and these packages.
Other people with this problem seemed to be having issues with their sysfonts install (like it needed to be updated, etc.) but that didn't work for me, instead I got an error when using trying to load both the sysfonts and the emojifont package. If you look at this line in the error "Library not loaded: /opt/X11/lib/libfreetype.6.dylib", that seems to be missing in the error message of people with only the sysfonts problem.
Hope this saves someone the 2 hours I just spent searching!
Installed RStudio using Anaconda Navigator even though I already had RStudio and it was working fine before. The package 'imager' didn't load so I removed the application from Navigator and completely uninstall R and RStudio from my Macbook and reinstalled R and the application through Navigator, but that didn't fix things. Other packages install just fine. The following is the error message:
library(imager)
Error: package or namespace load failed for ‘imager’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/omeedkashef/Library/R/3.4/library/imager/libs/imager.so':
dlopen(/Users/omeedkashef/Library/R/3.4/library/imager/libs/imager.so, 6): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Users/omeedkashef/Library/R/3.4/library/imager/libs/imager.so
Reason: image not found
I had this same problem. I did not have a problem installing imager from CRAN but did get an error message when trying to load the CRAN-installed package. When I tried installing from GitHub I got the more useful error message saying that X11 was not found (same as #andrii above). I solved all issues by installing X11 by downloading from this site: https://www.xquartz.org/
EDIT: I should mention that this is not a problem with RStudio per se, as the header of the question suggests, but rather just a dependency issue of one package (imager) on a not-explicitly R piece of sofware (X11).
I upgraded my R version today from 3.1 to 3.2. In doing so, I kept a copy of my original libraries in a separate folder. After installing version 3.2, I pasted the libraries in the libraries folder of R 3.2.
After doing so, I upgraded Bioconductor, and updated all its packages.
However, when I try to load some (not all) bioconductor packages right now in R, I get the following error:
library(ballgown)
Error : .onLoad failed in loadNamespace() for 'XML', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/user/Library/R/3.2/library/XML/libs/XML.so':
dlopen(/Users/user/Library/R/3.2/library/XML/libs/XML.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib
Referenced from: /Users/user/Library/R/3.2/library/XML/libs/XML.so
Reason: image not found
Error: package or namespace load failed for ‘ballgown’
It looks like he's still looking for something in the older 3.1 version, but I deleted that folder.
Here is my library path in R:
.libPaths()
[1] "/Users/user/Library/R/3.2/library"
[2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"
Remarkably, when loading the same packages in RStudio, the error does not pop up. How can I still fix this?
Thanks.
I recently updated my R (on Mac) from Version 3.0.2 to 3.1.1. I tried to load a package by using library(WRScpp)
But I got an error as shown below:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/WRScpp/libs/WRScpp.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/WRScpp/libs/WRScpp.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libRlapack.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/WRScpp/libs/WRScpp.so
Reason: image not found
Error: package or namespace load failed for ‘WRScpp’
It seems that R tried to load libRlapack.dylib by looking for it in the wrong directory (it looked for it in the Version 3.0 directory). I wonder what can be done to direct R to search the correct directory?