we are trying to load the edgeR and Glimma packages on a Mac OS version 11.0. We have installed and loaded other packages successfully from Bioconductor including limma. It appears that the install of both was successful, but when trying to load the packages we get the following error messages:
library(edgeR)
Error: package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so, 6): Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
Referenced from: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so (which was built for Mac OS X 13.0)
Expected in: /usr/lib/libc++.1.dylib
> library(Glimma)
Error: package or namespace load failed for ‘Glimma’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/DESeq2/libs/DESeq2.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/DESeq2/libs/DESeq2.so, 6): Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
Referenced from: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/DESeq2/libs/DESeq2.so (which was built for Mac OS X 13.0)
Expected in: /usr/lib/libc++.1.dylib
The RStudio version is 2022.12.0+353
The macOS is 11.2.2 BigSur
Related
Until yesterday, I could run library(car) just fine. But after running yay -Syyu and upgrading as many packages as I can, this no longer works.
> library(car)
Loading required package: carData
Error: package or namespace load failed for ‘car’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/my-name/R/x86_64-pc-linux-gnu-library/4.0/stringi/libs/stringi.so':
libicui18n.so.68: cannot open shared object file: No such file or directory
I am running this on Arch Linux.
We can install the 'stringi' package
install.packages('stringi')
I installed the xlsx package in R, but when I tried to load the library I got the following message:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
The Mac is version 10.14.1 Mojave. R is version 3.5.1. Java version is 1.8.0_73. Java and Mac are both 64 bits as I saw that as an issue with other question submissions. Is this a problem related to the newest macOS Mojave?
I am trying to install the ROracle library but I get this error:
Error: package or namespace load failed for ‘ROracle’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ROracle/libs/ROracle.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ROracle/libs/ROracle.so, 6): Symbol not found: _OCIArrayDescriptorAlloc
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ROracle/libs/ROracle.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ROracle/libs/ROracle.so
I tried to follow different approach like this but nevertheless I can't fix it.
I am using macOS Sierra 10.12.6 and R version 3.5.1.
I am attempting to install R 'sf' on a Centos machine. After extended problems with gdal (now fixed by building from source), I now get:
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/my_user_name/R/x86_64-redhat-linux-gnu-
library/3.4/sf/libs/sf.so':
/home/my_user_name/R/x86_64-redhat-linux-gnu-library/3.4/sf/libs/sf.so:
undefined symbol: ZN15OGRMultiSurface18CastToMultiPolygonEPS
How can I resolve this error?
So, this problem was apparently caused by my manual install of gdal not correctly linking to geos.
So I just reinstalled gdal following these instructions (https://trac.osgeo.org/gdal/wiki/BuildingOnUnix) with --with-geos=yes as a flag to ./configure.
This solved the problem.
I'm trying to install an R package called ChemoSpec and am receiving the following error:
Error : .onLoad failed in loadNamespace() for 'rgl', details: call:
dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared
object
'/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgl/libs/rgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgl/libs/rgl.so,
6): Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgl/libs/rgl.so
Reason: image not found Error: package or namespace load failed for
‘ChemoSpec’
I'm running R version 3.3 using R Studio on OS X 10.10.5
Any help would be great! Thanks.
The problem is almost certainly that you do not have X11 installed. This in turn prevents rgl from installing, and in turn, ChemoSpec. Macs used to ship with X11 installed, but since OSX 10.6 they have not (info). You can install X11 from here. After that, try:
install.packages("rgl")
and if that is successful, do:
install.packages("ChemoSpec")
and you should be ready to go.