Loading required package: xml2
Loading required package: rJava
Loading required package: methods
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: #rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/r Java.so
Reason: image not found
Error: package ‘rJava’ could not be loaded
Execution halted
I'm getting this error a day after I installed version 3.4 of R. I tried solutions from other pages but it didn't work. I can't run R scripts through the terminal but I run scripts on RStudio. I'm thinking that it might be a problem with paths, but I just wanted to double check here and confirm instead of getting myself into a deeper mess.
Related
I have installed XLConnect package though my R studio. When I try to load the library I get the following error
> library(XLConnect)
Loading required package: XLConnectJars
Error: package or namespace load failed for ‘XLConnectJars’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: #rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
Reason: image not found
Error: package ‘XLConnectJars’ could not be loaded
I checked the /Library/Frameworks/R.framework/Versions/3.4/Resources/library folder and I am noticed all three mentioned libraries(XLConnect, XLConnectJars, rJava) already present.
I have problem with installing R package XVector.
I've tried to install it using biocLite:
Error: package or namespace load failed for ‘XVector’ in
dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object
'/home/fedorovaad/R/XVector/libs/XVector.so':
/home/fedorovaad/R/XVector/libs/XVector.so: undefined symbol:egzrewind
Error: loading failed
Execution halted
ERROR: loading failed
Also I used R CMD INSTALL XVector_0.16.0.tar.gz (the same error).
Besides I remove old version of Xvector (the same error...)
How can I fix it?
When I try to install the bioconductor workflow 'highthroughputassays' as follows (and as described here):
> source("http://bioconductor.org/workflows.R")
> workflowInstall("highthroughputassays")
It installs a lot of dependent packages, but just before ending the installation it gives the following errors:
No man pages found in package ‘highthroughputassays’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'rgl', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so':
dlopen(/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
Referenced from: /Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/johansenkh/Library/R/3.3/library/highthroughputassays’
Warning in install.packages :
installation of package ‘highthroughputassays’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/hb/sc3x6vtj0ys009qnyplbp2_h1g5hgm/T/RtmpDkWkRH/downloaded_packages’
Because of those errors, the workflow does not load;
library(flowStats)
gives a similar error after installing packages as described above.
I have tried it on 3 different Mac computers (all with the newest OS X, but one of them had the 3.3.1 version of R (The newest version is 3.3.2))
When trying library(rgl) I get the following error:
Error : .onLoad failed in loadNamespace() for 'rgl', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so':
dlopen(/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
Referenced from: /Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so
Reason: image not found
Error: package or namespace load failed for ‘rgl’
I solved the problem as follows:
The problem was with loading 'rgl'.
By installing XQUARTZ (www.XQUARTZ.com) followed by restarting OS X (Log out and log in) the rgl-package worked. Thereafter the workflow installed as indicated above.
I just recently updated my Rstudio to the 0.98.1103 release and now I'm unable to load ggplot it keeps throwing the following error. Any ideas what is going on?
> library(ggplot2)
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /usr/X11/lib/libXft.2.dylib
Referenced from: /usr/local/lib/libtk8.6.dylib
Reason: image not found
Error: package or namespace load failed for ‘ggplot2
I tried removing the tcltk library and ggplot2 and reinstalling them now I'm getting a different set of errors:
> library(ggplot2)
Error : package ‘tcltk’ does not have a namespace
Error: package or namespace load failed for ‘ggplot2’
> library(tcltk)
Error in library(tcltk) : ‘tcltk’ is not a valid installed package
Seems like X11 is not installed on your system. Try installing xorg (if you're running Linux) or XQuartz if you're on OSX.
I'm using R 3.0.2 and RStudio 0.98.945 for Mac.
Loading 'ks' package gives this error message.
Loading required package: rgl
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/3.0/Resources/library/rgl/libs/rgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/rgl/libs/r gl.so, 6): Library not loaded: /usr/X11/lib/libGLU.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/rgl/libs/rgl.so
Reason: image not found
Error: package ‘rgl’ could not be loaded
Loading 'rgl' package gives the same error message.
How can I solve this?