I am trying to install Deseq2, however I get this error. The same appears for all other packages I try to install with BiocLite...I wonder what is the problem? I installed R and rstudio with anaconda on my ubuntu 16.04. R version 3.3.2. Any help is much appreciated.
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/dani/anaconda2/lib/R/library/tidyr/libs/tidyr.so':
/home/dani/anaconda2/lib/R/library/tidyr/libs/tidyr.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1ERKS4_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/dani/anaconda2/lib/R/library/tidyr’
* restoring previous ‘/home/danianaconda2/lib/R/library/tidyr’
does it has something to do with this error at the beginning?
Makevars:21: Makevars.local: No such file or directory
touch: "Makevars.local"
I know this is not the best solution: I was using anaconda version 4.3.1 and I changed it to 4.1.1 and reinstalled all using this version, R remained always v 3.3.2. So I don't know if there is a bug or some incompatibility problem with Rcpp package or else in the last version of conda.
Related
I installed tidyverse in R Studio, but I'm having a problem running it.
I ran library("tidyverse") but I keep getting an error.
error: package or namespace load failed for ‘tidyverse’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so, 6): Symbol not found: _EXTPTR_PTR
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
Expected in: /Library/Frameworks/R.framework/Resources/lib/libR.dylib
in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
In addition: Warning message:
package ‘tidyverse’ was built under R version 4.0.2
I also tried uninstalling and reinstalling but that didn't seem to work.
We answered that a few times. It is an unfortunate error in R 4.0.0 and R 4.0.1 which changed a minor detail about EXTPTR_PTR.
Upgrade to R 4.0.2 and the issue will go away.
The error is also encountered in installing Rcpp package and it is seems can be solved by upgrading the R version to 4.02.
I'm trying to install the Homals package - library(homals), but keep getting this error message:
library(homals)
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
‘homals’
I have a couple of my colleagues to run the same code, the same thing happens. I have re-install R studio to the newest version.
install.packages("rgl")
install.packages("homals")
library(homals)
Any solutions for this? thank you.
I was able to successfully install on both Windows and Mac. I believe the root cause here is that you have R version 3.3 installed when you require at least v3.5.3 as per below:
library(homals)
Warning message:
package ‘homals’ was built under R version 3.5.3
I've got a server running RStudio, and recently another user updated what version of gcc was on it for another project. I attempted to install Rcpp, and get the following error:
Error: package or namespace load failed for ‘Rcpp’ in dyn.load(file,
DLLpath = DLLpath, ...): unable to load shared object
'/home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so':
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by
/home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so)
Error: loading failed Execution halted ERROR: loading failed
Oddly, this doesn't occur when using R from the command line, which makes me think that RStudio Server is having trouble finding GLIBCXX_3.4.20, rather than it being genuinely missing.
Does anyone know how to sort this error out?
After updating to the latest version of Rstudio (R version 3.4.1 (2017-06-30) -- "Single Candle") I cannot seem to get the XLConnect Package to load. This is the error message I get:
> 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
R also throws a similar error message when I try to load the rJava package as well. I have tried uninstalling both Java and R and have scoured SO for answers, but nothing seems to work.
I am running macOS Sierra (10.12.6)
Would anyone be willing to offer any help?
The error suggests that there is an issue loading rJava. Try updating the Java configuration variables via R CMD javareconf or sudo R CMD javareconf.
I installed the R caret package using install.packages command and did library(caret). I am recieving the following error
>library(caret)
Loading required package: lattice
Loading required package: 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/local/lib/libtcl8.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
Error: package or namespace load failed for ‘caret’
I searched other posts and also installed OSX tcltk package from http://cran.us.r-project.org/bin/macosx/tools/ but it still does not seem to work. I also installed tcltk2 package from R but still does not work.. Kindly help
I have met the same problem with the same error message but unfortunately, just reinstalling R1.3 didn't solve the problem for me.
To solve it, I had to install X-Quartz as explained here in the "Mac OS X Trouble-shooting" section and the problems related to tcltk.
Do this and it will resolve the problem
install.packages("quantreg")
What version of R are you using? Do you use Mavericks? You may need to update to a version which includes Mavericks updates.
http://cran.r-project.org/bin/macosx/
I had the same issue. Reinstalling Quartz solved the issue
Try this, worked for me.
install.packages("caret", dependencies = T)
Once that is done, run
install.packages("pbkrtest", dependencies = T)