How can I install the ridge package in R without getting the following undefined symbol error?
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘ridge’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/qwr/R/x86_64-pc-linux-gnu-library/3.4/ridge/libs/ridge.so':
/home/qwr/R/x86_64-pc-linux-gnu-library/3.4/ridge/libs/ridge.so: undefined symbol: regression_wrapper_function
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/qwr/R/x86_64-pc-linux-gnu-library/3.4/ridge’
The downloaded source packages are in
‘/tmp/Rtmp5AEXdl/downloaded_packages’
Warning message:
In install.packages("ridge") :
installation of package ‘ridge’ had non-zero exit status
Looking at the installation message, I see GSL (GNU Scientific Library) must be installed:
* installing *source* package ‘ridge’ ...
** package ‘ridge’ successfully unpacked and MD5 sums checked
checking for gsl-config... no
configure: WARNING: gsl-config not found, is GSL installed?
configure: WARNING: ridge will be installed but some functions will be unavailable
configure: creating ./config.status
Install (on Ubuntu 18.04) with sudo apt install libgsl-dev
Related
When i install gdalcubes on ubuntu 20.04 with R, i have this error :
installing to /home/obstetar/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-gdalcubes/00new/gdalcubes/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
munmap_chunk(): invalid pointer
Aborted (core dumped)
ERROR: loading failed
removing ‘/home/obstetar/R/x86_64-pc-linux-gnu-library/4.1/gdalcubes’
Warning in install.packages :
installation of package ‘gdalcubes’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp6dZFPa/downloaded_packages’
To install another package that depends on vroom (which failed) on a HPC node, I sought to install vroom manually.
I tried to install the package manually but it fails too:
My code:
install.packages("vroom")
error message:
installing to /home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-vroom/00new/vroom/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘vroom’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-vroom/00new/vroom/libs/vroom.so':
/home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-vroom/00new/vroom/libs/vroom.so: undefined symbol: __cxa_init_primary_exception
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/vroom’
Warning in install.packages :
installation of package ‘vroom’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpgPcp9Y/downloaded_packages’
I have tried under different R versions (3.5.3 up to 4.1.1) but keep having the same issue no matter what version I chose.
I have also deleted any 00LOCK-"package-name" folder that might have arisen in the process in the corresponding R Version package folder, but to no avail.
Can anybody help me out here?
Many thanks in advance,
Philibertus88
I have tried installing the rtracklayer package using Bioconductor on R 4.0.2 and CentOS 7 without success. This is the error that I get:
installing to ~/bin/R/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '~/bin/R/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/rtracklayer.so':
~/bin/R/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/rtracklayer.so: undefined symbol: CRYPTO_set_locking_callback
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘~/bin/R/lib64/R/library/rtracklayer’
The downloaded source packages are in
‘/tmp/Rtmpet2cyn/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
installation of package ‘rtracklayer’ had non-zero exit status
I haven't been able to fix this. Note: I've changed the absolute address of my home folder to "~"
I get the following trying to install gpclib package in R 3.6.2:
Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘gpclib’
These will not be installed
I have already installed Rtools.
I tried with the code:
install.packages("gpclib")
Trying with
install.packages("gpclib", type="source")
the message is:
installing *source package 'gpclib' ...
** package 'gpclib' successfully unpacked and MD5 sums checked **
using staged installation ** libs *** arch - i386 Warning in system(cmd) :
'make' not found ERROR: compilation failed for package 'gpclib' *
removing 'C:/Users/Juan/Documents/R/win-library/3.6/gpclib'
Warning message: In install.packages("gpclib", type = "source") :
installation of package ‘gpclib’ had non-zero exit status*
I am trying to build a package which has the namespace files as follows:
exportPattern("^[[:alpha:]]+")
importFrom(rClr, clrLoadAssembly)
rClr is installed in my system.
I build my package using devtools::build and it successfully builds.
When I install the package using the following command install.packages("C:/Package/Utils_0.1.0.tar.gz", repos = NULL, type = "source")
I get the following error:
* installing *source* package 'Utils' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error : .onLoad failed in loadNamespace() for 'rClr', details:
call: fun(libname, pkgname)
error: 'msvcr120.dll' was not found on this Windows system.
You are probably missing the Visual C++ Redistributable for Visual Studio 2013.
Check instructions at https://r2clr.codeplex.com/wikipage?title=Installing%20R%20packages&referringTitle=Documentation
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/S.Bista/Documents/R/R-3.3.2/library/Utils'
* restoring previous 'C:/Users/S.Bista/Documents/R/R-3.3.2/library/Utils'
Warning in install.packages :
running command '"C:/Users/S~1.BIS/DOCUME~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\S.Bista\Documents\R\R-3.3.2\library" "C:/Package/Utils_0.1.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Package/Utils_0.1.0.tar.gz’ had non-zero exit status
Loading fails for i386 but I have x64 system.