Hi gurus,
I attempted to install nlmixr package on Rstudio Cloud
These all went smoothly
############################################################
Install packages
############################################################
pip install --upgrade --user pip
pip install sympy --user
pip install numpy --user
pip install nose --user
pip install tornado --user
pip install pandas --user
library(reticulate)
use_python("/usr/bin/python")
import numpy and specify no automatic Python to R conversion
np <- import("numpy", convert = FALSE)
do some array manipulations with NumPy
a <- np$array(c(1:4))
sum <- a$cumsum()
convert to R explicitly at the end
py_to_r(sum)
install_github("nlmixrdevelopment/RxODE")
install_github("nlmixrdevelopment/SnakeCharmR")
library(RxODE)
demo("demo1","RxODE")
rxSymPyVersion()
rxTest(full = F) # run all of the unit tests
install.packages("Rcpp")
install.packages("RcppArmadillo")
library(Rcpp)
library(RcppArmadillo)
However, these final steps returned an error
library(devtools)
install_github("nlmixrdevelopment/nlmixr")
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/dparser/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/RxODE/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/StanHeaders/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/lbfgsb3c/include" -I/usr/local/include -g -Id -I../inst/include -DBOOST_DISABLE_ASSERTS -I""/opt/R/3.6.0/lib/R/bin/Rscript" -e 'cat(file.path(find.package("RcppArmadillo"),"include"))'" -fpic -g -O2 -c RcppExportMod.cpp -o RcppExportMod.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
make: *** [RcppExportMod.o] Error 4
/opt/R/3.6.0/lib/R/etc/Makeconf:176: recipe for target 'RcppExportMod.o' failed
ERROR: compilation failed for package ‘nlmixr’
- removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/nlmixr’
Error in i.p(...) :
(converted from warning) installation of package ‘/tmp/RtmpwzuhsB/file14002aa9ff6b/nlmixr_1.1.0-8.tar.gz’ had non-zero exit status
Any clue what needs to be done?
Much appreciated!
Tao