Hi Ben, thanks for your quick response. Unfortunately, this addition made no change. Any other thoughts?
As a side note, when is it expected that the updated package will be available from CRAN?
cheers
Hi Ben, thanks for your quick response. Unfortunately, this addition made no change. Any other thoughts?
As a side note, when is it expected that the updated package will be available from CRAN?
cheers
Hi Ben, tried another version of the compiler with rstan suggested (RStan Getting Started · stan-dev/rstan Wiki · GitHub).
It appears to download the development version of rstanarm with this installed (refer session_info()), but when I use help(package = “rstanarm”) to get the version it returns the Cran version. I also don’t have access to stan_surv.
I assume it has something to do with this error:
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
Which appears frequently throughout the download process.
I have remove chunks from the below pertaining to mver, lm, jm, binomial, count, due to space. I have attached the full output.rstanarm dev installation.txt (34.5 KB)
> remove.packages("rstan")
Removing package from ‘C:/Users/21307937/OneDrive/R Packages’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘rstan’
> remove.packages("rstanarm")
Removing package from ‘C:/Users/21307937/OneDrive/R Packages’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘rstanarm’
> if (file.exists(".RData")) file.remove(".RData")
> **# compiler from Rstan**
> dotR <- file.path(Sys.getenv("HOME"), ".R")
> if (!file.exists(dotR)) dir.create(dotR)
> M <- file.path(dotR, "Makevars.win")
> if (!file.exists(M)) file.create(M)
> cat("\nCXX14FLAGS=-O3 -march=corei7 -mtune=corei7",
+ "CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y",
+ "CXX11FLAGS=-O3 -march=corei7 -mtune=corei7",
+ file = M, sep = "\n", append = TRUE)
> # Install rstan
> # From suggestion online mc-discourse
> install.packages("rstan", type = "win.binary", dependencies = TRUE)
Installing package into ‘C:/Users/21307937/OneDrive/R Packages’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rstan_2.19.3.zip'
Content type 'application/zip' length 4734192 bytes (4.5 MB)
downloaded 4.5 MB
package ‘rstan’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\21307937\AppData\Local\Temp\RtmpIntU98\downloaded_packages
> install.packages( "https://win-builder.r-project.org/9256KcZ01L9C/StanHeaders_2.19.2.zip", repos = NULL, type = "win.binary")
Installing package into ‘C:/Users/21307937/OneDrive/R Packages’
(as ‘lib’ is unspecified)
trying URL 'https://win-builder.r-project.org/9256KcZ01L9C/StanHeaders_2.19.2.zip'
Content type 'application/x-zip-compressed' length 2260970 bytes (2.2 MB)
downloaded 2.2 MB
package ‘StanHeaders’ successfully unpacked and MD5 sums checked
> pkgbuild::has_build_tools(debug = TRUE)
[1] TRUE
> if (!require(devtools)) {
+ install.packages("devtools")
+ library(devtools)
+ }
Loading required package: devtools
Loading required package: usethis
> devtools::install_github("stan-dev/rstanarm", build_vignettes = FALSE)
Downloading GitHub repo stan-dev/rstanarm@master
stan-dev-rstanarm-8709540/tests/testthat/include: Can't create '\\\\?\\C:\\Users\\21307937\\AppData\\Local\\Temp\\RtmpIntU98\\remotes17ab47b414359\\stan-dev-rstanarm-8709540\\tests\\testthat\\include'
stan-dev-rstanarm-8709540/tests/testthat/stan_files: Can't create '\\\\?\\C:\\Users\\21307937\\AppData\\Local\\Temp\\RtmpIntU98\\remotes17ab47b414359\\stan-dev-rstanarm-8709540\\tests\\testthat\\stan_files'
tar.exe: Error exit delayed from previous errors.
√ checking for file 'C:\Users\21307937\AppData\Local\Temp\RtmpIntU98\remotes17ab47b414359\stan-dev-rstanarm-8709540/DESCRIPTION' (588ms)
- preparing 'rstanarm': (776ms)
√ checking DESCRIPTION meta-information ...
- cleaning src
- running 'cleanup.win' (606ms)
- checking for LF line-endings in source and make files and shell scripts (735ms)
- checking for empty or unneeded directories
- looking to see if a 'data/datalist' file should be added
- building 'rstanarm_2.19.3.tar.gz'
Warning: file 'rstanarm/cleanup' did not have execute permissions: corrected
Installing package into ‘C:/Users/21307937/OneDrive/R Packages’
(as ‘lib’ is unspecified)
* installing *source* package 'rstanarm' ...
** libs
*** arch - i386
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/continuous.stan
Wrote C++ file "stan_files/continuous.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/continuous.cc -o stan_files/continuous.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/polr.stan
Wrote C++ file "stan_files/polr.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/polr.cc -o stan_files/polr.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan
Wrote C++ file "stan_files/bernoulli.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/bernoulli.cc -o stan_files/bernoulli.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/count.stan
Wrote C++ file "stan_files/count.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/count.cc -o stan_files/count.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/binomial.stan
Wrote C++ file "stan_files/binomial.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/binomial.cc -o stan_files/binomial.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/mvmer.stan
Wrote C++ file "stan_files/mvmer.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/mvmer.cc -o stan_files/mvmer.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan
Wrote C++ file "stan_files/lm.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/lm.cc -o stan_files/lm.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/jm.stan
Wrote C++ file "stan_files/jm.cc"
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/jm.cc -o stan_files/jm.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c init.cpp -o init.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -shared -s -static-libgcc -o rstanarm.dll tmp.def stan_files/continuous.o stan_files/mvmer.o stan_files/polr.o stan_files/bernoulli.o stan_files/jm.o stan_files/count.o stan_files/binomial.o stan_files/lm.o init.o -LC:/Users/21307937/OneDrive/RPACKA~1/RCPPPA~1/lib/i386 -ltbb -ltbbmalloc -LC:/PROGRA~1/R/R-35~1.2/bin/i386 -lR
rm stan_files/jm.cc stan_files/binomial.cc stan_files/lm.cc stan_files/continuous.cc stan_files/bernoulli.cc stan_files/polr.cc stan_files/count.cc stan_files/mvmer.cc
installing to C:/Users/21307937/OneDrive/R Packages/rstanarm/libs/i386
*** arch - x64
"C:/PROGRA~1/R/R-35~1.2/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/continuous.stan
Wrote C++ file "stan_files/continuous.cc"
C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/continuous.cc -o stan_files/continuous.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/polr.stan
Wrote C++ file "stan_files/polr.cc"
C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/polr.cc -o stan_files/polr.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
"C:/PROGRA~1/R/R-35~1.2/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan
Wrote C++ file "stan_files/bernoulli.cc"
C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c stan_files/jm.cc -o stan_files/jm.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-35~1.2/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -I"C:/Users/21307937/OneDrive/R Packages/StanHeaders/include" -I"C:/Users/21307937/OneDrive/R Packages/rstan/include" -I"C:/Users/21307937/OneDrive/R Packages/BH/include" -I"C:/Users/21307937/OneDrive/R Packages/Rcpp/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppEigen/include" -I"C:/Users/21307937/OneDrive/R Packages/RcppParallel/include" -O3 -march=corei7 -mtune=corei7 -c init.cpp -o init.o
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'CxxFlags' not found
Calls: ::: -> get
Execution halted
C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -shared -s -static-libgcc -o rstanarm.dll tmp.def stan_files/continuous.o stan_files/mvmer.o stan_files/polr.o stan_files/bernoulli.o stan_files/jm.o stan_files/count.o stan_files/binomial.o stan_files/lm.o init.o -LC:/Users/21307937/OneDrive/RPACKA~1/RCPPPA~1/lib/x64 -ltbb -ltbbmalloc -LC:/PROGRA~1/R/R-35~1.2/bin/x64 -lR
rm stan_files/jm.cc stan_files/binomial.cc stan_files/lm.cc stan_files/continuous.cc stan_files/bernoulli.cc stan_files/polr.cc stan_files/count.cc stan_files/mvmer.cc
installing to C:/Users/21307937/OneDrive/R Packages/rstanarm/libs/x64
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'Rcpp' was built under R version 3.5.3
** help
No man pages found in package 'rstanarm'
*** installing help indices
converting help for package 'rstanarm'
finding HTML links ... done
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Warning: package 'Rcpp' was built under R version 3.5.3
*** arch - x64
Warning: package 'Rcpp' was built under R version 3.5.3
* DONE (rstanarm)
In R CMD INSTALL
Warning message:
In utils::untar(tarfile, ...) :
‘tar.exe -zxf "C:\Users\21307937\AppData\Local\Temp\RtmpIntU98\file17ab450f917cd.tar.gz" -C "C:/Users/21307937/AppData/Local/Temp/RtmpIntU98/remotes17ab47b414359"’ returned error code 1
library(rstanarm)
Loading required package: Rcpp
rstanarm (Version 2.19.3, packaged: 2020-04-18 00:23:44 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- bayesplot theme set to bayesplot::theme_default()
* Does not affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
Warning message:
package ‘Rcpp’ was built under R version 3.5.3
> help(package = "rstanarm")
# returns Documentation for package ‘rstanarm’ version 2.19.3
> ?stan_surv
No documentation for ‘stan_surv’ in specified packages and libraries:
you could try ‘??stan_surv’
session_info()
- Session info ---------------------------------------------------------------------------------------------------------------
setting value
version R version 3.5.2 (2018-12-20)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Australia.1252
ctype English_Australia.1252
tz Australia/Perth
date 2020-04-18
- Packages -------------------------------------------------------------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.5.3)
backports 1.1.4 2019-04-10 [1] CRAN (R 3.5.3)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.5.0)
bayesplot 1.7.1 2019-12-01 [1] CRAN (R 3.5.3)
boot 1.3-20 2017-08-06 [2] CRAN (R 3.5.2)
callr 3.4.3 2020-03-28 [1] CRAN (R 3.5.3)
cli 2.0.2 2020-02-28 [1] CRAN (R 3.5.3)
codetools 0.2-15 2016-10-05 [2] CRAN (R 3.5.2)
colorspace 1.4-0 2019-01-13 [1] CRAN (R 3.5.2)
colourpicker 1.0 2017-09-27 [1] CRAN (R 3.5.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1)
crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.5.1)
curl 3.3 2019-01-10 [1] CRAN (R 3.5.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.1)
devtools * 2.3.0 2020-04-10 [1] CRAN (R 3.5.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 3.5.3)
dplyr 0.8.4 2020-01-31 [1] CRAN (R 3.5.3)
DT 0.13 2020-03-23 [1] CRAN (R 3.5.3)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 3.5.3)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.5.3)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.5.2)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.5.3)
ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.5.3)
ggridges 0.5.1 2018-09-27 [1] CRAN (R 3.5.3)
glue 1.4.0 2020-04-03 [1] CRAN (R 3.5.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.1)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.0)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1)
htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.5.3)
httpuv 1.4.5.1 2018-12-18 [1] CRAN (R 3.5.2)
igraph 1.2.4 2019-02-13 [1] CRAN (R 3.5.3)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.5.3)
later 0.8.0 2019-02-11 [1] CRAN (R 3.5.2)
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.5.2)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.1)
lme4 1.1-21 2019-03-05 [1] CRAN (R 3.5.3)
loo 2.2.0 2019-12-19 [1] CRAN (R 3.5.3)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1)
markdown 0.9 2018-12-07 [1] CRAN (R 3.5.3)
MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.5.3)
Matrix 1.2-15 2018-11-01 [2] CRAN (R 3.5.2)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.5.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.1)
mime 0.6 2018-10-05 [1] CRAN (R 3.5.2)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 3.5.1)
minqa 1.2.4 2014-10-09 [1] CRAN (R 3.5.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1)
nlme 3.1-137 2018-04-07 [2] CRAN (R 3.5.2)
nloptr 1.2.1 2018-10-03 [1] CRAN (R 3.5.3)
packrat 0.5.0 2018-11-14 [1] CRAN (R 3.5.2)
pillar 1.4.3 2019-12-20 [1] CRAN (R 3.5.3)
pkgbuild 1.0.6.9000 2020-04-17 [1] Github (r-lib/pkgbuild@a475485)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.2)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.3)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.5.3)
promises 1.0.1 2018-04-13 [1] CRAN (R 3.5.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.2)
purrr 0.3.3 2019-10-18 [1] CRAN (R 3.5.3)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.5.2)
Rcpp * 1.0.1 2019-03-17 [1] CRAN (R 3.5.3)
remotes 2.1.1 2020-02-15 [1] CRAN (R 3.5.3)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.2)
rlang 0.4.5 2020-03-01 [1] CRAN (R 3.5.3)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1)
rsconnect 0.8.15 2019-07-22 [1] CRAN (R 3.5.3)
rstan 2.19.3 2020-02-11 [1] CRAN (R 3.5.3)
rstanarm * 2.19.3 2020-04-18 [1] Github (stan-dev/rstanarm@8709540)
rstantools 2.0.0 2019-09-15 [1] CRAN (R 3.5.3)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.5.3)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.3)
shiny 1.2.0 2018-11-02 [1] CRAN (R 3.5.2)
shinyjs 1.0 2018-01-08 [1] CRAN (R 3.5.1)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 3.5.3)
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 3.5.3)
StanHeaders 2.19.2 2019-09-07 [1] CRAN (R 3.6.3)
stringi 1.3.1 2019-02-13 [1] CRAN (R 3.5.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.2)
survival 2.43-3 2018-11-26 [2] CRAN (R 3.5.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 3.5.3)
threejs 0.3.1 2017-08-13 [1] CRAN (R 3.5.3)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.5.3)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.2)
usethis * 1.6.0 2020-04-09 [1] CRAN (R 3.5.2)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1)
xtable 1.8-3 2018-08-29 [1] CRAN (R 3.5.1)
xts 0.11-2 2018-11-05 [1] CRAN (R 3.5.2)
zoo 1.8-7 2020-01-10 [1] CRAN (R 3.5.3)
[1] C:/Users/21307937/OneDrive/R Packages
[2] C:/Program Files/R/R-3.5.2/library
When you do
you need to specify ref = "feature/survival"
.
Elite. Thank you. Worked well.
Thanks for solving this Ben! I sort of wonder whether it is worth having something in the Wiki (or somewhere similar) about installing the feature/survival
development branch, since this might keep happening a bit otherwise.
I am continuing this thread as I have problems installing the feature/survival
branch from Github on OSX Catalina.
I followed Rstan getting started and Installing Rstan from source on a Mac, installed first the macOS R toolchain, then Rcpp and Rstan (version 2.19.3) with
install.packages("Rcpp", repos = "https://rcppcore.github.io/drat")
install.packages("rstan", type = "source")
After this I have succesfully installed and used rstanarm
from CRAN
install.packages("rstanarm", type="source")
Also these installations succeed
install.packages("rstanarm")
devtools::install_github("stan-dev/rstanarm", build_vignettes = FALSE)
However, when I try to install the feature/survival
branch from github, it fails:
devtools::install_github("stan-dev/rstanarm@feature/survival", build_vignettes = FALSE)
(Note that below I show only the end of the R output. The full log is very long, as it has some seemingly unrelated warnings that also show up in the successful installations)
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rstanarm’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so’:
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so, 6): Symbol not found: __ZN20model_polr_namespace24csr_matrix_times_vector2IdN4stan4math3varEEEN5Eigen6MatrixIN5boost4math5tools12promote_argsIT_T0_ffffE4typeELin1ELi1ELi0ELin1ELi1EEERKiSG_RKNS5_ISA_Lin1ELi1ELi0ELin1ELi1EEERKNSt3__16vectorIiNSK_9allocatorIiEEEESQ_RKNS5_ISB_Lin1ELi1ELi0ELin1ELi1EEEPNSK_13basic_ostreamIcNSK_11char_traitsIcEEEE
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstanarm’
Error: Failed to install ‘rstanarm’ from GitHub:
(converted from warning) installation of package ‘/var/folders/st/bd1mw1z533d4pwb1xxd2vf540000gn/T//RtmpSpPhb2/file15724720f6586/rstanarm_2.19.1.tar.gz’ had non-zero exit status
The same happens if I download the repo and try to install it manually from Rstudio.
This error message seems very similar to the one reported here, but that did not help me forward.
Curiously, I was able to install and use the survival branch on Debian GNU/Linux 10 (buster)
.
So I have a problem that seems to be specific to the survival branch and OSX. Could it be that rstanarm
master branch has been updated recently to cope with OSX Catalina, but the survival branch has not? Or maybe the survival branch is incompatible with rstan
version 2.19.3
, and I should install an older rstan
version first?
Could either @sambrilleman or @bgoodri help me out here?
I managed to solve the issue at least partially. The problem appears to be some lines in my .R/Makevars
.
After my initial installation of rstan
and rstanarm
(2.19.3.), I had updated my .R/Makevars
based on this and this (if I remember correctly), and it looked like this:
# clang: start
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/l$
SHLIB_CXXLDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
SHLIB_CXX11LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
# clang: end
CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256
After commenting out all lines in .R/Makevars
, I managed to successfully install the survival branch with
devtools::install_github("stan-dev/rstanarm@feature/survival", build_vignettes = FALSE)
and it seems to work properly.
However, trying to install the downloaded repo manually from RStudio produces the same error as above.
I am also having trouble installing the development version of rstanarm. I’m working on a windows 10 machine with 32gb of ram, but get the following error after running
devtools::install_github("stan-dev/rstanarm",ref = "feature/survival", build_vignettes = FALSE)
cc1plus.exe: out of memory allocating 15696248 bytes
make: *** [C:/PROGRA~1/R/R-40~1.1/etc/i386/Makeconf:227: stan_files/jm.o] Error 1
rm stan_files/jm.cc stan_files/binomial.cc stan_files/lm.cc stan_files/continuous.cc stan_files/bernoulli.cc stan_files/polr.cc stan_files/surv.cc stan_files/count.cc stan_files/mvmer.cc
ERROR: compilation failed for package ‘rstanarm’
Trying to install from the downloaded zipfile has the identical result.
Are you using R4.0 and rtools4? These kinds of errors can occur when upgrading your R and RTools version to the latest versions.
Can you try the instructions in the post below and see if they fix the problem?
I am using rtools4 and R version 4.0.1.
I followed these instructions and am having the same problem.
Alrighty, just to check the existing configuration, can you post the outputs from the following commands:
Sys.which("make")
Sys.getenv("BINPREF")
Sys.getenv("PATH")
readLines("~/.R/Makevars.win")
Sys.which("make")
make
“C:\rtools40\usr\bin\make.exe”
Sys.getenv("BINPREF")
[1] “”
Sys.getenv("PATH")
[1] “C:\rtools40\usr\bin;C:\Program Files\R\R-4.0.1\bin\x64;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Rtools\bin;C:\Program Files\ImageMagick-7.0.9-Q16;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\Git\cmd;c:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;c:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Users\shauh\AppData\Local\Microsoft\WindowsApps;”
readLines("~/.R/Makevars.win")
[1] “” “CXX14FLAGS=-O3 -march=corei7 -mtune=corei7”
[3] “CXX14 = (BINPREF)g++ -m(WIN) -std=c++1y” “CXX11FLAGS=-O3 -march=corei7 -mtune=corei7”
Can you remove this line from your Makevars.win
file:
“CXX14 = (BINPREF)g++−m (WIN) -std=c++1y”
Then restart R and try again?
Sorry, I’m not sure how to do that. Could you please explain how to implement that?
In your ‘My Documents’ folder, you should have a folder called ‘.R’, in that folder will be your Makevars.win file. If you open that with a text editor (like Notepad), you can remove the line that I mentioned
Thanks for that. I removed that line and tried to install rstanarm again but get the identical problem.
Can you check if the RStan example model compiles and samples:
library(rstan)
example(stan_model,run.dontrun = TRUE,verbose=TRUE)
Looks like it compiled successfully
That means the compiler and Stan installation are all working well, so the issue is elsewhere.
Looking at the original error, it looks like it only ran out of memory by ~15mb. This can happen if you’re compiling multiple models simultaneously, with each model taking ~2-3gb.
Can you trying installing with fewer cores:
Sys.setenv(MAKEFLAGS="-j2")
devtools::install_github("stan-dev/rstanarm",ref = "feature/survival", build_vignettes = FALSE)
Same issue infortunately
cc1plus.exe: out of memory allocating 15636264 bytes
make: *** [C:/PROGRA~1/R/R-40~1.1/etc/i386/Makeconf:227: stan_files/jm.o] Error 1
rm stan_files/jm.cc stan_files/binomial.cc stan_files/lm.cc stan_files/continuous.cc stan_files/bernoulli.cc stan_files/polr.cc stan_files/surv.cc stan_files/count.cc stan_files/mvmer.cc
ERROR: compilation failed for package ‘rstanarm’
removing ‘C:/Users/shauh/Documents/R/win-library/4.0/rstanarm’
Error: Failed to install ‘rstanarm’ from GitHub:
(converted from warning) installation of package ‘C:/Users/shauh/AppData/Local/Temp/RtmpWQjLOl/file2c7862e42f7e/rstanarm_2.19.1.tar.gz’ had non-zero exit status
In addition: Warning message:
In utils::untar(tarfile, …) :
‘tar.exe -xf “C:\Users\shauh\AppData\Local\Temp\RtmpWQjLOl\file2c7818aa2ef6.tar.gz” -C “C:/Users/shauh/AppData/Local/Temp/RtmpWQjLOl/remotes2c78789e2e32”’ returned error code 1