Compilation of 'rstanarm' survival extension failed
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Description
Using the code:
install.packages("rstanarm", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
devtools::install_github("stan-dev/rstanarm", ref = "feature/survival", build_vignettes = FALSE)
I am trying to install the survival extension of the rstanarm packages into my R version 4.2 on a Windows 10 computer.
It runs until:
C:/Users/wilhch00/AppData/Local/R/win-library/4.2/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes]
"C:/PROGRA1/R/R-421.3/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/surv.stan
and then the error states that:
Error in rstan::stanc(file, allow_undefined = TRUE, obfuscate_model_name = FALSE) :
0
Semantic error in 'string', line 404, column 2 to line 411, column 3:
402: }
403:
404: vector quadrature_log_cdf(vector qwts, vector log_hazard, int qnodes, int N) {
^
405: int M = rows(log_hazard);
406: vector[M] hazard = exp(log_hazard);
Real return type required for probability functions ending in _log, _lpdf, _lupdf, _lpmf, _lupmf, _cdf, _lcdf, or _lccdf.
Calls: make_cc ->
Execution halted
make: *** [Makevars.win:28: stan_files/surv.cc] Error 1
rm stan_files/polr.cc stan_files/mvmer.cc stan_files/count.cc stan_files/lm.cc stan_files/jm.cc stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc
ERROR: compilation failed for package 'rstanarm'
- removing 'C:/Users/wilhch00/AppData/Local/R/win-library/4.2/rstanarm'
- restoring previous 'C:/Users/wilhch00/AppData/Local/R/win-library/4.2/rstanarm'
Warning messages:
1: In utils::untar(tarfile, ...) :
‘tar.exe -xf "C:\Users\wilhch00\AppData\Local\Temp\RtmpcphJws\file12c849956fc.tar.gz" -C "C:/Users/wilhch00/AppData/Local/Temp/RtmpcphJws/remotes12c83388f58"’ returned error code 1
2: In i.p(...) :
installation of package ‘C:/Users/wilhch00/AppData/Local/Temp/RtmpcphJws/file12c83b9a3c1e/rstanarm_2.26.1.tar.gz’ had non-zero exit status
I have tried to also download the survival extension and building the package from R studio as well.
But the same issue reoccurs.
Any help would be greatly appreciated.
Charlotte
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- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the reported Windows installation command and the failure in stan_files/surv.stan, especially the quadrature_log_cdf declaration around line 404. Read tools/make_cc.R and Makevars.win to trace how the Stan file is compiled, then reproduce the install failure and determine the compatible declaration or dependency state needed for the survival extension to build.
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Assessment
- Tech stack
- r
- Domain
- build-system
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100