Installation Errors - Githubissues

Summary:

Trouble installing on two systems with different operating systems.

Description:

I had Rstan and RStanarm working on a previous build of R (3.6.-). I tried installing the Development version, as I want to access stan_surv for a model I am attempting. Failed to install. Updated my R and Rstudio to the latest versions - purged all packages. Followed instruction to reinstall Rstan (https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started). No issues. Tried installing development version of RStanarm, both with and without vignettes = TRUE, no luck!

Reproducible Steps:

Reproduced this on a different Fedora 30 system, but I think that error is upstream with the C++, G++.

RStanARM Version:

Development

R Version:

4.0.0

Operating System:

Windows 10 (but also tried on Fedora 30)

Errors:

Error Vignettes FALSE C:/Users/Alex/Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/mat/fun/quad_form.hpp:92:5: required from 'void stan::math::internal::quad_form_vari<Ta, Ra, Ca, Tb, Rb, Cb>::chain() [with Ta = double; int Ra = -1; int Ca = -1; Tb = stan::math::var; int Rb = -1; int Cb = 1]' C:/Users/Alex/Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/mat/fun/quad_form.hpp:89:16: required from here C:/Users/Alex/Documents/R/win-library/4.0/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(4) double'} [-Wignored-attributes]

cc1plus.exe: out of memory allocating 2763176 bytes make: *** [C:/PROGRA~1/R/R-40~1.0/etc/i386/Makeconf:227: stan_files/continuous.o] Error 1 rm stan_files/continuous.cc ERROR: compilation failed for package 'rstanarm'

removing 'C:/Users/Alex/Documents/R/win-library/4.0/rstanarm'
restoring previous 'C:/Users/Alex/Documents/R/win-library/4.0/rstanarm' Error: Failed to install 'rstanarm' from GitHub: (converted from warning) installation of package ‘C:/Users/Alex/AppData/Local/Temp/RtmpIZN646/file21084e907f27/rstanarm_2.19.3.tar.gz’ had non-zero exit status In addition: Warning message: In utils::untar(tarfile, ...) : ‘tar.exe -xf "C:\Users\Alex\AppData\Local\Temp\RtmpIZN646\file21086b6ba7f.tar.gz" -C "C:/Users/Alex/AppData/Local/Temp/RtmpIZN646/remotes21087d2329f3"’ returned error code 1

Error Vignettes TRUE

C:/Users/Alex/Documents/R/win-library/4.0/RcppEigen/include/Eigen/src/Core/arch/AVX/Complex.h:387:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cd,Packet4d) ^~~~~~~~ C:/rtools40/mingw64/bin/g++ -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/Alex/Documents/R/win-library/4.0/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/PROGRA~1/R/R-40~1.0/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/Alex/AppData/Local/Temp/RtmpWSND4y/Rinst22cc50e8444f/00LOCK-rstanarm/00new/rstanarm/libs/x64 R data moving datasets to lazyload DB demo inst byte-compile and prepare package for lazy loading 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 from temporary location Error: package or namespace load failed for 'rstanarm' in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'C:/Users/Alex/AppData/Local/Temp/RtmpWSND4y/Rinst22cc50e8444f/00LOCK-rstanarm/00new/rstanarm/libs/x64/rstanarm.dll': LoadLibrary failure: The specified module could not be found.

Error: loading failed Execution halted ERROR: loading failed

removing 'C:/Users/Alex/AppData/Local/Temp/RtmpWSND4y/Rinst22cc50e8444f/rstanarm'

ERROR: package installation failed Error: Failed to install 'rstanarm' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: package or namespace load failed for 'rstanarm' in inDL(x, as.logical(local), as.logical(now), ...): E> unable to load shared object 'C:/Users/Alex/AppData/Local/Temp/RtmpWSND4y/Rinst22cc50e8444f/00LOCK-rstanarm/00new/rstanarm/libs/x64/rstanarm.dll': E> LoadLibrary failure: The specified module could not be found. E> E> Error: loading failed E> Execution halted E> ERROR: loading failed E> * removing 'C:/Users/Alex/AppData/Local/Temp/RtmpWSND4y/Rinst22cc50e8444f/rstanarm' E> ----------------------------------- E> ERROR: package installation failed In addition: Warning message: In utils::untar(tarfile, ...) : ‘tar.exe -xf "C:\Users\Alex\AppData\Local\Temp\RtmpIZN646\file210867033528.tar.gz" -C "C:/Users/Alex/AppData/Local/Temp/RtmpIZN646/remotes210870c87fa8"’ returned error code 1

Just a follow-up - I am still unable to get this to work. I was concerend that devtools install_github was trying to go through a bad download.file.method, so I tried cycling through those (wininet, curl, libcurl, auto). I ended up manually downloading a zip of the the feature/surv from https://github.com/stan-dev/rstanarm/tree/feature/survival . Then using devtools::install_local to use that zip. I run into a similar error on the Windows 10 machine.

For the Fedora machine, I ended up doing a wipe on it and installing a clean system Fedora 32. I got the rstanarm development version to work, BUT still no go on the feature/survival. I will update if I get that system to work.

On the Windows machine, I ran build_vignettes both as false and true, similar errors at the same line. install_local("~/surv.zip", build_vignettes = FALSE)

C:/Users/Alex/Documents/R/win-library/4.0/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here C:/Users/Alex/Documents/R/win-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(4) double'} [-Wignored-attributes]

cc1plus.exe: out of memory allocating 4926368 bytes make: *** [C:/PROGRA~1/R/R-40~1.0/etc/i386/Makeconf:227: stan_files/surv.o] Error 1 rm stan_files/surv.cc ERROR: compilation failed for package 'rstanarm'

removing 'C:/Users/Alex/Documents/R/win-library/4.0/rstanarm' Error: Failed to install 'surv.zip' from local: (converted from warning) installation of package ‘C:/Users/Alex/AppData/Local/Temp/RtmpsF81IQ/remotes23bc60405830/rstanarm-feature-survival’ had non-zero exit status

So, I seem to need more memory for CC1Plus on the Windows machine - it's running 64-bit architecture. I have a large page file set, and the machine has 4 gig RAM - not a lot, but thought it would be enough?

Any ideas for a workaround, preferably with additional instructions on how to undo said workaround?

Sorry it's not working for you!

In my comment at https://github.com/stan-dev/rstanarm/issues/429#issuecomment-640897528 I linked to some comments on the Stan forums from @bgoodri that helped a Windows users else get this installed. I'm not sure this is the same exact issue but maybe.

If that's not the issue then perhaps the 4 GB of RAM isn't enough for the compilation (I think the feature/survival branch consumes a decent bit more RAM than the master branch). In that case ideally maybe somebody could build you Windows binary of the feature/survival branch to install. I'm on mac unfortunately, but if you ask on the Stan forums a windows user might be able to help out with that. Sorry for the hassle!

@rok-cesnovar @sambrilleman This could be a good candidate for the new https://github.com/stan-dev/r-packages. We could host binaries of the feature/survival branch since a lot of people want to use it but it's not on CRAN and it's not easy to install via install_github().

Thanks very much for the response! Yes, I had followed your instructions. I also tried purging my .Rprofile and changing the R_INSTALL_TAR/tar environment variable. I guess Windows sometimes blocks permissions. I reinstalled Rstan and played around with the version of StanHeaders. I am having issues, too, on my Fedora 32 system, but I assume those errors are upstream.

Thanks for the other potential option; I did not realize people could build packages for Windows installation. I have asked a friend to try running one version of my model. If that works, then I will pursue this suggestion, since I will need to run about 30 more models.

I really appreciate the time you took to respond!

@jgabry cheers, yeah I wasn't aware of https://github.com/stan-dev/r-packages. That could be a great idea! Perhaps later this week I will look into it. Yeah the whole survival dev branch installation problem is a headache that keeps cropping up. I am on a Windows machine so maybe I can make a Windows binary, although each time I've tried to build a binary in the past I've encountered some form of error, but will try give it another crack! 😃

@sambrilleman Sounds good! We should definitely try to provide an easy way to install the survival branch until it's CRAN-able. In terms of building the windows binary, if you can't build that successfully then maybe open an issue at https://github.com/stan-dev/r-packages and @rok-cesnovar or @serban-nicusor-toptal may be able to help. Unfortunately I'm pretty useless when it comes to Windows.

Mac binaries for the feature/survival branch would be much appreciated too! 🙏🏻

(On my machine (macOS 10.14.6 + R 3.6.3), I managed to install the feature/survival branch. However, I was unable to do so after upgrading to R 4.0.2).

** 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 '/Users/anddis/Library/R/4.0/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so':
  dlopen(/Users/anddis/Library/R/4.0/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: /Users/anddis/Library/R/4.0/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so
  Expected in: flat namespace
 in /Users/anddis/Library/R/4.0/library/00LOCK-rstanarm/00new/rstanarm/libs/rstanarm.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/anddis/Library/R/4.0/library/rstanarm’
Error: Failed to install 'rstanarm' from GitHub:
  (converted from warning) installation of package ‘/var/folders/20/frdftm5x0cz3wz5rvdgws18c0000gp/T//RtmpiqKfwh/filea9b2e07b214/rstanarm_2.19.1.tar.gz’ had non-zero exit status

@sambrilleman When you have a chance can you update the feature/survival branch with the changes from master (hopefully there aren't many conflicts)? I think that's probably necessary in order for us to build working binaries.

@jgabry No worries! It may have to be this weekend if it is a big-ish job.

Hey @jgabry -- looks like @bgoodri has already updated feature/survival with the latest changes from master. Hopefully that went smoothly. Let me know if there is anything I can do to assist.

I still can't build either master or feature/survival from source on my local machine though. I tried the installation instructions mentioned for rstan but encountered a 404 error on the rstan binary. I can install the CRAN versions of rstan and rstanarm and run the example model, but I can't build from source. I'll just sit tight for now until some of the Windows issues are resolved.

fyi, the error I am getting when trying to build rstanarm master from source is:

==> roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))

Loading rstanarm
Re-compiling rstanarm
-  installing *source* package 'rstanarm' ... (365ms)
   ** using staged installation
   cp: cannot overwrite non-directory 'tests/testthat/stan_files' with directory 'src/stan_files'
   cp: cannot overwrite non-directory 'tests/testthat/include' with directory 'inst/include'
   ** libs
   "C:/PROGRA~1/R/R-40~1.2/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 -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'C:/Program Files/R/R-4.0.2/library/StanHeaders/include' -I'C:/Program Files/R/R-4.0.2/library/rstan/include' -I'C:/Program Files/R/R-4.0.2/library/BH/include' -I'C:/Program Files/R/R-4.0.2/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.2/library/RcppEigen/include' -I'C:/Program Files/R/R-4.0.2/library/RcppParallel/include'     `"C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "StanHeaders:::CxxFlags()"`   -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2  -c stan_files/continuous.cc -o stan_files/continuous.o
   g++.exe: error: Files/R/R-4.0.2/library/RcppParallel/include": No such file or directory
   make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:227: stan_files/continuous.o] Error 1
   rm stan_files/continuous.cc
   ERROR: compilation failed for package 'rstanarm'
-  removing 'C:/Users/SBRILL~1/AppData/Local/Temp/Rtmp6jlzvV/devtools_install_21bc1f475483/rstanarm'

Error: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr:
E> * installing *source* package 'rstanarm' ...
E> ** using staged installation
E> cp: cannot overwrite non-directory 'tests/testthat/stan_files' with directory 'src/stan_files'
E> cp: cannot overwrite non-directory 'tests/testthat/include' with directory 'inst/include'
E> ** libs
E> "C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/continuous.stan
E> Wrote C++ file "stan_files/continuous.cc"
E> 
E> 
E> C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'C:/Program Files/R/R-4.0.2/library/StanHeaders/include' -I'C:/Program Files/R/R-4.0.2/library/rstan/include' -I'C:/Program Files/R/R-4.0.2/library/BH/include' -I'C:/Program Files/R/R-4.0.2/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.2/library/RcppEigen/include' -I'C:/Program Files/R/R-4.0.2/library/RcppParallel/include'     `"C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "StanHeaders:::CxxFlags()"`   -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2  -c stan_files/continuous.cc -o stan_files/continuous.o
E> g++.exe: error: Files/R/R-4.0.2/library/RcppParallel/include": No such file or directory
E> make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:227: stan_files/continuous.o] Error 1
E> rm stan_files/continuous.cc
E> ERROR: compilation failed for package 'rstanarm'
E> * removing 'C:/Users/SBRILL~1/AppData/Local/Temp/Rtmp6jlzvV/devtools_install_21bc1f475483/rstanarm'

 Stack trace:

 1. base:::suppressPackageStartupMessages({ ...
 2. base:::withCallingHandlers(expr, packageStartupMessage = function(c) tryInv ...
 3. roxygen2::roxygenize(".", roclets = c("rd", "collate", "namespace"))
 4. roxygen2:::load_code(base_path)
 5. pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
 6. pkgbuild::compile_dll(path, quiet = quiet)
 7. pkgbuild:::install_min(path, dest = install_dir, components = "libs",  ...
 8. pkgbuild:::rcmd_build_tools("INSTALL", c(path, paste("--library=",  ...
 9. pkgbuild:::with_build_tools(callr::rcmd_safe(..., env = env,  ...
 10. withr::with_path(rtools_path(), code)
 11. base:::force(code)
 12. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE,  ...
 13. callr:::run_r(options)
 14. base:::with(options, with_envvar(env, do.call(processx::run,  ...
 15. base:::with.default(options, with_envvar(env, do.call(processx::run,  ...
 16. base:::eval(substitute(expr), data, enclos = parent.frame())
 17. base:::eval(substitute(expr), data, enclos = parent.frame())
 18. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
 19. base:::force(code)
 20. base:::do.call(processx::run, c(list(bin, args = real_cmdargs,  ...
 21. (function (command = NULL, args = character(), error_on_status = TRUE,  ...
 22. throw(new_process_error(res, call = sys.call(), echo = echo,  ...

 x System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr:
E> * installing *source* package 'rstanarm' ...
E> ** using staged installation
E> cp: cannot overwrite non-directory 'tests/testthat/stan_files' with directory 'src/stan_files'
E> cp: cannot overwrite non-directory 'tests/testthat/include' with directory 'inst/include'
E> ** libs
E> "C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/continuous.stan
E> Wrote C++ file "stan_files/continuous.cc"
E> 
E> 
E> C:/Rtools/mingw_64/bin/g++ -m64 -std=c++1y -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I"../inst/include" -I"C:/Program Files/R/R-4.0.2/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'C:/Program Files/R/R-4.0.2/library/StanHeaders/include' -I'C:/Program Files/R/R-4.0.2/library/rstan/include' -I'C:/Program Files/R/R-4.0.2/library/BH/include' -I'C:/Program Files/R/R-4.0.2/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.2/library/RcppEigen/include' -I'C:/Program Files/R/R-4.0.2/library/RcppParallel/include'     `"C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-40~1.2/bin/x64/Rscript" -e "StanHeaders:::CxxFlags()"`   -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2  -c stan_files/continuous.cc -o stan_files/continuous.o
E> g++.exe: error: Files/R/R-4.0.2/library/RcppParallel/include": No such file or directory
E> make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:227: stan_files/continuous.o] Error 1
E> rm stan_files/continuous.cc
E> ERROR: compilation failed for package 'rstanarm'
E> * removing 'C:/Users/SBRILL~1/AppData/Local/Temp/Rtmp6jlzvV/devtools_install_21bc1f475483/rstanarm' 

Execution halted

Exited with status 1.

Can you try installing the RStan binaries again that @bgoodri linked to on discourse? I think @bgoodri updated the links in that discourse post and you shouldn't get a 404 anymore. I bet that's probably necessary for you to be able to compile this (at least I think so).

stan-dev / rstanarm

Installation Errors #439