stan-dev / stan-dev/rstanarm

Cannot install development version

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Description

Summary:

I'm trying to build the feature/survival branch from source, using "Install and Restart" in the RStudio console for the rstanarm.Rproj R project.

But after taking forever (some time overnight), it eventually fails, this time with this error in the build window:

E> C:/Rpackages/StanHeaders/include/stan/math/rev/mat/fun/quad_form.hpp:70:13: required from 'void stan::math::internal::quad_form_vari<Ta, Ra, Ca, Tb, Rb, Cb>::chainB(Eigen::Matrix<stan::math::var, Rb, Cb>&, const Eigen::Matrix<double, R, C>&, const Eigen::Matrix<double, Rb, Cb>&, const Eigen::Matrix<double, Cb, Cb>&) [with Ta = double; int Ra = -1; int Ca = -1; Tb = stan::math::var; int Rb = -1; int Cb = 1]
E> C:/Rpackages/StanHeaders/include/stan/math/rev/mat/fun/quad_form.hpp:79:5: required from 'void stan::math::internal::quad_form_vari<Ta, Ra, Ca, Tb, Rb, Cb>::chainAB(Eigen::Matrix<T, R, C>&, Eigen::Matrix<T2, R2, C2>&, const Eigen::Matrix<double, R, C>&, const Eigen::Matrix<double, Rb, Cb>&, const Eigen::Matrix<double, Cb, Cb>&) [with Ta = double; int Ra = -1; int Ca = -1; Tb = stan::math::var; int Rb = -1; int Cb = 1]
E> C:/Rpackages/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]
E> C:/Rpackages/StanHeaders/include/stan/math/rev/mat/fun/quad_form.hpp:89:16: required from here
E> C:/Rpackages/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8:warning: noring attributes on template argument 'Eigen::internal::packet_traits<double>::type{aka '__vector(2) double-Wignored-attributes
E> In file included from C:/Rpackages/StanHeaders/include/stan/math/rev/core.hpp:46
E>                  from C:/Rpackages/StanHeaders/include/stan/math/rev/mat.hpp:6
E>                  from C:/Rpackages/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4
E>                  from C:/Rpackages/StanHeaders/include/src/stan/model/test_gradients.hpp:7
E>                  from C:/Rpackages/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10
E>                  from C:/Rpackages/rstan/include/rstan/stan_fit.hpp:35
E>                  from C:/Rpackages/rstan/include/rstan/rstaninc.hpp:4
E>                  from stan_files/continuous.hpp:18
E>                  from stan_files/continuous.cc:3
E> C:/Rpackages/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:t global scope:
E> C:/Rpackages/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13:warning: void stan::math::set_zero_all_adjoints()ined but not used [-Wunused-function
E>  static void set_zero_all_adjoints
E>              ^~~~~~~~~~~~~~~~~~~~~
E> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: stan_files/continuous.o: too many sections (79359)
E> C:\Users\SBRILL~1\AppData\Local\Temp\ccKCIkOw.s: Assembler messages:
E> C:\Users\SBRILL~1\AppData\Local\Temp\ccKCIkOw.s: Fatal error: can't write 56 bytes to section .text of stan_files/continuous.o: 'file too big'
E> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: stan_files/continuous.o: too many sections (79359)
E> C:\Users\SBRILL~1\AppData\Local\Temp\ccKCIkOw.s: Fatal error: can't close stan_files/continuous.o: file too big
E> make: *** [C:/PROGRA~1/R/R-40~1.3/etc/x64/Makeconf:227: stan_files/continuous.o] Error 1
E> rm stan_files/continuous.cc stan_files/surv.cc
E> ERROR: compilation failed for package 'rstanarm'
E> * removing 'C:/Users/SBRILL~1/AppData/Local/Temp/RtmpoFuIY3/devtools_install_175069105387/rstanarm' 

Execution halted

Exited with status 1.
Reproducible Steps:

As described above.

RStanARM Version:

feature/survival branch.

R Version:

4.0.3

Operating System:

Windows 10

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the development-branch installation on Windows 10 with R 4.0.3 and inspect the compiler output for stan_files/continuous.cc, especially the assembler "too many sections" and "file too big" errors. Compare the package build configuration and the R Makeconf referenced in the log; done means the feature/survival branch installs successfully.

Written by the indexing model from the issue text.

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

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