Dear all,
I am working on a package using rstantools. It compiles perfectly fine and fast enough (~1min) on linux but gets stuck on Windows (10) when linking (aborted ld.exe after 30 min). The Windows toolchain is set up correctly. I can compile the very same stan model using rstan::stan_model() directly.
There seems to be an MD5 mismatch for my RCppParallel, installation it from source fails. I wonder whether that can be the issue if compiling directly from an interactive session works though.
Any ideas what could be the issue?
Thanks!
- OS Win10/CentOS
- RStan Version 2.21.15, rstantools: 2.2.0
src/Makevars.win:
STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= 2.26, '-DUSE_STANC3',''))")
PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 $(STANC_FLAGS)
PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
CXX_STD = CXX14
CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
devtools::session_info("rstan")
- Session info -------------------------------------------------------------------------------------------------------------
setting value
version R version 4.1.2 (2021-11-01)
os Windows 10 x64 (build 19042)
system x86_64, mingw32
ui RStudio
language en_US.utf8
collate English_United States.1252
ctype English_United States.1252
tz -----------
date 2022-07-24
rstudio 2021.09.1+372 Ghost Orchid (desktop)
pandoc NA
- Packages -----------------------------------------------------------------------------------------------------------------
! package * version date (UTC) lib source
backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2)
BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.1.2)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.2)
checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.1.3)
cli 3.2.0 2022-02-14 [1] CRAN (R 4.1.2)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.3)
crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.3)
desc 1.4.1 2022-03-06 [1] CRAN (R 4.1.3)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.3)
farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.2)
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.1.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.2)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.1.2)
isoband 0.2.5 2021-07-13 [1] CRAN (R 4.1.2)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.1)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.1.2)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2)
loo 2.5.1 2022-03-24 [1] CRAN (R 4.1.3)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.2)
Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.1.3)
matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.1.3)
mgcv 1.8-38 2021-10-06 [2] CRAN (R 4.1.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2)
nlme 3.1-153 2021-09-07 [2] CRAN (R 4.1.2)
pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.2)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.2)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.3)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.1.3)
Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.1.3)
RcppEigen 0.3.3.9.2 2022-04-08 [1] CRAN (R 4.1.3)
D RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.1.3)
rlang 1.0.2 2022-03-04 [1] CRAN (R 4.1.3)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.1.3)
rstan * 2.21.5 2022-04-11 [1] CRAN (R 4.1.3)
scales 1.2.0 2022-04-13 [1] CRAN (R 4.1.3)
StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 4.1.2)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.3)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.3)
[1] C:/Users/------/Documents/R/4.1.2
[2] C:/Program Files/R/R-4.1.2/library
D -- DLL MD5 mismatch, broken installation.
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