Install issue - splitting "Application Support" path to RcppParallel

[daeh]

Summary:

clang error when installing rstanarm. Path to RcppParallel is not being shell escaped and is being split at space in "Application Support".

Description:

I'm trying to install rstanarm on an arm64 Mac and am getting the error,

clang: error: no such file or directory: 'Support/renv/cache/v5/R-4.2/aarch64-apple-darwin21.6.0/RcppParallel/5.1.5/f3e94e34ff656a7c8336ce01207bc2b8/RcppParallel/include''
make: *** [stan_files/bernoulli.o] Error 1
rm stan_files/bernoulli.cc
ERROR: compilation failed for package ‘rstanarm’

The path should be ~/Library/Application Support/renv/cache/v5/R-4.2/aarch64-apple-darwin21.6.0/RcppParallel/5.1.5/f3e94e34ff656a7c8336ce01207bc2b8/RcppParallel/include/RcppParallel.h

So something is not escaping the space, which is causing the path to get split. I'm not sure where to start troubleshooting so any pointers would be greatly appreciated. My ~/.R/Makevars was initially

FC      = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran
F77     = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran
FLIBS   = -L/opt/homebrew/Cellar/gcc/12.2.0/lib

and I've tried adding various things, e.g.

CXX=clang++
CXX_STD = CXX11
PKG_LIBS += $(shell ${R_HOME}/bin/Rscript -e "RcppParallel::RcppParallelLibs()")

but nothing seems to change the error. I use homebrew for gcc and clang.

Thanks a ton.

Reproducible Steps:

install.packages("rstanarm")

RStanARM Version:

latest, both from CRAN and from install.packages("rstanarm", type = "source")

R Version:

4.2.2

Operating System:

OS X 12.6.1

[jgabry]

@bgoodri Any ideas? These compilation errors are not my area of expertise.

@daeh Are you able to successfully install the binary from CRAN in the meantime? Or are there issues with that too and not just installing from source?

[daeh]

Thanks a ton for looking into it.

Trying to install from CRAN (i.e. install.packages("rstanarm")) runs into the same Application Support/renv/cache issue, which I guess means that it isn't able to locate an appropriate binary?

Installing a downloaded binary

renv::install(file.path(wdir, "packagesource/rstanarm_2.21.3.tgz"), repos= NULL)

doesn't raise any errors during the install, but then rstanarm can't find libR.dylib: dlopen(~/.../renv/library/R-4.2/aarch64-apple-darwin21.6.0/rstanarm/libs/rstanarm.so, 0x0006): Library not loaded: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libR.dylib'

The libR.dylib issue seems like something I can probably resolve. Will report back when I have a chance to look at it.

[mikegilchrist]

I am having the same issue with the same error line on 22.04. Neither "install.github" nor "install.packages" works. rstan and StanHeaders are installed from github and work.

> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods   base     

other attached packages:
[1] devtools_2.4.5 usethis_2.1.6 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        compiler_4.2.2    later_1.3.0       urlchecker_1.0.1 
 [5] prettyunits_1.1.1 profvis_0.3.7     remotes_2.4.2     tools_4.2.2      
 [9] digest_0.6.31     pkgbuild_1.4.0    pkgload_1.3.2     memoise_2.0.1    
[13] lifecycle_1.0.3   rlang_1.0.6       shiny_1.7.4       cli_3.5.0        
[17] curl_4.3.2        fastmap_1.1.0     withr_2.5.0       stringr_1.5.0    
[21] desc_1.4.2        fs_1.5.2          htmlwidgets_1.6.0 rprojroot_2.0.3  
[25] glue_1.6.2        R6_2.5.1          processx_3.8.0    sessioninfo_1.2.2
[29] callr_3.7.3       purrr_0.3.4       magrittr_2.0.3    ps_1.7.2         
[33] promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.4   mime_0.12        
[37] xtable_1.8-4      httpuv_1.6.7      stringi_1.7.8     miniUI_0.1.1.1   
[41] cachem_1.0.6      crayon_1.5.2