To build an R package from source fails: Win10, RStudio

Question

Installing a package from source fails for me on my windows machine. I uninstalled RStudio, R and deleted rtools40 folder, restarted and reinstalled those items. I believe I have the path set up appropriately.

Here's the code I tried, using some troubleshooting help from here:

#troubleshooting installation
pkgbuild::find_rtools()
pkgbuild::has_rtools(TRUE)
pkgbuild::check_rtools(TRUE)
pkgbuild::rtools_path()
pkgbuild::check_build_tools(TRUE)
pkgbuild::check_compiler(TRUE)
Sys.getenv("PATH")
Sys.getenv('BINPREF')
sessionInfo()

#Test installation from source via CRAN
pkgbuild::with_build_tools(install.packages("lme4", type = "source"))

And here is the output:

Restarting R session...

> #troubleshooting installation
> pkgbuild::find_rtools()
[1] TRUE
> pkgbuild::has_rtools(TRUE)
[1] TRUE
> pkgbuild::check_rtools(TRUE)
[1] TRUE
> pkgbuild::rtools_path()
[1] "C:\\rtools40/usr/bin"
> pkgbuild::check_build_tools(TRUE)
Your system is ready to build packages!
> pkgbuild::check_compiler(TRUE)
Trying to compile a simple C file
Running "C:/PROGRA~1/R/R-40~1.3/bin/x64/Rcmd.exe" SHLIB foo.c
Warning message:
In system(cmd) : 'make' not found
Error: Failed to compile C code
> Sys.getenv("PATH")
[1] "C:\\Program Files\\R\\R-4.0.3\\bin\\x64;C:\\rtools40\\bin;C:\\rtools40\\mingw64\\bin;C:\\Program Files (x86)\\Microsoft SDKs\\Azure\\CLI2\\wbin;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files\\Pandoc\\;C:\\Program Files\\Git\\cmd;C:\\Program Files\\dotnet\\;C:\\Program Files\\Microsoft SQL Server\\130\\Tools\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\Client SDK\\ODBC\\170\\Tools\\Binn\\;C:\\Users\\nealm\\AppData\\Local\\Microsoft\\WindowsApps;C:\\ProgramData\\Anaconda3;C:\\ProgramData\\Anaconda3\\Scripts;C:\\Users\\nealm\\.conda\\pkgs\\conda-4.7.5-py37_0\\Scripts;C:\\ProgramData\\Anaconda3\\Library\\bin;C:\\Users\\nealm\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\nealm\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\nealm\\AppData\\Roaming\\TinyTeX\\bin\\win32;"
> Sys.getenv('BINPREF')
[1] "C:/rtools40/mingw64/bin/"
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252    LC_MONETARY=English_New Zealand.1252
[4] LC_NUMERIC=C                         LC_TIME=English_New Zealand.1252    

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

loaded via a namespace (and not attached):
 [1] processx_3.4.5      compiler_4.0.3      assertthat_0.2.1    R6_2.5.0            cli_2.2.0           livecode_0.1.0.9000
 [7] prettyunits_1.1.1   tools_4.0.3         glue_1.4.2          rstudioapi_0.13     Rcpp_1.0.5          remotes_2.2.0      
[13] crayon_1.3.4        fansi_0.4.1         callr_3.5.1         ps_1.4.0            pkgbuild_1.1.0     
> 
> #Test installation from source via CRAN
> pkgbuild::with_build_tools(install.packages("lme4", type = "source"))
Installing package into ‘C:/Rpackages’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-26.tar.gz'
Content type 'application/x-gzip' length 3297635 bytes (3.1 MB)
downloaded 3.1 MB

* installing *source* package 'lme4' ...
** package 'lme4' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/rtools40/mingw64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Rpackages/Rcpp/include' -I'C:/Rpackages/RcppEigen/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c external.cpp -o external.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Rpackages/Rcpp/include' -I'C:/Rpackages/RcppEigen/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c glmFamily.cpp -o glmFamily.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Rpackages/Rcpp/include' -I'C:/Rpackages/RcppEigen/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c optimizer.cpp -o optimizer.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Rpackages/Rcpp/include' -I'C:/Rpackages/RcppEigen/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c predModule.cpp -o predModule.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Rpackages/Rcpp/include' -I'C:/Rpackages/RcppEigen/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c respModule.cpp -o respModule.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o lme4.dll tmp.def external.o glmFamily.o optimizer.o predModule.o respModule.o -LC:/PROGRA~1/R/R-40~1.3/bin/i386 -lR
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: skipping incompatible C:/PROGRA~1/R/R-40~1.3/bin/i386/R.dll when searching for -lR
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: skipping incompatible C:/PROGRA~1/R/R-40~1.3/bin/i386/R.dll when searching for -lR
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lR
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'lme4'
* removing 'C:/Rpackages/lme4'
* restoring previous 'C:/Rpackages/lme4'
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status

The downloaded source packages are in
    ‘C:\Users\nealm\AppData\Local\Temp\RtmpwPwykm\downloaded_packages’
>

The problem does not appear to be specific to the lme4 package.

Answer 1

This is more of a work around than a proper answer. The alternative to installing and building from source is to install a pre-built binary. If one is not available, you can build it remotely. In this case, for the package of interest for me, rundel/livecode on github, I:

1. Forked the repo (in this case rundel/livecode). This step might be optional.
2. Downloaded the tar.gz (remotes::install_github("markbneal/livecode") which doesn't install it, but the error tells you where it saves the .tar.gz file locally.
3. Used rhub to build the package binary for windows, go to this website https://builder.r-hub.io/ and upload your tar.gz file, ensuring rhub has your email address (click "advanced" button to provide your email address as alternate - you will need to validate it). That emails me a zip 5 minutes later.
4. Then copy the livecode folder in the zip that is emailed to me to my "R packages" folder location. Package should now work for you, in my case library(livecode)

Edited six months later when I had to use this process again!