[R-SIG-Mac] Trouble compiling packages in R

Wed Jan 26 18:01:13 CET 2022

On 26/01/2022 05:46, Simon Urbanek wrote:
> Jarrett,
> 
> you seem to have some ancient compilers in /usr/local. In order to avoid issue, I would strongly recommend removing the content of /usr/local (or putting it aside - see below). You don't need any extra tools on Big Sur, only standard Apple Xcode or CLT are needed (see R documentation).

Unless you need to compile Fortran code ... on x86_64 the manuals 
recommend installing gfortran in /usr/local/gfortran and using a 
complete path.

For some packages you need other tools such as pkg-config, and the 
Tcl/Tk support code is installed under /usr/local (as are some 
symlinks).  So I would nuance Simon's suggestion by adding that you 
should re-install R (preferably 4.1.2) once /usr/local/* has been moved 
aside.

> 
> Also please note that your github repository (https://github.com/jphill01/HACSim.R) has binary files checked in which is a bad idea, so you may want to fix that problem first.
> 
> Cheers,
> Simon
> 
> 
> to remove all files from /usr/local:
> sudo rm -rf /usr/local/*
> 
> to put them aside:
> sudo -i
> cd /usr/local
> mkdir .bak
> mv * .bak/
> 
> to restore  if needed:
> sudo -i
> cd /usr/local
> mv .bak/* .
> rmdir .bak
> 
> 
> 
> 
> 
>> On Jan 26, 2022, at 5:43 PM, Jarrett Phillips <phillipsjarrett1 using gmail.com> wrote:
>>
>> Hi All,
>> I am new to the list and am running RStudio Version 1.4.1717 on macOS Big
>> Sur 11.4 and have R 4.1.1 installed.
>>
>> I just re-installed Xcode as well as Command Line Tools via instructions at
>> https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
>>
>> I am attempting to build my package using devtools::build I have verified
>> that both Rcpp and RcppArmadillo are working properly.
>>
>> However, when I build, I get the following error message
>>
>> Error: package or namespace load failed for ‘HACSim’ in dyn.load(file,
>> DLLpath = DLLpath, ...):
>>     unable to load shared object
>> '/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/00LOCK-HACSim/00new/HACSim/libs/HACSim.so':
>>
>> dlopen(/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/00LOCK-HACSim/00new/HACSim/libs/HACSim.so,
>> 6): Symbol not found: ___addtf3
>>      Referenced from: /usr/local/lib/libquadmath.0.dylib
>>      Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
>>     in /usr/local/lib/libquadmath.0.dylib
>>    Error: loading failed
>>    Execution halted
>>    ERROR: loading failed
>> ─  removing
>> ‘/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/HACSim’
>>          -----------------------------------
>>    ERROR: package installation failed
>> Error in (function (command = NULL, args = character(), error_on_status =
>> TRUE,  :
>>   System command 'R' failed, exit status: 1, stdout + stderr (last 10
>> lines):
>> E>
>> dlopen(/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/00LOCK-HACSim/00new/HACSim/libs/HACSim.so,
>> 6): Symbol not found: ___addtf3
>> E>   Referenced from: /usr/local/lib/libquadmath.0.dylib
>> E>   Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
>> E>  in /usr/local/lib/libquadmath.0.dylib
>> E> Error: loading failed
>> E> Execution halted
>> E> ERROR: loading failed
>> E> * removing
>> ‘/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/HACSim’
>> E>       -----------------------------------
>> E> ERROR: package installation failed
>> Type .Last.error.trace to see where the error occurred
>>
>> Here is the traceback:
>>
>> Stack trace:
>>
>> 1. devtools:::build("HACSim_OO")
>> 2. pkgbuild::build(path = pkg, dest_path = path, binary = binary,  ...
>> 3. withr::with_temp_libpaths(rcmd_build_tools(options$cmd, c(options$path,
>> ...
>> 4. base:::force(code)
>> 5. pkgbuild:::rcmd_build_tools(options$cmd, c(options$path, options$args),
>> ...
>> 6. pkgbuild:::with_build_tools(callr::rcmd_safe(..., env = env,  ...
>> 7. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE,  ...
>> 8. callr:::run_r(options)
>> 9. base:::with(options, with_envvar(env, do.call(processx::run,  ...
>> 10. base:::with.default(options, with_envvar(env, do.call(processx::run,
>> ...
>> 11. base:::eval(substitute(expr), data, enclos = parent.frame())
>> 12. base:::eval(substitute(expr), data, enclos = parent.frame())
>> 13. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args =
>> real_c ...
>> 14. base:::force(code)
>> 15. base:::do.call(processx::run, c(list(bin, args = real_cmdargs,  ...
>> 16. (function (command = NULL, args = character(), error_on_status = TRUE,
>> ...
>> 17. throw(new_process_error(res, call = sys.call(), echo = echo,  ...
>>
>> x System command 'R' failed, exit status: 1, stdout + stderr (last 10
>> lines):
>> E>
>> dlopen(/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/00LOCK-HACSim/00new/HACSim/libs/HACSim.so,
>> 6): Symbol not found: ___addtf3
>> E>   Referenced from: /usr/local/lib/libquadmath.0.dylib
>> E>   Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
>> E>  in /usr/local/lib/libquadmath.0.dylib
>> E> Error: loading failed
>> E> Execution halted
>> E> ERROR: loading failed
>> E> * removing
>> ‘/private/var/folders/wv/4_z4h7ns57g7qvd600qgd__w0000gn/T/RtmpGe2Cqt/Rinst118e1e9f13a0/HACSim’
>> E>       -----------------------------------
>> E> ERROR: package installation failed
>>
>>
>> Any ideas?
>>
>> Any assistance is warmly welcomed and greatly appreciated.
>>
>> Cheers,
>>
>> Jarrett
>>
>> 	[[alternative HTML version deleted]]
>>
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> 
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-- 
Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford