[R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

[Jarrett Phillips]

Hi Rodney,

When I paste the directories into the Terminal, I get

no such file or directory:



suggesting that they don't exist.


Seems like I need to create them (I'm a newbie)?


What should be my next steps?


Thanks!


Cheers,


Jarrett




On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips <phillipsjarrett1 using gmail.com>
wrote:

> Hi Rodney,
>
> When I paste the directories into the Terminal, I get
>
> no such file or directory:
>
>
>
> suggesting that they don't exist.
>
>
> Seems like I need to create them (I'm a newbie)?
>
>
> What should be my next steps?
>
>
> Thanks!
>
>
> Cheers,
>
>
> Jarrett
>
>
>
>
>
> On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney <rsparapa using mcw.edu>
> wrote:
>
>> Hi Jarrett:
>>
>>
>>
>> Do the two directories exist that clang is warning you about?
>>
>>
>>
>> '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>> '/opt/R/arm64/gfortran/lib'
>>
>>
>>
>> --
>>
>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>>
>> Director, Wisconsin Chapter of the American Statistical Association
>>
>> Institute for Health and Equity, Division of Biostatistics
>>
>> Medical College of Wisconsin, Milwaukee Campus
>>
>>
>>
>> *From: *R-SIG-Mac <r-sig-mac-bounces using r-project.org> on behalf of Jarrett
>> Phillips <phillipsjarrett1 using gmail.com>
>> *Date: *Wednesday, May 17, 2023 at 11:54 AM
>> *To: *r-sig-mac using r-project.org <r-sig-mac using r-project.org>
>> *Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
>> devtools::build()
>>
>> ATTENTION: This email originated from a sender outside of MCW. Use
>> caution when clicking on links or opening attachments.
>> ________________________________
>>
>> Hi All,
>>
>> I'm trying to generate a `tar.gz` file on a Mac for R package submission
>> to
>> CRAN but am having issues.
>>
>> I'm using `devtools`, specifically `build()` and `install()`.
>>
>> My package relies on compiled code via `Rcpp/RcppArmadillo`.
>>
>>     build("HACSim_OO")
>>     ── R CMD build
>> ─────────────────────────────────────────────────────────────────
>>     ✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
>> simulation/HACSim_OO/DESCRIPTION’ ...
>>     ─  preparing ‘HACSim’:
>>     ✔  checking DESCRIPTION meta-information ...
>>     ─  cleaning src
>>     ─  installing the package to process help pages
>>          -----------------------------------
>>     ─  installing *source* package ‘HACSim’ ...
>>        ** using staged installation
>>        ** libs
>>        clang++ -arch arm64 -std=gnu++11 -
>> I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>>
>>  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
>>
>> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
>> -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall
>> -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
>>        clang++ -arch arm64 -std=gnu++11
>> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>>
>>  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
>>
>> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
>> -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall
>> -pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
>>        clang++ -arch arm64 -std=gnu++11 -dynamiclib
>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
>> -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
>> -L/opt/R/arm64/lib -o HACSim.so RcppExports.o accumulate.o
>> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
>> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
>> -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
>> -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>>        ld: warning: directory not found for option
>> '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>>        ld: warning: directory not found for option
>> '-L/opt/R/arm64/gfortran/lib'
>>        ld: library not found for -lgfortran
>>        clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>>        make: *** [HACSim.so] Error 1
>>        ERROR: compilation failed for package ‘HACSim’
>>     ─  removing
>>
>> ‘/private/var/folders/r4/xm5blbcd2tn06tjv00lm1c780000gn/T/RtmpN4uaYR/Rinstdf4219594de/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: <printed>
>>      ---
>>     Type .Last.error to see the more details.
>>
>> `clang` is installed (since I am able to run the code within my package)
>> and I've verified by typing `gcc` in the Mac Terminal. I've also installed
>> `Homebrew` and `gfortran`, verifying via typing in the Terminal.
>>
>> Any idea on what's going on and how to fix the issue(s)?
>>
>> Thanks!
>>
>> Cheers,
>>
>> Jarrett
>>
>> P.S. - I've asked on the R package dev list and after trying a number of
>> solutions was suggested to try here as it seems to be a macOS issue.
>>
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