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

Simon Urbanek @|mon@urb@nek @end|ng |rom R-project@org
Wed May 17 22:59:18 CEST 2023


Jarrett,

Duncan's suggestion was correct, but you are using older R, so I'd recommend simply upgrading R to the latest release.

If you want to use old R, you have to install the older Fortran binaries that match your R version, but that's not entirely trivial so it's easier to just upgrade R instead.

Cheers,
Simon


> On 18/05/2023, at 6:43 AM, Jarrett Phillips <phillipsjarrett1 using gmail.com> wrote:
> 
> Hi Duncan,
> 
> I did exactly that, but still got the error above when I try building in
> both RStudio via devtools::build() and the Terminal via R CMD build.
> 
> To confirm that the right gfortran successfully installed in the correct
> location, I did
> 
> jarrettphillips using Jarretts-MacBook-Pro ~ % /opt/gfortran/bin/gfortran
> 
> *aarch64-apple-darwin20.0-gfortran:* *fatal error: *no input files
> 
> compilation terminated.
> 
> 
> Any other ideas?
> 
> 
> 
> 
> On Wed, May 17, 2023 at 2:13 PM Duncan Murdoch <murdoch.duncan using gmail.com>
> wrote:
> 
>> I think the simplest solution is to remove the gfortran you installed,
>> and then install it back using the installer on
>> 
>>   https://mac.r-project.org/tools/
>> 
>> Duncan Murdoch
>> 
>> On 17/05/2023 1:26 p.m., Jarrett Phillips 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 1:25 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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>>>>> 
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