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

Prof Brian Ripley r|p|ey @end|ng |rom @t@t@@ox@@c@uk
Thu May 18 07:40:55 CEST 2023 

On 17/05/2023 21:59, Simon Urbanek wrote:
> 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.

It is possible to use a binary R installation with a version of gfortran 
other than it was built with (I have occasionally needed to use a later 
gfortran).  This is discussed in the manual, at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS-packages
and
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Customizing-package-compilation

The crucial part is that FLIBS (in etc/Makeconf or overridden in a 
personal or site Makevars) has to match the compiler in use.

To reduce confusion I always specify the full path to gfortran in FC.

> 
> 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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>>>>>>
>>>>>
>>>>
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-- 
Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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