[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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