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

Wed May 17 20:43:21 CEST 2023

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.
> >>>
> >>>          [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac using r-project.org
> >>>
> >>>
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> >>> <
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> >
> >>>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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>

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