[R-SIG-Mac] Problems compiling with R CMD build and devtools::build()
Jarrett Phillips
ph||||p@j@rrett1 @end|ng |rom gm@||@com
Wed May 17 23:30:58 CEST 2023
Thanks Simon,
Removing the old gfortran and updating R to the latest version (4.3.0)
fixed everything.
Now I'm able to build and install without issues.
I'll be sure to update R every time a new version is released.
Cheers,
Jarrett
On Wed, May 17, 2023 at 4:59 PM Simon Urbanek <simon.urbanek using r-project.org>
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.
>
> 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.
> >>>>>
> >>>>> [[alternative HTML version deleted]]
> >>>>>
> >>>>> _______________________________________________
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> >>>>>
> >>>>>
> >>
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