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 <phillipsjarre...@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@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.dun...@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 <
phillipsjarre...@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 <rspar...@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-boun...@r-project.org> on behalf of
Jarrett
Phillips <phillipsjarre...@gmail.com>
*Date: *Wednesday, May 17, 2023 at 11:54 AM
*To: *r-sig-mac@r-project.org <r-sig-mac@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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Emeritus Professor of Applied Statistics, University of Oxford
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