After a recent upgrade of "R" I have many broken links that never resolve

[Kenneth Wolcott]

Could not open /opt/local/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib:
Error opening or reading file (referenced from
/opt/local/Library/Frameworks/R.framework/Versions/4.6/Resources/library/cluster/libs/cluster.so)
Could not open /opt/local/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.dylib:
Error opening or reading file (referenced from
/opt/local/Library/Frameworks/R.framework/Versions/4.6/Resources/library/KernSmooth/libs/KernSmooth.so)
--->  Found 3 broken files, matching files to ports
--->  Found 2 broken ports, determining rebuild order
You can always run 'port rev-upgrade' again to fix errors.
The following ports will be rebuilt:
 R-KernSmooth @2.23-24+gcc15
 R-cluster @2.1.8+gcc15
Continue? [Y/n]: y
Error: R: Variant gcc14 conflicts with gcc15
Error: Unable to open port: Error evaluating variants
Error: rev-upgrade failed: Error rebuilding R-KernSmooth
Error: Follow https://guide.macports.org/#project.tickets if you
believe there is a bug.

On Wed, Jun 10, 2026 at 6:06 PM Kenneth Wolcott
<kennethwolcott at gmail.com> wrote:
>
> A more complete error capture:
>
> Could not open /opt/local/Library/Frameworks/R.framework/Versions/4.5/Resources/lib/libR.dylib:
> Error opening or reading file (referenced from
> /opt/local/Library/Frameworks/R.framework/Versions/4.5/Resources/library/foreign/libs/foreign.so)
> Could not open /opt/local/Library/Frameworks/R.framework/Versions/4.5/Resources/lib/libRblas.dylib:
> Error opening or reading file (referenced from
> /opt/local/Library/Frameworks/R.framework/Versions/4.5/Resources/library/Matrix/libs/Matrix.so)
> Could not open /opt/local/Library/Frameworks/R.framework/Versions/4.5/Resources/lib/libRlapack.dylib:
> Error opening or reading file (referenced from
> /opt/local/Library/Frameworks/R.framework/Versions/4.5/Resources/library/Matrix/libs/Matrix.so)
> --->  Found 33 broken files, matching files to ports
> --->  Found 29 broken ports, determining rebuild order
> You can always run 'port rev-upgrade' again to fix errors.
> The following ports will be rebuilt:
>  R-foreign @0.8-87
>  R-lattice @0.22-6
>  R-MASS @7.3-61
>  R-class @7.3-22
>  R-Matrix @1.7-1+gcc14
>  R-nlme @3.1-166+gcc14
>  R-mgcv @1.9-1+gcc14
>  R-nnet @7.3-19
>  R-rpart @4.1.23
>  R-spatial @7.3-17
>  R-survival @3.7-0
>  R-gmp @0.7-5
>  R-Rmpfr @1.0-0
>  R-base64enc @0.1-3
>  R-cli @3.6.3
>  R-glue @1.8.0
>  R-magrittr @2.0.3
>  R-rlang @1.1.4
>  R-vctrs @0.6.5
>  R-digest @0.6.37
>  R-stringi @1.8.4
>  R-app @1.82
>  R-jsonlite @1.8.9
>  R-purrr @1.0.2
>  R-xml2 @1.3.6
>  R-backports @1.5.0
>  R-gtools @3.9.5
>  R-proxy @0.4-27
>  R-e1071 @1.7-16
> Continue? [Y/n]:
>
> On Wed, Jun 10, 2026 at 4:24 PM Kenneth Wolcott
> <kennethwolcott at gmail.com> wrote:
> >
> > How to fix this?
> >
> > I hope that these ports are arm64 and not universal...
> >
> > Here is an excerpt of the last attempt when I agree to an revbuild:
> >
> > DEBUG: universal_variant is false, so not adding the default universal variant
> > DEBUG: Executing variant gcc14 provides gcc14
> > Error: R-Matrix: Variant gcc14 conflicts with gcc15
> > DEBUG: Error evaluating variants
> >     while executing
> > "error "Error evaluating variants""
> >     (procedure "mportopen" line 72)
> >     invoked from within
> > "mportopen $porturl $interp_options $installedvariations"
> > Error: Unable to open port: Error evaluating variants
> > DEBUG: Rebuilding port R-backports finished with status 1
> > DEBUG: rev-upgrade failed: Error rebuilding R-backports
> >     while executing
> > "error "Error rebuilding $portname""
> >     (procedure "revupgrade_scanandrebuild" line 489)
> >     invoked from within
> > "revupgrade_scanandrebuild broken_port_counts $opts"
> > Error: rev-upgrade failed: Error rebuilding R-backports
> > Error: Follow https://guide.macports.org/#project.tickets if you
> > believe there is a bug.
> > ~:
> >
> >
> > R-app @1.82
> >  R-MASS @7.3-61
> >  R-class @7.3-22
> >  R-backports @1.5.0
> >  R-base64enc @0.1-3
> >  R-cli @3.6.3
> >  R-digest @0.6.37
> >  R-foreign @0.8-87
> >  R-glue @1.8.0
> >  R-gmp @0.7-5
> >  R-Rmpfr @1.0-0
> >  R-gtools @3.9.5
> >  R-jsonlite @1.8.9
> >  R-lattice @0.22-6
> >  R-Matrix @1.7-1+gcc14
> >  R-magrittr @2.0.3
> >  R-nlme @3.1-166+gcc14
> >  R-mgcv @1.9-1+gcc14
> >  R-nnet @7.3-19
> >  R-proxy @0.4-27
> >  R-e1071 @1.7-16
> >  R-rlang @1.1.4
> >  R-rpart @4.1.23
> >  R-spatial @7.3-17
> >  R-stringi @1.8.4
> >  R-survival @3.7-0
> >  R-vctrs @0.6.5
> >  R-purrr @1.0.2
> >  R-xml2 @1.3.6
> > Continue? [Y/n]:
> >
> > Every time I say yes, it dies...
> >
> > Thanks,
> > Ken Wolcott