Unable to upgrade R language

[vkuznet (Valentin Kuznetsov)]

Hi, for several release iterations I can't upgrade R to newer version. My R port is outdated with version saying 4.1.3_0 < 4.2.1_0. I supply main.log and config.log which fails due to the following:

:info:configure checking how to get verbose linking output from /opt/local/bin/gfortran-mp-12... configure: WARNING: compilation failed
:info:configure checking for Fortran libraries of /opt/local/bin/gfortran-mp-12...
:info:configure checking how to get verbose linking output from /opt/local/bin/clang-mp-14... configure: WARNING: cannot determine how to obtain linking information from /opt/local/bin/clang-mp-14
:info:configure checking for C libraries of /opt/local/bin/clang-mp-14...
:info:configure checking for dummy main to link with Fortran libraries... none
:info:configure checking for Fortran name-mangling scheme... configure: error: in `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-4.2.1':
:info:configure configure: error: cannot compile a simple Fortran program
:info:configure See `config.log' for more details

[vkuznet (Valentin Kuznetsov)]

main log

[vkuznet (Valentin Kuznetsov)]

config log file

[ryandesign (Ryan Carsten Schmidt)]

Looks like a problem with the gcc12 port, which has recently had updates. Make sure you've received all the available updates (with sudo port selfupdate and sudo port upgrade outdated). If you already have, then there may be a problem that needs to be fixed in that port.

[vkuznet (Valentin Kuznetsov)]

I should stated this in a ticket, yes, I do have full selfupdate and the only port which is outdated is this one. I also did not report it for couple of weeks since I thought something will pop up in updates but finally after several weeks and several selfupdates I confirm that I still have this issue. Here is my current status:

port outdated
The following installed ports are outdated:
R                              4.1.3_0 < 4.2.1_0

[cjones051073 (Chris Jones)]

Problem is not an issue with gcc12 per se, but almost certainly just a consequence of upstreams decision to start to use rpath. If a port exclusively uses gcc, its handled consistently. This though is quite uncommon. Much more common is for ports to mix using clang and gcc, as here, and this can lead to issues, as clang of course knows nothing if gcc’s rpath requirements. (Reading between the lines I feel this mixing is something upstream has not properly taken into account in their decision to start to use rpath)..

[cjones051073 (Chris Jones)]

Cannot reproduce...

I configured and built R just fine locally, using the example same variants as you use above (you add +accelerate which is not active by default).

I also just triggered a rebuild in the build bots, to pick up the newer gcc variant that is now the default (gcc11 -> gcc12) and that also is showing no signs of any problems.

​https://ports.macports.org/port/R/builds/

So am I afraid whatever the issue is it appears specific to your setup. Can you make sure your ports tree is m*really* update to date

sudo port -d sync

then try again.

[vkuznet (Valentin Kuznetsov)]

Hi, I run port -d sync but the issue remained. So, I decided to uninstall the port and got the following error:

sudo port install R
Error: Requested variants "+builtin_lapack+cairo+gcc12+openmp+recommended+x11" do not match those the build was started with: "+accelerate+cairo+gcc12+openmp+recommended+x11".
Error: Please use the same variants again, or run 'port clean R' first to remove the existing partially completed build.
Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
Error: Processing of port R failed

Therefore, I did port clean R and then finally reinstall the R port. Since set of variants has changed I think this was the root of the problem. Since issue is fixed after clean action and reinstalling the port we may close this ticket.

[mascguy (Christopher Nielsen)]

Replying to vkuznet:

Therefore, I did port clean R and then finally reinstall the R port. Since set of variants has changed I think this was the root of the problem. Since issue is fixed after clean action and reinstalling the port we may close this ticket.

Great, glad the issue is resolved!