Created attachment 186661 [details] Compilation logs When LTO is set: OPTIONS_FILE_SET+=LTO port fails to compile - see attached log.
Matching the settings in your build, but in a clean environment (poudriere), the build finishes successfully. http://pkg.awarnach.mathstat.dal.ca/data/11amd64-default/2017-09-24_10h20m09s/logs/R-3.4.1_7.log Could you try again with the suggestion at the end of your build? That is, try `make MAKE_JOBS_UNSAFE=yes build`.
I haven't updated ports for about two weeks. Maybe something is already fixed. I will double check. I will schedule the compilation today and should have the result by tomorrow.
I've been able to reproduce this now. I am considering just removing the LTO option. It's not turned on by default upstream and it's been a lot of trouble for questionable benefit.
Thank you for this hint: I have been having trouble building math/R under portmaster for the bast few months; when I saw this report, I checked: sure enough, I had the LTO option set. So I un-set it; this morning, the update of math/R from R-3.4.1_7 to R-3.4.1_8 using portmaster "Just Worked." (In my case, the apparent symptom seemed to involve the attempted use of an "ar" executable that was from a different toolchain than expected: a command-line option had been specified that the "ar" that was actually invoked failed to understand.)
(In reply to david from comment #4) David, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=220481
Thanks for reporting. The LTO option has been removed with the upgrade to 3.4.2.