R fails to upgrade with fortran compiler error

[r1pp3r@…]

Trying to upgrade the R port fails, due to a Fortran configure error:

checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for /usr/bin/clang option to accept ISO C99... none needed
checking for /usr/bin/clang option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether /usr/bin/clang supports -c -o FILE.lo... yes
checking how to get verbose linking output from /opt/local/bin/gfortran-mp-4.8... configure: WARNING: compilation failed

checking for Fortran 77 libraries of /opt/local/bin/gfortran-mp-4.8... 
checking how to get verbose linking output from /usr/bin/clang... configure: WARNING: cannot determine how to obtain linking information from /usr/bin/clang

checking for C libraries of /usr/bin/clang... 
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 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-3.1.0':
configure: error: cannot compile a simple Fortran program
See `config.log' for more details
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.1.0" && ./configure --prefix=/opt/local/Library/Frameworks --enable-R-framework --enable-R-shlib --enable-BLAS-shlib --disable-openmp --with-readline --with-aqua --without-tcltk --with-libpng --with-ICU --with-included-gettext --without-internal-tzcode --with-blas="-framework vecLib" --with-lapack="-framework vecLib" --with-x --with-jpeglib --x-include=/opt/local/include/X11 --x-lib=/opt/local/lib --with-cairo --with-recommended-packages 
Exit code: 1
Error: Failed to configure R, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.1.0/config.log
Error: org.macports.configure for port R returned: configure failure: command execution failed
Warning: targets not executed for R: org.macports.install org.macports.configure org.macports.build org.macports.destroot
Please see the log file for port R for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets

[mf2k (Frank Schima)]

In the future, please Cc the port maintainers (port info --maintainers R).

[cooljeanius (Eric Gallager)]

Cc Me!

[petrrr]

Cc Me!

[kjellpk (Kjell Konis)]

Maintainer here: sorry for the late reply (was on vacation). So I am not able to reproduce this. For me, the R port builds fine on an up-to-date MacPorts installation on Mavericks. Is your gcc48 port up-to-date?

[mf2k (Frank Schima)]

Please attach the complete main.log after cleaning the port.

[r1pp3r@…]

Hi, sorry for the late reply. I attached the main.log file. And yes, the gcc48 is up-to-date. Any help is highly appreciated?

[cooljeanius (Eric Gallager)]

Could you post the config.log file as well? I have a feeling as to what issue this might be, but we would need to see the config.log as well to know for sure...

[kjellpk (Kjell Konis)]

The config.log is attached as R-config.log. The problem is

<built-in>:0:0: internal compiler error: Abort trap: 6
364	gfortran-mp-4.8: internal compiler error: Abort trap: 6 (program f951)
365	./configure: line 2204: 23971 Abort trap: 6           $F77 -c $FFLAGS conftest.$ac_ext 1>&5
366	configure:7393: $? = 134
367	configure: failed program was:
368	|       program main
369	|
370	|       end

which is very similar to something I remember seeing fixed a while ago.

OP: if you run 'port info gcc48' does the first line of output say

gcc48 @4.8.2_2 (lang)

[cooljeanius (Eric Gallager)]

Replying to kjell.konis@…:

The config.log is attached as R-config.log.

Oops, missed that one, thanks for pointing it out.

The problem is

<built-in>:0:0: internal compiler error: Abort trap: 6
gfortran-mp-4.8: internal compiler error: Abort trap: 6 (program f951)
./configure: line 2204: 23971 Abort trap: 6           $F77 -c $FFLAGS conftest.$ac_ext 1>&5
configure:7393: $? = 134
configure: failed program was:
|       program main
|
|       end

which is very similar to something I remember seeing fixed a while ago.

OK, that's what I was guessing... iirc it was due to at least one of gmp/mpfr/libmpc being mis-built, which could have been revealed by running their test suites. The following tickets are still open about that:

• #40548
• #41753
• #42752
• #42940
• #42732 (and, by extension, #42731)
• #42733

[petrrr]

Cc Me!