[MacPorts] #44084: R fails to upgrade with fortran compiler error
#44084: R fails to upgrade with fortran compiler error -------------------------+-------------------------------- Reporter: r1pp3r@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Keywords: R, gfortran | Port: R -------------------------+-------------------------------- 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 }}} -- Ticket URL: <https://trac.macports.org/ticket/44084> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Changes (by mf2k@…): * owner: macports-tickets@… => kjell.konis@… * keywords: R, gfortran => Comment: In the future, please Cc the port maintainers ({{{port info --maintainers R}}}). -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Comment (by 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? -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Comment (by mf2k@…): Please attach the complete main.log after cleaning the port. -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Comment (by 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? -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Comment (by egall@…): 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... -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Comment (by 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) }}} -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#44084: R fails to upgrade with fortran compiler error -----------------------+--------------------------- Reporter: r1pp3r@… | Owner: kjell.konis@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: R | -----------------------+--------------------------- Comment (by egall@…): Replying to [comment:8 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 -- Ticket URL: <https://trac.macports.org/ticket/44084#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
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