gildas @201512a: Undefined symbols _ftvers_

[jpinedaf (Jaime Pineda)]

Hi,

I tried to install Gildas on my desktop which I just upgraded to ElCapitan. The Macports installation is fresh, and I already have the latest XCode and gcc installed. I also used port select to select the macport installed gcc. However I get the following error message:

(cd ./built/x86_64-darwin-gfortran && /opt/local/bin/gfortran-mp-5  -dynamiclib   -L/opt/local/lib -Wl,-headerpad_max_install_names -shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so getcar.o ctrlc.o import-c.o sic-message-c.o sic-sicimport.o gmaster-c.o sic_python.o sic_parse_mod.o sic_inter_mod.o sic-interfaces-public.o sic-interfaces-private.o sic-interfaces.o aliasvar.o argauto.o abbrev.o analyse.o argumexp.o codefunc.o compute.o controlc.o defvar.o delete.o delvar.o desc.o dofunc.o dofuncl.o dofuncs.o dofuncd.o dofunci.o editor.o error.o evaluate.o examine.o execsic.o expand_macro.o expr.o fill.o fits.o foreign.o forme.o get.o getcom.o getlin.o hashing.o header.o help.o import.o inicli.o inihel.o interstate.o intrinsic.o let.o liste.o loop.o lun.o macro.o math.o minimize.o modify.o operand.o powell.o procedure.o prompt.o read.o reduce.o sicfits.o gmessage.o sicopt.o sic-package.o sic-python-f.o sicsay.o sicset.o sicsub.o sicvms.o siman.o sort.o stack.o symbol.o task.o transpose.o varexp.o varexp-generic.o vector.o wrpro.o xvariable.o zroutines.o gmaster.o sic-message.o \
        -o /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib -L/opt/local/lib -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -L/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/  -lggui -lgcore -lgio -lgwcs -lgmath -lgsys -lginc -lslatec -framework Accelerate -lcfitsio  -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -ldl -framework CoreFoundation -lpython2.7  -lm -ldl -install_name @executable_path/../lib/libsic.so)
Undefined symbols for architecture x86_64:
  "_ftvers_", referenced from:
      _sicapropos_ in sicset.o
      _sicapropos_cfitsio_vers_ in sicset.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[3]: *** [/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so] Error 1
make[2]: *** [default-install] Error 1
make[1]: *** [default-install] Error 1
make: *** [default-install] Error 1
Command failed: source admin/gildas-env.sh -c /opt/local/bin/gfortran-mp-5 -s /opt/local/include:/opt/local/lib:/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/ && export GAG_SLDFLAGS='-shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@) -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@)' && export DYLD_LIBRARY_PATH=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib && make install
Exit code: 2
Error: org.macports.build for port gildas returned: command execution failed
Warning: targets not executed for gildas: org.macports.activate org.macports.build org.macports.destroot org.macports.install
Please see the log file for port gildas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port gildas failed

The last lines of the log report gives this information:

:info:build (cd ./built/x86_64-darwin-gfortran && /opt/local/bin/gfortran-mp-5  -dynamiclib   -L/opt/local/lib -Wl,-headerpad_max_install_names -shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so getcar.o ctrlc.o import-c.o sic-message-c.o sic-sicimport.o gmaster-c.o sic_python.o sic_parse_mod.o sic_inter_mod.o sic-interfaces-public.o sic-interfaces-private.o sic-interfaces.o aliasvar.o argauto.o abbrev.o analyse.o argumexp.o codefunc.o compute.o controlc.o defvar.o delete.o delvar.o desc.o dofunc.o dofuncl.o dofuncs.o dofuncd.o dofunci.o editor.o error.o evaluate.o examine.o execsic.o expand_macro.o expr.o fill.o fits.o foreign.o forme.o get.o getcom.o getlin.o hashing.o header.o help.o import.o inicli.o inihel.o interstate.o intrinsic.o let.o liste.o loop.o lun.o macro.o math.o minimize.o modify.o operand.o powell.o procedure.o prompt.o read.o reduce.o sicfits.o gmessage.o sicopt.o sic-package.o sic-python-f.o sicsay.o sicset.o sicsub.o sicvms.o siman.o sort.o stack.o symbol.o task.o transpose.o varexp.o varexp-generic.o vector.o wrpro.o xvariable.o zroutines.o gmaster.o sic-message.o \
:info:build 	-o /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib -L/opt/local/lib -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -L/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/  -lggui -lgcore -lgio -lgwcs -lgmath -lgsys -lginc -lslatec -framework Accelerate -lcfitsio  -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -ldl -framework CoreFoundation -lpython2.7  -lm -ldl -install_name @executable_path/../lib/libsic.so)
:info:build Undefined symbols for architecture x86_64:
:info:build   "_ftvers_", referenced from:
:info:build       _sicapropos_ in sicset.o
:info:build       _sicapropos_cfitsio_vers_ in sicset.o
:info:build ld: symbol(s) not found for architecture x86_64
:info:build collect2: error: ld returned 1 exit status
:info:build make[3]: *** [/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so] Error 1
:info:build make[2]: *** [default-install] Error 1
:info:build make[1]: *** [default-install] Error 1
:info:build make: *** [default-install] Error 1
:info:build Command failed: source admin/gildas-env.sh -c /opt/local/bin/gfortran-mp-5 -s /opt/local/include:/opt/local/lib:/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/ && export GAG_SLDFLAGS='-shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@) -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@)' && export DYLD_LIBRARY_PATH=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib && make install
:info:build Exit code: 2
:error:build org.macports.build for port gildas returned: command execution failed
:debug:build Error code: NONE
:debug:build Backtrace: command execution failed
    while executing
"proc-org.macports.build-build-0 org.macports.build"
    ("eval" body line 1)
    invoked from within
"eval $procedure $targetname"
:info:build Warning: targets not executed for gildas: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port gildas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/main.log

Cheers,
Jaime

[smaret (Sebastien Maret)]

Could you please try to install the gfortran variant of the fftw port:

sudo port install fftw-3 +gfortran

and then try to rebuild gildas?

[jpinedaf (Jaime Pineda)]

I installed fftw-3 but that does not fix the problem

bash-3.2$ sudo port install fftw-3 +gfortran
--->  Computing dependencies for fftw-3
--->  Fetching archive for fftw-3
--->  Attempting to fetch fftw-3-3.3.4_1+gfortran.darwin_15.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/fftw-3
--->  Attempting to fetch fftw-3-3.3.4_1+gfortran.darwin_15.x86_64.tbz2 from http://lil.fr.packages.macports.org/fftw-3
--->  Attempting to fetch fftw-3-3.3.4_1+gfortran.darwin_15.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/fftw-3
--->  Fetching distfiles for fftw-3
--->  Attempting to fetch fftw-3.3.4.tar.gz from http://nue.de.distfiles.macports.org/macports/distfiles/fftw-3
--->  Verifying checksums for fftw-3
--->  Extracting fftw-3
--->  Applying patches to fftw-3
--->  Configuring fftw-3
--->  Building fftw-3
--->  Staging fftw-3 into destroot
--->  Installing fftw-3 @3.3.4_1+gfortran
--->  Deactivating fftw-3 @3.3.4_1
--->  Cleaning fftw-3
--->  Activating fftw-3 @3.3.4_1+gfortran
--->  Cleaning fftw-3
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.
bash-3.2$  sudo port install gildas
--->  Computing dependencies for gildas
--->  Building gildas
Error: org.macports.build for port gildas returned: command execution failed
Please see the log file for port gildas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port gildas failed

the error log file gives the following information:

bash-3.2$ more     /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/main.log

:info:build (cd ./built/x86_64-darwin-gfortran && /opt/local/bin/gfortran-mp-5  -dynamiclib   -L/opt/local/lib -Wl,-headerpad_max_install_names -shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so getcar.o ctrlc.o import-c.o sic-message-c.o sic-sicimport.o gmaster-c.o sic_python.o sic_parse_mod.o sic_inter_mod.o sic-interfaces-public.o sic-interfaces-private.o sic-interfaces.o aliasvar.o argauto.o abbrev.o analyse.o argumexp.o codefunc.o compute.o controlc.o defvar.o delete.o delvar.o desc.o dofunc.o dofuncl.o dofuncs.o dofuncd.o dofunci.o editor.o error.o evaluate.o examine.o execsic.o expand_macro.o expr.o fill.o fits.o foreign.o forme.o get.o getcom.o getlin.o hashing.o header.o help.o import.o inicli.o inihel.o interstate.o intrinsic.o let.o liste.o loop.o lun.o macro.o math.o minimize.o modify.o operand.o powell.o procedure.o prompt.o read.o reduce.o sicfits.o gmessage.o sicopt.o sic-package.o sic-python-f.o sicsay.o sicset.o sicsub.o sicvms.o siman.o sort.o stack.o symbol.o task.o transpose.o varexp.o varexp-generic.o vector.o wrpro.o xvariable.o zroutines.o gmaster.o sic-message.o \
:info:build     -o /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib -L/opt/local/lib -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -L/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/  -lggui -lgcore -lgio -lgwcs -lgmath -lgsys -lginc -lslatec -framework Accelerate -lcfitsio  -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -ldl -framework CoreFoundation -lpython2.7  -lm -ldl -install_name @executable_path/../lib/libsic.so)
:info:build Undefined symbols for architecture x86_64:
:info:build   "_ftvers_", referenced from:
:info:build       _sicapropos_ in sicset.o
:info:build       _sicapropos_cfitsio_vers_ in sicset.o
:info:build ld: symbol(s) not found for architecture x86_64
:info:build collect2: error: ld returned 1 exit status
:info:build make[3]: *** [/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so] Error 1
:info:build make[2]: *** [default-install] Error 1
:info:build make[1]: *** [default-install] Error 1
:info:build make: *** [default-install] Error 1
:info:build Command failed: source admin/gildas-env.sh -c /opt/local/bin/gfortran-mp-5 -s /opt/local/include:/opt/local/lib:/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/ && export GAG_SLDFLAGS='-shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@) -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@)' && export DYLD_LIBRARY_PATH=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib && make install
:info:build Exit code: 2
:error:build org.macports.build for port gildas returned: command execution failed
:debug:build Error code: NONE
:debug:build Backtrace: command execution failed
    while executing
"proc-org.macports.build-build-0 org.macports.build"
    ("eval" body line 1)
    invoked from within
"eval $procedure $targetname"
:info:build Warning: targets not executed for gildas: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port gildas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/main.log

Any ideas?

[smaret (Sebastien Maret)]

Sorry, I meant fftw-3-single, not fftw-3:

sudo port install fftw-3-single +gfortran

[jpinedaf (Jaime Pineda)]

that didn't work neither

bash-3.2$ sudo port install fftw-3-single +gfortran
Password:
--->  Computing dependencies for fftw-3-single
--->  Fetching archive for fftw-3-single
--->  Attempting to fetch fftw-3-single-3.3.4_1+gfortran.darwin_15.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/fftw-3-single
--->  Attempting to fetch fftw-3-single-3.3.4_1+gfortran.darwin_15.x86_64.tbz2 from http://lil.fr.packages.macports.org/fftw-3-single
--->  Attempting to fetch fftw-3-single-3.3.4_1+gfortran.darwin_15.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/fftw-3-single
--->  Fetching distfiles for fftw-3-single
--->  Verifying checksums for fftw-3-single
--->  Extracting fftw-3-single
--->  Applying patches to fftw-3-single
--->  Configuring fftw-3-single
--->  Building fftw-3-single
--->  Staging fftw-3-single into destroot
--->  Installing fftw-3-single @3.3.4_1+gfortran
--->  Activating fftw-3-single @3.3.4_1+gfortran
--->  Cleaning fftw-3-single
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.       

bash-3.2$ sudo port install gildas
--->  Computing dependencies for gildas
--->  Fetching archive for gildas
--->  Attempting to fetch gildas-201512a_0+gcc5.darwin_15.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/gildas
--->  Attempting to fetch gildas-201512a_0+gcc5.darwin_15.x86_64.tbz2 from http://lil.fr.packages.macports.org/gildas
--->  Attempting to fetch gildas-201512a_0+gcc5.darwin_15.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/gildas
--->  Fetching distfiles for gildas
--->  Verifying checksums for gildas
--->  Extracting gildas
--->  Applying patches to gildas
--->  Configuring gildas
--->  Building gildas
Error: org.macports.build for port gildas returned: command execution failed
Please see the log file for port gildas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port gildas failed

the error message in the logfile is:

:info:build (cd ./built/x86_64-darwin-gfortran && /opt/local/bin/gfortran-mp-5  -dynamiclib   -L/opt/local/lib -Wl,-headerpad_max_install_names -shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/libsic.so getcar.o ctrlc.o import-c.o sic-message-c.o sic-sicimport.o gmaster-c.o sic_python.o sic_parse_mod.o sic_inter_mod.o sic-interfaces-public.o sic-interfaces-private.o sic-interfaces.o aliasvar.o argauto.o abbrev.o analyse.o argumexp.o codefunc.o compute.o controlc.o defvar.o delete.o delvar.o desc.o dofunc.o dofuncl.o dofuncs.o dofuncd.o dofunci.o editor.o error.o evaluate.o examine.o execsic.o expand_macro.o expr.o fill.o fits.o foreign.o forme.o get.o getcom.o getlin.o hashing.o header.o help.o import.o inicli.o inihel.o interstate.o intrinsic.o let.o liste.o loop.o lun.o macro.o math.o minimize.o modify.o operand.o powell.o procedure.o prompt.o read.o reduce.o sicfits.o gmessage.o sicopt.o sic-package.o sic-python-f.o sicsay.o sicset.o sicsub.o sicvms.o siman.o sort.o stack.o symbol.o task.o transpose.o varexp.o varexp-generic.o vector.o wrpro.o xvariable.o zroutines.o gmaster.o sic-message.o \
:info:build     -o /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib -L/opt/local/lib -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -L/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/  -lggui -lgcore -lgio -lgwcs -lgmath -lgsys -lginc -lslatec -framework Accelerate -lcfitsio  -L/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -ldl -framework CoreFoundation -lpython2.7  -lm -ldl -install_name @executable_path/../lib/libsic.so)
:info:build Undefined symbols for architecture x86_64:
:info:build   "_ftvers_", referenced from:
:info:build       _sicapropos_ in sicset.o
:info:build       _sicapropos_cfitsio_vers_ in sicset.o
:info:build ld: symbol(s) not found for architecture x86_64
:info:build collect2: error: ld returned 1 exit status
:info:build make[3]: *** [/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib/libsic.so] Error 1
:info:build make[2]: *** [default-install] Error 1
:info:build make[1]: *** [default-install] Error 1
:info:build make: *** [default-install] Error 1
:info:build Command failed: source admin/gildas-env.sh -c /opt/local/bin/gfortran-mp-5 -s /opt/local/include:/opt/local/lib:/System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/ && export GAG_SLDFLAGS='-shared -o /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@) -install_name /opt/local/lib/gildas/x86_64-darwin-gfortran/lib/$(notdir $@)' && export DYLD_LIBRARY_PATH=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gildas/gildas/work/gildas-src-dec15a/integ/x86_64-darwin-gfortran/lib && make install

[smaret (Sebastien Maret)]

Do you have IRAF installed on your computer? Apparently it ships its own version of CFITSIO, and I wonder if somehow GILDAS is built against it if it is present.

[smaret (Sebastien Maret)]

Indeed the bug seems to be related to the Fortran interface of the CFITSIO, which is missing in the default variant of the corresponding port. Please try the following:

sudo port install cfitsio +gcc5
sudo port clean gildas
sudo port install gildas

and let me know if this solves the problem.

[smaret (Sebastien Maret)]

This should be fixed by r145605.

[jpinedaf (Jaime Pineda)]

yes, this fixes it! thanks a lot