arpack @3.1.3: Undefined symbols

[steven.levis@…]

Here's the log file. Already tried clean --all and upgrade outdated

version:1
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:main Executing org.macports.main (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.archivefetch (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.configure (arpack)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Sat Nov  9 22:14:49 PST 2013
:notice:build --->  Building arpack
:debug:build Executing org.macports.build (arpack)
:debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3" && /usr/bin/make -j8 -w all'
:debug:build Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3" && /usr/bin/make -j8 -w all 
:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3'
:info:build Making all in UTIL
:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3/UTIL'
:info:build make[1]: Nothing to be done for `all'.
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3/UTIL'
:info:build Making all in SRC
:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3/SRC'
:info:build make[1]: Nothing to be done for `all'.
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3/SRC'
:info:build Making all in .
:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3'
:info:build /bin/sh ./libtool --tag=F77   --mode=link /opt/local/bin/gfortran-mp-4.8  -O2 -m64 -no-undefined -version-info 2:0 /usr/lib/libblas.dylib /usr/lib/liblapack.dylib -o libarpack.la -rpath /opt/local/lib  ./SRC/libarpacksrc.la ./UTIL/libarpackutil.la -lblas -llapack  
:info:build libtool: link: /opt/local/bin/gfortran-mp-4.8 -dynamiclib  -o .libs/libarpack.2.dylib   -Wl,-force_load,./SRC/.libs/libarpacksrc.a -Wl,-force_load,./UTIL/.libs/libarpackutil.a  -lblas -llapack  -O2 -m64   -install_name  /opt/local/lib/libarpack.2.dylib -compatibility_version 3 -current_version 3.0 -Wl,-single_module
:info:build Undefined symbols for architecture x86_64:
:info:build   "_cgeqr2_", referenced from:
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_clacpy_", referenced from:
:info:build       _cnapps_ in libarpacksrc.a(cnapps.o)
:info:build       _cneigh_ in libarpacksrc.a(cneigh.o)
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_clahqr_", referenced from:
:info:build       _cneigh_ in libarpacksrc.a(cneigh.o)
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_clanhs_", referenced from:
:info:build       _cnaitr_ in libarpacksrc.a(cnaitr.o)
:info:build       _cnapps_ in libarpacksrc.a(cnapps.o)
:info:build   "_clarnv_", referenced from:
:info:build       _cgetv0_ in libarpacksrc.a(cgetv0.o)
:info:build   "_clartg_", referenced from:
:info:build       _cnapps_ in libarpacksrc.a(cnapps.o)
:info:build   "_clascl_", referenced from:
:info:build       _cnaitr_ in libarpacksrc.a(cnaitr.o)
:info:build   "_claset_", referenced from:
:info:build       _cnapps_ in libarpacksrc.a(cnapps.o)
:info:build       _cneigh_ in libarpacksrc.a(cneigh.o)
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_ctrevc_", referenced from:
:info:build       _cneigh_ in libarpacksrc.a(cneigh.o)
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_ctrsen_", referenced from:
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_cunm2r_", referenced from:
:info:build       _cneupd_ in libarpacksrc.a(cneupd.o)
:info:build   "_dgeqr2_", referenced from:
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build       _dseupd_ in libarpacksrc.a(dseupd.o)
:info:build   "_dlabad_", referenced from:
:info:build       _dlaqrb_ in libarpacksrc.a(dlaqrb.o)
:info:build       _dnaitr_ in libarpacksrc.a(dnaitr.o)
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build       _znaitr_ in libarpacksrc.a(znaitr.o)
:info:build       _znapps_ in libarpacksrc.a(znapps.o)
:info:build   "_dlacpy_", referenced from:
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build       _dneigh_ in libarpacksrc.a(dneigh.o)
:info:build       _dsapps_ in libarpacksrc.a(dsapps.o)
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build       _dseupd_ in libarpacksrc.a(dseupd.o)
:info:build   "_dlaev2_", referenced from:
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build   "_dlahqr_", referenced from:
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build   "_dlamch_", referenced from:
:info:build       _dlaqrb_ in libarpacksrc.a(dlaqrb.o)
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build       _dnaitr_ in libarpacksrc.a(dnaitr.o)
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build       _dnaup2_ in libarpacksrc.a(dnaup2.o)
:info:build       _dnaupd_ in libarpacksrc.a(dnaupd.o)
:info:build       _dnconv_ in libarpacksrc.a(dnconv.o)
:info:build       ...
:info:build   "_dlanhs_", referenced from:
:info:build       _dlaqrb_ in libarpacksrc.a(dlaqrb.o)
:info:build       _dnaitr_ in libarpacksrc.a(dnaitr.o)
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build   "_dlanst_", referenced from:
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build   "_dlanv2_", referenced from:
:info:build       _dlaqrb_ in libarpacksrc.a(dlaqrb.o)
:info:build   "_dlapy2_", referenced from:
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build       _dsortc_ in libarpacksrc.a(dsortc.o)
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build       _dnaup2_ in libarpacksrc.a(dnaup2.o)
:info:build       _dnconv_ in libarpacksrc.a(dnconv.o)
:info:build       _dneigh_ in libarpacksrc.a(dneigh.o)
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build       ...
:info:build   "_dlarf_", referenced from:
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build   "_dlarfg_", referenced from:
:info:build       _dlaqrb_ in libarpacksrc.a(dlaqrb.o)
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build   "_dlarnv_", referenced from:
:info:build       _dgetv0_ in libarpacksrc.a(dgetv0.o)
:info:build   "_dlartg_", referenced from:
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build       _dsapps_ in libarpacksrc.a(dsapps.o)
:info:build   "_dlascl_", referenced from:
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build       _dnaitr_ in libarpacksrc.a(dnaitr.o)
:info:build       _dsaitr_ in libarpacksrc.a(dsaitr.o)
:info:build   "_dlaset_", referenced from:
:info:build       _dnapps_ in libarpacksrc.a(dnapps.o)
:info:build       _dsapps_ in libarpacksrc.a(dsapps.o)
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build   "_dlasr_", referenced from:
:info:build       _dstqrb_ in libarpacksrc.a(dstqrb.o)
:info:build   "_dorm2r_", referenced from:
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build       _dseupd_ in libarpacksrc.a(dseupd.o)
:info:build   "_dsteqr_", referenced from:
:info:build       _dseupd_ in libarpacksrc.a(dseupd.o)
:info:build   "_dtrevc_", referenced from:
:info:build       _dneigh_ in libarpacksrc.a(dneigh.o)
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build   "_dtrsen_", referenced from:
:info:build       _dneupd_ in libarpacksrc.a(dneupd.o)
:info:build   "_sgeqr2_", referenced from:
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build       _sseupd_ in libarpacksrc.a(sseupd.o)
:info:build   "_slabad_", referenced from:
:info:build       _slaqrb_ in libarpacksrc.a(slaqrb.o)
:info:build       _snaitr_ in libarpacksrc.a(snaitr.o)
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build       _cnaitr_ in libarpacksrc.a(cnaitr.o)
:info:build       _cnapps_ in libarpacksrc.a(cnapps.o)
:info:build   "_slacpy_", referenced from:
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build       _sneigh_ in libarpacksrc.a(sneigh.o)
:info:build       _ssapps_ in libarpacksrc.a(ssapps.o)
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build       _sseupd_ in libarpacksrc.a(sseupd.o)
:info:build   "_slaev2_", referenced from:
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build   "_slahqr_", referenced from:
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build   "_slamch_", referenced from:
:info:build       _slaqrb_ in libarpacksrc.a(slaqrb.o)
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build       _snaitr_ in libarpacksrc.a(snaitr.o)
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build       _snaup2_ in libarpacksrc.a(snaup2.o)
:info:build       _snaupd_ in libarpacksrc.a(snaupd.o)
:info:build       _snconv_ in libarpacksrc.a(snconv.o)
:info:build       ...
:info:build   "_slanhs_", referenced from:
:info:build       _slaqrb_ in libarpacksrc.a(slaqrb.o)
:info:build       _snaitr_ in libarpacksrc.a(snaitr.o)
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build   "_slanst_", referenced from:
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build   "_slanv2_", referenced from:
:info:build       _slaqrb_ in libarpacksrc.a(slaqrb.o)
:info:build   "_slapy2_", referenced from:
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build       _ssortc_ in libarpacksrc.a(ssortc.o)
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build       _snaup2_ in libarpacksrc.a(snaup2.o)
:info:build       _snconv_ in libarpacksrc.a(snconv.o)
:info:build       _sneigh_ in libarpacksrc.a(sneigh.o)
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build       ...
:info:build   "_slarf_", referenced from:
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build   "_slarfg_", referenced from:
:info:build       _slaqrb_ in libarpacksrc.a(slaqrb.o)
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build   "_slarnv_", referenced from:
:info:build       _sgetv0_ in libarpacksrc.a(sgetv0.o)
:info:build   "_slartg_", referenced from:
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build       _ssapps_ in libarpacksrc.a(ssapps.o)
:info:build   "_slascl_", referenced from:
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build       _snaitr_ in libarpacksrc.a(snaitr.o)
:info:build       _ssaitr_ in libarpacksrc.a(ssaitr.o)
:info:build   "_slaset_", referenced from:
:info:build       _snapps_ in libarpacksrc.a(snapps.o)
:info:build       _ssapps_ in libarpacksrc.a(ssapps.o)
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build   "_slasr_", referenced from:
:info:build       _sstqrb_ in libarpacksrc.a(sstqrb.o)
:info:build   "_sorm2r_", referenced from:
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build       _sseupd_ in libarpacksrc.a(sseupd.o)
:info:build   "_ssteqr_", referenced from:
:info:build       _sseupd_ in libarpacksrc.a(sseupd.o)
:info:build   "_strevc_", referenced from:
:info:build       _sneigh_ in libarpacksrc.a(sneigh.o)
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build   "_strsen_", referenced from:
:info:build       _sneupd_ in libarpacksrc.a(sneupd.o)
:info:build   "_zgeqr2_", referenced from:
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build   "_zlacpy_", referenced from:
:info:build       _znapps_ in libarpacksrc.a(znapps.o)
:info:build       _zneigh_ in libarpacksrc.a(zneigh.o)
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build   "_zlahqr_", referenced from:
:info:build       _zneigh_ in libarpacksrc.a(zneigh.o)
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build   "_zlanhs_", referenced from:
:info:build       _znaitr_ in libarpacksrc.a(znaitr.o)
:info:build       _znapps_ in libarpacksrc.a(znapps.o)
:info:build   "_zlarnv_", referenced from:
:info:build       _zgetv0_ in libarpacksrc.a(zgetv0.o)
:info:build   "_zlartg_", referenced from:
:info:build       _znapps_ in libarpacksrc.a(znapps.o)
:info:build   "_zlascl_", referenced from:
:info:build       _znaitr_ in libarpacksrc.a(znaitr.o)
:info:build   "_zlaset_", referenced from:
:info:build       _znapps_ in libarpacksrc.a(znapps.o)
:info:build       _zneigh_ in libarpacksrc.a(zneigh.o)
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build   "_ztrevc_", referenced from:
:info:build       _zneigh_ in libarpacksrc.a(zneigh.o)
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build   "_ztrsen_", referenced from:
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build   "_zunm2r_", referenced from:
:info:build       _zneupd_ in libarpacksrc.a(zneupd.o)
:info:build ld: symbol(s) not found for architecture x86_64
:info:build collect2: error: ld returned 1 exit status
:info:build make[1]: *** [libarpack.la] Error 1
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3'
:info:build make: *** [all-recursive] Error 1
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/work/arpack-ng-3.1.3" && /usr/bin/make -j8 -w all 
:info:build Exit code: 2
:error:build org.macports.build for port arpack returned: command execution failed
:debug:build Error code: CHILDSTATUS 60940 2
:debug:build Backtrace: command execution failed
    while executing
"system -nice 0 $fullcmdstring"
    ("eval" body line 1)
    invoked from within
"eval system $notty $nice \$fullcmdstring"
    invoked from within
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: targets not executed for arpack: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:error:build Failed to install arpack
:debug:build couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory
    while executing
"open [file join $dir tclIndex]"
:notice:build Please see the log file for port arpack for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_arpack/arpack/main.log

[ryandesign (Ryan Carsten Schmidt)]

The log is incomplete. Please ​clean and try again, then attach (not paste) the new log to this ticket.

[ryandesign (Ryan Carsten Schmidt)]

Oh sorry, I now see you did attach a complete log, in addition to the incomplete pasted one.

[mamoll (Mark Moll)]

This doesn't seem to happen for me on Mavericks. I noticed that on my machine, configure used "/opt/local/bin/gsed", while on yours it used "/usr/bin/sed". This seems like a minor thing, but could you try the following:

sudo port clean arpack
sudo port uninstall arpack
sudo port install gsed arpack

[steven.levis@…]

Still the same missing symbols after installing gsed. I confirmed that configure is using gsed. I'm starting to suspect gfortran since there is no macport for it. I am using gfortran-4.9

[steven.levis@…]

Replying to steven.levis@…:

Still the same missing symbols after installing gsed. I confirmed that configure is using gsed. I'm starting to suspect gfortran since there is no macport for it. I am using gfortran-4.9

nvm about that gfortran-4.9 comment. I see that gcc48 installs gfortran-mp-4.8, which is apparently what is being used in building arpack

[mamoll (Mark Moll)]

I am also using gcc48. I don't understand what is different between your setup and mine.

[steven.levis@…]

How can I replay, step-through, and debug the port build on my machine? Any pointers, links, etc., would be appreciated. I have experience building / configuring software on linux platforms.

[weibel@…]

I added a log (main2.log) file that seems to be similar to Stevens. I'm on OSX 10.10 and tried to build Arpack 3.1.5 while installing Octave.

[mamoll (Mark Moll)]

I am also on 10.10. I cannot reproduce this I tried both with and without atlas. In both cases, I used gcc49 as the fortran compiler. See attached log files main-atlas.log and main-noatlas.log.

[mamoll (Mark Moll)]

Presumably fixed by now. The current version is 3.6.2. Feel free to reopen if this is not fixed.