gnudatalanguage build fails due to libtool "version mismatch error"

[davidagalvan@…]

Hello,

I am trying to install gnudatalanguage on my Intel MacBook Pro (OS 10.6.3). The port install went well until the very end, when it failed. I was directed by the screen text to look at the logfile "/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log"

The last part of that log file reported: "Version mismatch error. This is libtool 2.2.6b, but the definition of this LT_INIT comes from libtool 2.2.10. You should recreate aclocal.m4 with macros from libtool 2.2.6b and run autoconf again."

How do I do what it suggests? I'd like to get GDL running as soon as possible.

More of that logfile below: (Thanks in advance for any help you can provide!)

--->  Computing dependencies for gnudatalanguage
--->  Building gnudatalanguage
Error: Target org.macports.build returned: shell command failed
Log for gnudatalanguage is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>
dgalvan-09153112037:~ dgalvan$ vi /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log
dgalvan-09153112037:~ dgalvan$ vi /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log

:info:build libtool: Version mismatch error.  This is libtool 2.2.6b, but the
:info:build libtool: definition of this LT_INIT comes from libtool 2.2.10.
:info:build libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b
:info:build libtool: and run autoconf again.
:info:build make[3]: *** [gdl] Error 63
:info:build make[2]: *** [all-recursive] Error 1
:info:build make[1]: *** [all-recursive] Error 1
:info:build make: *** [all] Error 2
:info:build shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/work/gdl-0.9rc4" && /usr/bin/make -j2 all " returned error 2
:error:build Target org.macports.build returned: shell command failed
:debug:build Backtrace: shell command failed
    while executing
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: the following items did not execute (for gnudatalanguage): org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Log for gnudatalanguage is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log

[ryandesign (Ryan Carsten Schmidt)]

Please remember to preview before submitting, to use WikiFormatting, and to Cc the maintainers of the port.

[nerdling (Jeremy Lavergne)]

It looks like your libtool is outdated. Please do the following and let us know if it worked for you:

sudo port selfupdate
sudo port upgrade libtool
sudo port clean gnudatalanguage
sudo port install gnudatalanguage

[davidagalvan@…]

I ran the suggested commands. Same problem persists: "Shell command failed", and then in the logfile I see the version mismatch error again.

The selfupdate, upgrade libtool, and clean gnudatalanguage commands seemed to work with no reported problems. But the install gnudatalanguage command failed at the same place. Here is the command line response for that last part:

dgalvan-09153112037:~ dgalvan$ port version
Version: 1.9.1
dgalvan-09153112037:~ dgalvan$ sudo port install gnudatalanguage
--->  Computing dependencies for gnudatalanguage
--->  Building gnudatalanguage
Error: Target org.macports.build returned: shell command failed
Log for gnudatalanguage is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>

And now, the last part of that logfile:

:msg:main --->  Building gnudatalanguage:debug:build build phase started at Mon Jun 21 08:20:38 PDT 2010:debug:build Executing org.macports.build (gnudatalanguage):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_ports_math_gnudatalanguage/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.6':debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/work/gdl-0.9rc4" && /usr/bin/make -j2 all':info:build /usr/bin/make  all-recursive:info:build Making all in src:info:build Making all in antlr:info:build make[3]: Nothing to be done for `all'.:info:build Making all in pro:info:build Making all in dicom:info:build make[4]: Nothing to be done for `all'.:info:build make[4]: Nothing to be done for `all-am'.:info:build /bin/sh ../libtool --tag=CXX   --mode=link /usr/bin/g++-4.2  -pipe -O2 -arch x86_64  -L/opt/local/lib -arch x86_64 -L/opt/local/lib -L/opt/local/lib  -L/opt/local/lib -L/opt/local/lib -o gdl gdl-assocdata.o gdl-basic_fun_cl.o gdl-basic_fun.o gdl-basic_fun_jmg.o gdl-basic_op.o gdl-basic_pro.o gdl-basic_pro_jmg.o gdl-CFMTLexer.o gdl-color.o gdl-convert2.o gdl-datatypes.o gdl-dcommon.o gdl-dcompiler.o gdl-default_io.o gdl-dinterpreter.o gdl-dnode.o gdl-dpro.o gdl-dstructdesc.o gdl-dstructgdl.o gdl-dvar.o gdl-envt.o gdl-extrat.o gdl-FMTIn.o gdl-FMTLexer.o gdl-fmtnode.o gdl-FMTOut.o gdl-FMTParser.o gdl-gdleventhandler.o gdl-gdlexception.o gdl-gdlgstream.o gdl-GDLInterpreter.o gdl-GDLLexer.o gdl-GDLParser.o gdl-gdlpsstream.o gdl-gdlsvgstream.o gdl-gdlpython.o gdl-GDLTreeParser.o gdl-gdlwinstream.o gdl-gdlxstream.o gdl-getfmtast.o gdl-graphics.o gdl-gsl_fun.o gdl-ifmt.o gdl-initct.o gdl-initsysvar.o gdl-io.o gdl-libinit_cl.o gdl-libinit.o gd
l-libinit_jmg.o gdl-math_fun.o gdl-math_fun_jmg.o gdl-math_utl.o gdl-ncdf_att_cl
.o gdl-ncdf_cl.o gdl-ncdf_dim_cl.o gdl-ncdf_var_cl.o gdl-new.o gdl-objects.o gdl
-ofmt.o gdl-math_fun_ac.o gdl-libinit_ac.o gdl-math_fun_gm.o gdl-libinit_gm.o gd
l-math_fun_ng.o gdl-libinit_ng.o gdl-plotting.o gdl-print.o gdl-print_tree.o gdl
-read.o gdl-str.o gdl-terminfo.o gdl-topython.o gdl-typetraits.o gdl-hdf_fun.o g
dl-hdf_pro.o gdl-magick_cl.o gdl-gdlwidget.o gdl-widget.o gdl-basegdl.o gdl-hdf5
_fun.o gdl-libinit_mes.o gdl-file.o gdl-image.o gdl-gdljournal.o gdl-convol.o gd
l-convol_inc0.o gdl-convol_inc1.o gdl-convol_inc2.o gdl-sigfpehandler.o gdl-gdlz
stream.o gdl-arrayindex.o gdl-fftw.o gdl-mpi.o gdl-plot3d_nr.o gdl-grib.o gdl-pr
ognode.o gdl-prognodeexpr.o gdl-gdl.o ../src/antlr/libantlr.a -L/usr/X11R6/lib64
 -L/usr/X11R6/lib -lX11 -lmfhdf -lgslcblas -lgsl -L/opt/local/lib -L/opt/local -
lncurses -lpng -lopenjpeg -L/opt/local/lib -lreadline -lz -L/opt/local/lib -lgsl
 -lgslcblas -L/opt/local/lib -lplplotd -lplplotcxxd -L/opt/local/lib -lMagick++ 
-lMagickWand -lMagickCore -llcms -ltiff -lfreetype -ljpeg -L/opt/local/lib -lfon
tconfig -lexpat -lfreetype -lz -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -l
m -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework
/Versions/A/Libraries -lm -lpthread -lltdl -L/opt/local/lib -lnetcdf -L/opt/loca
l/lib -L/opt/local/lib/hdf -lmfhdf -ldf -ljpeg -lz -lsz -L/opt/local/lib -L/opt/
local/lib/hdf -L/opt/local/lib/hdf5 -lhdf5 -L/opt/local/lib -lfftw3 -L/opt/local
/lib -lfftw3f -L/opt/local/lib -lproj4 -L/opt/local/lib -ludunits2 -L/opt/local/
lib -lgrib_api -ljasper
:info:build libtool: Version mismatch error.  This is libtool 2.2.6b, but the
:info:build libtool: definition of this LT_INIT comes from libtool 2.2.10.
:info:build libtool: You should recreate aclocal.m4 with macros from libtool 2.2
.6b
:info:build libtool: and run autoconf again.
:info:build make[3]: *** [gdl] Error 63
:info:build make[2]: *** [all-recursive] Error 1
:info:build make[1]: *** [all-recursive] Error 1
:info:build make: *** [all] Error 2
:info:build shell command " cd "/opt/local/var/macports/build/_opt_local_var_mac
ports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/work/gdl-0.9
rc4" && /usr/bin/make -j2 all " returned error 2
:error:build Target org.macports.build returned: shell command failed
:debug:build Backtrace: shell command failed
    while executing
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: the following items did not execute (for gnudatalanguage): org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Log for gnudatalanguage is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_gnudatalanguage/main.log

I wonder. . . is it possible that I have two versions of libtool installed in two different places? When I run the command, whereis libtool I get:

dgalvan-09153112037:~ dgalvan$ whereis libtool
/usr/bin/libtool

And, MacPorts seem to be installing everything in another directory. Should I remove the libtool version in /usr/bin?

Also, I had first tried to install gnudatalanguage from HPC, here: ​http://hpc.sourceforge.net/, which I think put everything in /usr/local. Perhaps the two installs are interfering with each other? Is there a way I can uninstall the HPC-installed gnudatalanguage?

Thanks so much for your help!

[nerdling (Jeremy Lavergne)]

Oh boy, lots of stuff in /usr/local is going to be fun!

It might also be that the port simply needs use_autoreconf yes added. If you're comfortable editing the port file (you can undo it by doing a selfupdate again) try this:

sudo port edit gnudatalanguage

and just add use_autoreconf yes, then

sudo port clean gnudatalanguage
sudo port install gnudatalanguage

[davidagalvan@…]

That worked! I added use_autoreconf to the port file. I wasn't sure where to put it so I just put it under the "use autoconf yes" listing. See this snipped from the port file:

use_autoconf                yes
use_autoreconf 				yes
configure.env-append        LIBS=\"-lpng -lopenjpeg\"
configure.args              --with-plplotdir=${prefix} \
. . .

It appears to have worked, as I got the following when I ran sudo port install gnudatalanguage

dgalvan-09153112037:~ dgalvan$ sudo port install gnudatalanguage
--->  Computing dependencies for gnudatalanguage
--->  Fetching gnudatalanguage
--->  Verifying checksum(s) for gnudatalanguage
--->  Extracting gnudatalanguage
--->  Configuring gnudatalanguage
--->  Building gnudatalanguage
--->  Staging gnudatalanguage into destroot
--->  Installing gnudatalanguage @0.9rc4_2
--->  Activating gnudatalanguage @0.9rc4_2
--->  Cleaning gnudatalanguage
dgalvan-09153112037:~ dgalvan$ gdl

  GDL - GNU Data Language, Version 0.9rc4

- For basic information type HELP,/INFO
- Default library routine search path used (GDL_PATH/IDL_PATH env. var. not set): 
  /opt/local/share/gnudatalanguage/lib:/opt/local/share/gnudatalanguage/lib/dicom/opt/local/share/gnudatalanguage/lib/cmsvlib
- Please report bugs, feature or help requests and patches at:
  http://sourceforge.net/projects/gnudatalanguage/

Thanks very much for your help! Got me up and running again on this project! Now I just need to figure out how to set that GDL_PATH so GDL will see my *.pro files. . .

[tenomoto (Takeshi Enomoto)]

Sorry for slow response. Thank you for finding a solution. committed in r69056.

[tenomoto (Takeshi Enomoto)]

With autoreconf, autoconf is redundant. r69057 fixes the lint warning.