[EMBOSS] libnucleus.la

ajb at ebi.ac.uk ajb at ebi.ac.uk
Mon Mar 23 10:39:05 UTC 2009

Hello Sebastian,

That looks a bit like a libtool problem. I assume that
you've tried a fresh extraction (not just a 'make clean') and compilation
of EMBOSS and HMMER. That would eliminate various possibilities including
changes to libtool between compilation of EMBOSS and HMMER. I also
assume that you downloaded a fresh copy of HMMER from the
ftp site when you downloaded EMBOSS, otherwise there would be
problems, though probably not the one you've reported.

If the problem persists then it would be useful if you sent me
(not the list):

a) Operating system and version used.
b) The command line used to configure EMBOSS and the full
   output of it  (not just the stderr) e.g.
   ./configure [other options] > embossconfig.out 2>&1
   Also confirm that this version of EMBOSS works after
   Also confirm whether a 'make install' was done  or just
   a 'make'.
c) The command line used to configure HMMER and the full output e.g.
   ./configure [other options] > hmmerconfig.out 2>&1
d) The full output of the HMMER make e.g.
   make > hmmermake.out 2>&1

It would be useful to check whether there are any old libnucleus*
files in any standard system location (e.g. /usr/local/lib) before



> Hello,
> I am trying to install HMMER from EMBASSY.
> sb at dnalinux:~/EMBOSS-6.0.1/embassy/HMMER-2.3.2$ make 2> /tmp/xxx
> Making all in src
> make[1]: Entering directory
> `/home/sb/EMBOSS-6.0.1/embassy/HMMER-2.3.2/src'
> make[2]: Entering directory
> `/home/sb/EMBOSS-6.0.1/embassy/HMMER-2.3.2/src'
> gcc  -O2   -o ehmmcalibrate ehmmcalibrate.o
> ../../../nucleus/libnucleus.la ../../../ajax/libajax.la
> ../../../plplot/libeplplot.la -lX11  -lm  -lgd -lpng -lz -lm
> make[2]: Leaving directory `/home/sb/EMBOSS-6.0.1/embassy/HMMER-2.3.2/src'
> make[1]: Leaving directory `/home/sb/EMBOSS-6.0.1/embassy/HMMER-2.3.2/src'
> Here is the stderror:
> ../../../nucleus/libnucleus.la: file not recognized: File format not
> recognized
> collect2: ld returned 1 exit status
> make[2]: *** [ehmmcalibrate] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
> Here is the libnucleus.la:
> dlname='libnucleus.so.6'
> # Names of this library.
> library_names='libnucleus.so.6.0.0 libnucleus.so.6 libnucleus.so'
> # The name of the static archive.
> old_library='libnucleus.a'
> # Libraries that this one depends upon.
> dependency_libs=''
> # Version information for libnucleus.
> current=6
> age=0
> revision=0
> # Is this an already installed library?
> installed=yes
> # Should we warn about portability when linking against -modules?
> shouldnotlink=no
> # Files to dlopen/dlpreopen
> dlopen=''
> dlpreopen=''
> # Directory that this library needs to be installed in:
> libdir='/usr/local/lib'
> libnucleus.la is in:
> ~/EMBOSS-6.0.1/nucleus/libnucleus.la
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

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