[EMBOSS] Problem in profiling water and needle programs in the EMBOSS package

[ajb at ebi.ac.uk]

That is likely to be because, unless you do a 'make install' the files
in the 'emboss' directory are libtool scripts that call the true
executables (which are held in the 'emboss/.libs' subdirectory after
compilation).

You may get away with typing:
  gprof .libs/water gmon.out > gprof_water_ecoli01.txt

on some systems/configurations. However, the recommended way is
to use --prefix when you configure emboss (e.g. --prefix=/usr/local/emboss)
and do a 'make install'. Then use the true executable in (e.g.)
/usr/local/emboss/bin

HTH

Alan


> Hello all,
> I am having issues compiling the water and needle programs from the
> EMBOSS package.
> 1. I configured the package with --with-gccprofiling option which
> ensured that all the CFLAGS and LDFLAGS are set with -pg option.
> -bash-3.00$ ./water
> Smith-Waterman local alignment.
> Input sequence: ../../ncbi/build/myquery.txt
> Second sequence(s): ../../ncbi/build/ecoli.nt
> Gap opening penalty [10.0]:
> Gap extension penalty [0.5]:
> Output alignment [test1.water]:
> 2. the gmon.out file is created, however I get the foll. message
> -bash-3.00$ gprof water gmon.out > gprof_water_ecoli01.txt
> gprof: water: not in a.out format
>
> has anyone had this problem??
> Thanks in advance,
> Vivek
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