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

[ajb at ebi.ac.uk]

You probably also need to 'make clean' and then configure again,
this time also adding '--disable-shared' on the configuration
line. That will cause static libraries to be used.

HTH

Alan


> Thanks for the info.
> I reconfigured the package with options --prefix=$HOME and
> --with-gccprofiling.
> I executed the water program from the bin directory and this is what I
> got:
> -bash-3.00$ gprof water gmon.out > gprof_water_ecoli01.txt
> BFD: water(.rela.plt): relocation 0 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 1 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 2 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 3 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 4 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 5 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 6 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 7 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 8 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 9 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 10 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 11 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 12 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 13 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 14 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 15 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 16 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 17 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 18 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 19 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 20 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 21 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 22 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 23 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 24 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 25 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 26 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 27 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 28 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 29 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 30 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 31 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 32 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 33 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 34 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 35 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 36 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 37 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 38 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 39 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 40 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 41 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 42 has invalid symbol index 0
> BFD: water(.rela.plt): relocation 43 has invalid symbol index 0
> --------------------------
>
> what's going wrong now?? BTW I am using a linux-powerpc ppc64 machine.
> Thanks,
> Vivek
>
> On 4/12/07, ajb at ebi.ac.uk <ajb at ebi.ac.uk> wrote:
>> 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
>> > _______________________________________________
>> > EMBOSS mailing list
>> > EMBOSS at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/emboss
>> >
>>
>>
>>
>