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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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 > > [EMAIL PROTECTED] > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > _______________________________________________ EMBOSS mailing list [EMAIL PROTECTED] http://lists.open-bio.org/mailman/listinfo/emboss
