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
