I would very much like to see the first error that the CPAN shell gets - the errors you quote aren't useful. (They basically boil down to "something went wrong earlier").
That being said, your manual compilation attempt won't succeed because the first argument to perl isn't a perl script. Re-order your arguments and put Makefile.PL at the front:
~/.cpan/build/Tree-Suffix-0.12$ perl Makefile.PL CFLAGS="$CFLAGS -I$HO
+ME/MyBioTool/libstree-0.4.2/include" LDFLAGS="$LDFLAGS -L$HOME/MyBioT
+ool/libstree-0.4.2/lib"
followed by the command make and, only if the previous command was successful, make test and then (again, only if make test was successful) make install.
--
@/=map{[/./g]}qw/.h_nJ Xapou cets krht ele_ r_ra/;
map{y/X_/\n /;print}map{pop@$_}@/for@/
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