mlin
failed to compile
[jliu@login01 PhyloCSF]$ make
make -C lib/CamlPaml reinstall
make[1]: Entering directory /data/gpfs02/jliu/ding/tools/PhyloCSF/lib/CamlPaml' make uninstall make[2]: Entering directory /data/gpfs02/jliu/ding/tools/PhyloCSF/lib/CamlPaml'
ocamlfind remove CamlPaml
ocamlfind: [WARNING] No such file: /data/gpfs01/jliu/.opam/default/lib/CamlPaml/META
make[2]: Leaving directory /data/gpfs02/jliu/ding/tools/PhyloCSF/lib/CamlPaml' make install make[2]: Entering directory /data/gpfs02/jliu/ding/tools/PhyloCSF/lib/CamlPaml'
ocamlbuild -use-ocamlfind CamlPaml.cma CamlPaml.cmxa
- ocamlfind ocamlc -c -g -package gsl -pp ocaml+twt -o Code.cmo Code.ml
File "Code.ml", line 55, characters 11-24:
Warning 3: deprecated: Stdlib.String.create
Use Bytes.create instead.
File "Code.ml", line 57, characters 3-27:
Warning 3: deprecated: Stdlib.String.set
Use Bytes.set instead.
File "Code.ml", line 193, characters 32-46:
Warning 3: deprecated: Stdlib.Char.uppercase
Use Char.uppercase_ascii instead.
File "Code.ml", line 193, characters 50-64:
Warning 3: deprecated: Stdlib.Char.uppercase
Use Char.uppercase_ascii instead.
File "Code.ml", line 193, characters 68-82:
Warning 3: deprecated: Stdlib.Char.uppercase
Use Char.uppercase_ascii instead.
File "Code.ml", line 1:
Error: The implementation Code.ml does not match the interface Code.cmi:
...
In module DNA:
Values do not match:
val revcomp : string -> bytes
is not included in
val revcomp : string -> string
File "Code.mli", line 29, characters 1-31: Expected declaration
File "Code.ml", line 53, characters 5-12: Actual declaration
Command exited with code 2.
Compilation unsuccessful after building 53 targets (52 cached) in 00:00:00.
make[2]: *** [lib] Error 10
make[2]: Leaving directory
/data/gpfs02/jliu/ding/tools/PhyloCSF/lib/CamlPaml' make[1]: *** [reinstall] Error 2 make[1]: Leaving directory/data/gpfs02/jliu/ding/tools/PhyloCSF/lib/CamlPaml' make: *** [CamlPaml] Error 2
As the offical site tells, this problem may results by the difference between String and Bytes of the recent compiler.
To solve it, you can edit two Makefile in ./lib/CamlPaml and ./src/ and add -cflag '-unsafe-string' after each ocamlbuild as below:
- Before:
ocamlbuild -use-ocamlfind ${LIBNAME}.cma ${LIBNAME}.cmxa - After:
ocamlbuild -cflag '-unsafe-string' -use-ocamlfind ${LIBNAME}.cma ${LIBNAME}.cmxa
Just had the same issue - if any one else is struggling I reverted to older version of ocaml (4.02.3) and opam (2.0.0). With the current versions (ocaml 4.10.0 / opam 2.0.6) the above changes to the Makefiles was still resulting in errors as '-unsafe-string' is no longer compatible (at least with default configuration)
For me too, reverting to ocaml 4.02.3 did the trick, without having to do any changes to the Makefiles . After downloading opam, I just run :
opam init --switch==4.02.3
opam switch create 4.02.3
Not sure if the first command is necessary really. Making PhyloCSF then worked without a problem.
