failed to compile

[freedog8]

[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

[BioWu]

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

[rorycraig337]

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)

[Nikos22]

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.