[Debian-med-packaging] [covid-19] Help for ocaml package needed
Andreas Tille
andreas at an3as.eu
Sun May 24 19:16:21 BST 2020
Hi Pierra,
On Sun, May 24, 2020 at 05:11:59PM +0200, Pierre Boutillier wrote:
> Hi Andreas,
>
> (Someone NOT involved in debian (beyond following debian-ocaml-maint list)
> speaking here. I want for years taking the time to become involved but never
> did and won't in the near future :-/).
Its very cool that you provide this valuable information anyway.
> As Ralf told you, your first problem is that the software you're trying to
> package is using an old version of `ocamlbuild`. A quick and awful fix is
> (The correct thing would be to give the "origin" of the thing you're lexing
> instead of `"foobar"`):
>
> ```
>
> diff --git a/myocamlbuild.ml b/myocamlbuild.ml
> index fd877a9..cf75d2c 100644
> --- a/myocamlbuild.ml
> +++ b/myocamlbuild.ml
> @@ -14,7 +14,7 @@ open Ocamlbuild_plugin
>
> let run_and_read = Ocamlbuild_pack.My_unix.run_and_read
>
> -let blank_sep_strings = Ocamlbuild_pack.Lexers.blank_sep_strings
> +let blank_sep_strings = Ocamlbuild_pack.Lexers.blank_sep_strings "foobar"
>
> module OCamlFind =
> struct
> ```
>
> but I fear you will still be very far from home with only this. You'll then
> run into the failure:
>
> ```
> File "pplacer_src/guppy_mcl.ml", line 23, characters 2-9:
> Error: Unbound module Mcl
> ```
>
> I see you're the uploader of `mcl` in debian but what is needed here is not
> mcl binaries but "OCaml bindings to the mcl C functions" which looks to me
> not available in debian. Google found them at https://github.com/fhcrc/mcl.
> As you can see, it is a "fork" of mcl so it duplicates all its code which,
> if I'm correct, forbids to easily make a package out of it as duplication of
> code is forbidden in debian!
>
> From the other end, the situation is not better as, if I'm correct, mcl as
> packaged provides binaries but no C libraries you can link to. That means
> that it is not easy to take the `caml` folder of fhcrc/mcl and "simply"
> tweak the build system so that it finds the C functions in a "libmcs shared
> library" instead of in the C files it duplicated from mcl...
>
> Maybe, the """easiest""" path is to replace mcl pristine tarball by one from
> https://github.com/fhcrc/mcl (if only it is upto date...) so that mcl source
> package provides at the same time the binaries and an ocaml library...
I agree that this sounds very sensible approach. Mcl seems to be in
very low maintenance mode. In case the fork was done on top of the code
base which we have in Debian anyway I'd be in favour to follow your
suggestion and package the ocaml-enhanced code to enable us to package
pplacer (which is also used by other tools needed for covid-19 relevant
packages).
> Anyway, once the puzzle of packaging mcl OCaml bindings is solved, `make` in
> pplacer finally worked for me.
Thanks for checking all this.
Pranav or Nilesh, are you up for taking this challenge?
Kind regards
Andreas.
> For the record, here is how I managed to compile mcl OCaml bindings from
> https://github.com/fhcrc/mcl (in stable, Sorry I realize only now I should
> retry in sid...) :
>
> - I had to apply the following patch (because OCaml headers are not
> compatible with c89 anymore)
>
> ```
> diff --git a/_oasis b/_oasis
> index 22e106a..c0c93c3 100644
> --- a/_oasis
> +++ b/_oasis
> @@ -13,5 +13,5 @@ Library mcl
> Path: caml
> BuildTools: ocamlbuild
> CSources: caml_mcl.c
> - CCOpt: -fPIC -std=c89
> + CCOpt: -fPIC -std=c99
> Modules: Mcl
> diff --git a/caml/caml_mcl.c b/caml/caml_mcl.c
> index 37bd0d6..d5f92e0 100644
> --- a/caml/caml_mcl.c
> +++ b/caml/caml_mcl.c
> @@ -17,7 +17,7 @@ void caml_mcl_initialize(void)
> if (caml_mcl_initialized)
> return;
>
> - srandom(mcxSeed(315));
> + srand(mcxSeed(315));
> mclx_app_init(NULL);
> caml_mcl_initialized = 1;
> }
> diff --git a/myocamlbuild.ml b/myocamlbuild.ml
> index 2ff1223..e24475a 100644
> --- a/myocamlbuild.ml
> +++ b/myocamlbuild.ml
> @@ -602,7 +602,7 @@ let package_default =
> (["oasis_library_mcl_ccopt"; "compile"],
> [
> (OASISExpr.EBool true,
> - S [A "-ccopt"; A "-fPIC"; A "-ccopt"; A "-std=c89"])
> + S [A "-ccopt"; A "-fPIC"; A "-ccopt"; A "-std=c99"])
> ])
> ];
> includes = []
> diff --git a/setup.ml b/setup.ml
> index 2743646..28d9025 100644
> --- a/setup.ml
> +++ b/setup.ml
> @@ -6714,7 +6714,7 @@ let setup_t =
> bs_c_sources = ["caml_mcl.c"];
> bs_data_files = [];
> bs_ccopt =
> - [(OASISExpr.EBool true, ["-fPIC"; "-std=c89"])];
> + [(OASISExpr.EBool true, ["-fPIC"; "-std=c99"])];
> bs_cclib = [(OASISExpr.EBool true, [])];
> bs_dlllib = [(OASISExpr.EBool true, [])];
> bs_dllpath = [(OASISExpr.EBool true, [])];
> ```
>
> - Then I build by `ocaml setup.ml -all` and installed by hand with `ocaml
> setup.ml -install` (which simply runs `ocamlfind' install mcl caml/META
> _build/caml/mcl.cmx _build/caml/mcl.cmi _build/caml/mcl.cmxs
> _build/caml/mcl.a _build/caml/mcl.cmxa _build/caml/mcl.cma
> _build/caml/dllmcl_stubs.so _build/caml/libmcl_stubs.a caml/mcl.ml`)
>
> - To build debian packages instead, here comes the part where I humiliate
> myself because I've never managed to learn Ocaml packaging in debian so I
> know dh-ocaml provides all the automation necessary for these files put in
> their correct places to be spilt in a `libmcl-ocaml` and a
> `libmcl-ocaml-dev` but I can't spell it...
>
> Best,
> Pierre B.
>
> Le 23/05/2020 à 15:09, Andreas Tille a écrit :
> > Hi,
> >
> > in the Debian Med Covid-19 sprint we have a set of packages that can be
> > used to help researching the disease. To this set of packages belongs
> > pplacer which I injected into Salsa[1]. I admit I never packaged
> > software written in ocaml and my initial attempt was probably weak. It
> > ends with:
> >
> >
> > ...
> > make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
> > ocamlbuild pplacer.native
> > /usr/bin/ocamlopt.opt unix.cmxa -I /usr/lib/ocaml/ocamlbuild /usr/lib/ocaml/ocamlbuild/ocamlbuildlib.cmxa myocamlbuild.ml /usr/lib/ocaml/ocamlbuild/ocamlbuild.cmx -o myocamlbuild
> > + /usr/bin/ocamlopt.opt unix.cmxa -I /usr/lib/ocaml/ocamlbuild /usr/lib/ocaml/ocamlbuild/ocamlbuildlib.cmxa myocamlbuild.ml /usr/lib/ocaml/ocamlbuild/ocamlbuild.cmx -o myocamlbuild
> > File "myocamlbuild.ml", line 24, characters 6-78:
> > 24 | ......Lexing.from_string &
> > 25 | run_and_read "ocamlfind list | cut -d' ' -f1"
> > Error: This expression has type Lexing.lexbuf
> > but an expression was expected of type
> > Ocamlbuild_pack.Loc.source = string
> > Command exited with code 2.
> > make[2]: *** [Makefile:21: pplacer.native] Error 10
> > ...
> >
> >
> > Any hint what to do next and to fix this bug?
> >
> > Thanks for any help
> >
> > Andreas.
> >
> >
> > [1] https://salsa.debian.org/med-team/pplacer
> >
>
--
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