Re: [covid-19] Help for ocaml package needed
Hi again,
I've added Pierre Boutillier to CC since he once had made some
progress[3] with this package.
What I've done is the following:
1. Asked ftpmaster for fastprocessing of mcl to enable a smoother
access to the ocaml bindings of mcl
2. Tried to build pplacer with a local copy of libmcl-ocaml-dev
which ended up in
...
/usr/bin/ocamlmklib.opt -o pam_src/pplacer_pam pam_src/pam.o pam_src/caml_pam.o
/usr/bin/ocamlmklib.opt -o pplacer_src/pplacercside pplacer_src/linear_c.o pplacer_src/unix_support.o
ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules pplacer_src/rppr.ml > pplacer_src/rppr.ml.depends
+ ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules pplacer_src/rppr.ml > pplacer_src/rppr.ml.depends
ocamlfind: Package `mcl' not found
Command exited with code 2.
I have not checked the tutorials linked below. Ralf, I've added you as
developer for mcl and pplacer in salsa - hope this will enable you to
push changes. Anybody else is kindly invited to ask for push
permissions.
Kind regards
Andreas.
[3] https://lists.debian.org/debian-ocaml-maint/2020/05/msg00102.html
On Sun, Jun 14, 2020 at 05:13:13PM +0100, Shayan Doust wrote:
> Hello Ralf et al.,
>
> Apologies for the consecutive email. Kindly CC'ing to the mailing lists
> just in case someone has an idea as there are no sensitive info within
> the emails.
>
> I was just experimenting with this tutorial[1] on pplacer[2] and I've
> still hit no luck. The errors remain persistent as denoted below.
>
> I am sure the mcl library is compiled properly.
>
> $ocamlobjinfo /usr/lib/ocaml/mcl.cma
> File /usr/lib/ocaml/mcl.cma
> Force custom: no
> Extra C object files: -lmcl_stubs
> Extra C options:
> Extra dynamically-loaded libraries: -lmcl_stubs
> Unit name: Mcl
> Interfaces imported:
> ad45f251bbf98d3a0bf3b883546ecfc8 Stdlib
> 7fab99051af85dcaec18ca28f9f431c7 Mcl
> a2b1a9d869fd05813beb35645bd9cd94 CamlinternalFormatBasics
> Required globals:
> Uses unsafe features: YES
> Primitives declared in this module:
> caml_mcl
> Force link: no
>
>
> If anyone has got an idea with a possible solution, feel free to contribute.
>
> Kind regards,
> Shayan Doust
>
> [1]:
> https://www.mancoosi.org/~abate/ocamlbuild-stubs-and-dynamic-libraries.html
> [2]: https://salsa.debian.org/med-team/pplacer
>
> On 13/06/2020 20:54, Shayan Doust wrote:
> > Hello Ralf,
> >
> > Thanks for the patch, I've merged it.
> >
> > Running make after the usual build package procedures, we now see actual
> > ld errors (undefined reference) with regards to the mcl stubs:
> >
> > ```
> > ...
> > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getproto.o): in function
> > `unix_getprotobynumber':
> > (.text+0xe8): warning: Using 'getprotobynumber' in statically linked
> > applications requires at runtime the shared libraries from the glibc
> > version used for linking
> > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getproto.o): in function
> > `unix_getprotobyname':
> > (.text+0xc1): warning: Using 'getprotobyname' in statically linked
> > applications requires at runtime the shared libraries from the glibc
> > version used for linking
> > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getserv.o): in function
> > `unix_getservbyname':
> > (.text+0x109): warning: Using 'getservbyname' in statically linked
> > applications requires at runtime the shared libraries from the glibc
> > version used for linking
> > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getserv.o): in function
> > `unix_getservbyport':
> > (.text+0x159): warning: Using 'getservbyport' in statically linked
> > applications requires at runtime the shared libraries from the glibc
> > version used for linking
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(matrix.o): in function
> > `mclxMapTest':
> > (.text+0x71c): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(matrix.o): in function
> > `mclxScrub':
> > (.text+0x43d6): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(matrix.o): in function
> > `mclxFold':
> > (.text+0x5209): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(shadow.o): in function
> > `mcl_density_adjust':
> > (.text+0xce4): undefined reference to `mclgEdgeIterInit'
> > /usr/bin/ld: (.text+0xeca): undefined reference to `mclgEdgeInc'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(transform.o): in function
> > `mclgTFgraph':
> > (.text+0x13c6): undefined reference to `mclgKNNdispatch'
> > /usr/bin/ld: (.text+0x143f): undefined reference to `mclgKNNdispatch'
> > /usr/bin/ld: (.text+0x14b8): undefined reference to `mclgKNNdispatch'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(cat.o): in function
> > `clm_split_overlap':
> > (.text+0x233d): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(cat.o): in function
> > `clmEnstrict':
> > (.text+0x2669): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(clm.o): in function
> > `clmUGraphComponents':
> > (.text+0x1ecd): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(tab.o): in function `mclTabMap':
> > (.text+0x123d): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(interpret.o): in function
> > `calc_depth':
> > (.text+0x2b9): undefined reference to `mclgUnionv'
> > /usr/bin/ld: /usr/lib/ocaml/libmcl_stubs.a(interpret.o):(.text+0x4e1):
> > more undefined references to `mclgUnionv' follow
> > collect2: error: ld returned 1 exit status
> > File "caml_startup", line 1:
> > Error: Error during linking
> > Command exited with code 2.
> > Compilation unsuccessful after building 489 targets (273 cached) in
> > 00:00:22.
> > make[1]: *** [Makefile:21: guppy.native] Error 10
> > make[1]: Leaving directory '/pplacer'
> > make: *** [Makefile:16: guppy] Error 2
> >
> > ```
> >
> > I did more investigation and it seems like -ccopt -static flags are
> > actually executed. The following is executed before the linking warnings
> > and errors occur (I've truncated it as it is long):
> >
> > ocamlfind ocamlopt -ccopt -static -linkpkg -package batteries -package
> > csv -package xmlm -package gsl -package sqlite3 -package zip -package
> > mcl -thread -cclib -lpthread -cclib -lpplacercside -cclib -Lpplacer_src
> > -cclib -lcdd -cclib -Lcdd_src -cclib -lpplacer_pam -cclib -Lpam_src
> > -cclib -lgsl -I cdd_src -I common_src -I json_src -I pplacer_src -I
> > pam_src cdd_src/cdd.cmx common_src/ppr.cmx common_src/mapsSets.cmx ...
> >
> > It doesn't seem like we have the -lmcl flag (which could explain the
> > undefined reference issues at linking) but with my complete lack of
> > OCaml knowledge, I am not sure how -lmcl can be injected into this
> > command (although I am not sure if this is needed at all or not because
> > I would have thought ocamlfind would handle all of this seeing how we do
> > not have -lbatteries and -lsqlite3 and whatnot).
> >
> > Kind regards,
> > Shayan Doust
> >
> > On 13/06/2020 20:31, Ralf Treinen wrote:
> >> I updated my patch (pushed to the branch "ralf") so that compilation
> >> continues when typing "make" as you describe it, until it hits the
> >> next linking error.
> >>
> >> About the linking error, I guess one should try to engineer the
> >> "-ccopt -static" option into myocamlbuild.ml as described on the web
> >> page you found, but I didn't find yet how to do that.
> >>
> >> -Ralf.
> >>
> >> On Sat, Jun 13, 2020 at 07:10:03PM +0100, Shayan Doust wrote:
> >>> Hello Ralf,
> >>>
> >>> I merged the your branch into master and I can confirm I get these
> >>> warnings too. The odd thing is that these warnings shouldn't be
> >>> problematic (they're not errors) and I assume suppression is done using
> >>> musl as opposed to glib.
> >>>
> >>> Having looked online it seems like the ld complaints are related to
> >>> this: https://github.com/mmottl/sqlite3-ocaml/issues/31
> >>>
> >>> Other than that, I'm quite stuck myself as to how to solve this. What's
> >>> very strange is that (using pbuilder login to be more experimentative
> >>> and more hands on) dpkg-buildpackage generates these warnings and then
> >>> terminates as you've said, however running "make" afterwards does not
> >>> display these warnings, and instead now hits another error message:
> >>>
> >>> ```
> >>> ...
> >>> cp `readlink pplacer.native` bin/pplacer
> >>> rm pplacer.native
> >>> if [ ! -e bin ]; then mkdir bin; fi
> >>> make guppy.native
> >>> make[1]: Entering directory '/pplacer'
> >>> ocamlbuild guppy.native
> >>> Finished, 0 targets (0 cached) in 00:00:00.
> >>> File "_tags", line 4, characters 44-53:
> >>> Warning: the tag "pkg_oUnit" is not used in any flag or dependency
> >>> declaration, so it will have no effect; it may be a typo. Otherwise you
> >>> can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> >>> File "_tags", line 5, characters 22-31:
> >>> Warning: the tag "pkg_oUnit" is not used in any flag or dependency
> >>> declaration, so it will have no effect; it may be a typo. Otherwise you
> >>> can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> >>> File "_tags", line 8, characters 154-161:
> >>> Warning: the tag "pkg_str" is not used in any flag or dependency
> >>> declaration, so it will have no effect; it may be a typo. Otherwise you
> >>> can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> >>> File "_tags", line 8, characters 112-124:
> >>> Warning: the tag "pkg_bigarray" is not used in any flag or dependency
> >>> declaration, so it will have no effect; it may be a typo. Otherwise you
> >>> can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> >>> File "_tags", line 8, characters 102-110:
> >>> Warning: the tag "pkg_unix" is not used in any flag or dependency
> >>> declaration, so it will have no effect; it may be a typo. Otherwise you
> >>> can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> >>> + ocamlfind ocamlc -c -annot -w Z -package batteries -package csv
> >>> -package xmlm -package gsl -package sqlite3 -package zip -package mcl
> >>> -thread -I pplacer_src -I json_src -I pdprune_src -I pam_src -I
> >>> common_src -I tests -I cdd_src -I tests/pplacer -I tests/json -I
> >>> tests/rppr -I tests/guppy -o pplacer_src/guppy_squash.cmo
> >>> pplacer_src/guppy_squash.ml
> >>> File "pplacer_src/guppy_squash.ml", line 177, characters 51-77:
> >>> 177 | let prefix_of_int i = Filename.concat outdir (zero_pad_int
> >>> pad_width i) in
> >>>
> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^
> >>> Error: This expression has type Ppatteries.Bytes.t = bytes
> >>> but an expression was expected of type string
> >>> Command exited with code 2.
> >>> Compilation unsuccessful after building 320 targets (319 cached) in
> >>> 00:00:00.
> >>> make[1]: *** [Makefile:21: guppy.native] Error 10
> >>> make[1]: Leaving directory '/pplacer'
> >>> make: *** [Makefile:16: guppy] Error 2
> >>>
pub RSA 4096/19D02395 2019-09-04 Shayan Doust (Personal EMAIL) <hello@shayandoust.me>
>
--
http://fam-tille.de
Reply to: