Optional package deformation fails to build: mpir.h not found

[mkoeppe]

On homebrew-macos-maximal (https://github.com/mkoeppe/sage/runs/959683064) - which uses gmp from the system, not mpir...

 [deformation-d05941b.p0] error installing, exit status 1. End of log file:
  [deformation-d05941b.p0]   /Users/runner/work/sage/sage/.tox/local-homebrew-macos-maximal/local/var/tmp/sage/build/deformation-d05941b.p0/src/generics.h:12:10: fatal error: 'mpir.h' file not found
  [deformation-d05941b.p0]   #include <mpir.h>
  [deformation-d05941b.p0]            ^~~~~~~~
  [deformation-d05941b.p0]   In file included from zero.c:1:
  [deformation-d05941b.p0]   In file included from /Users/runner/work/sage/sage/.tox/local-homebrew-macos-maximal/local/var/tmp/sage/build/deformation-d05941b.p0/src/vec.h:8:
  [deformation-d05941b.p0]   /Users/runner/work/sage/sage/.tox/local-homebrew-macos-maximal/local/var/tmp/sage/build/deformation-d05941b.p0/src/generics.h:12:10: fatal error: 'mpir.h' file not found

Is this package still maintained?

Also on debian-bullseye:

 [deformation-d05941b.p0]       CC   ../build/perm/../perm.lo
  [deformation-d05941b.p0]   /usr/bin/ld: -r and -pie may not be used together
  [deformation-d05941b.p0]   collect2: error: ld returned 1 exit status

---

a straightforward modification of using GMP in place MPIR seems to work just fine, at least on 64-bit linux. Please review.

Depends on #31525

CC: @jpflori @videlec @kiwifb @slel @sagetrac-spancratz

Component: packages: experimental

Work Issues: fix C code on clang

Author: Matthias Koeppe, Dima Pasechnik

Branch/Commit: 44b1d0a

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/30325

[jpflori]

comment:2

I pushed a modif on my github repo for the debian issue.
For the homebrew one, I fear that the package is using some MPIR internals and cannot work with GMP, though that is just a very vague souvenir.

[mkoeppe]

comment:4

Setting new milestone based on a cursory review of ticket status, priority, and last modification date.

[mkoeppe]

comment:5

Replying to @jpflori:

I pushed a modif on my github repo for the debian issue.

Could you push a tag please so that there is a cleaner way to refer to this version?

[mkoeppe]

Branch: u/mkoeppe/optional_package_deformation_fails_to_build__mpir_h_not_found

[jpflori]

Commit: 9959a92

[jpflori]

comment:7

https://github.com/jpflori/deformation/tags
Just did.

---

New commits:

9959a92

WIP

[dimpase]

comment:8

we now have a release that uses GMP, and doesn't use MPIR at all.

[dimpase]

Author: Matthias Koeppe, Dima Pasechnik

[dimpase]

comment:9

this works and passes checks on Ubuntu and Fedora 32

---

New commits:

313c76b	WIP
dd68f33	updated to the latest fix, using GMP

[dimpase]

Changed branch from u/mkoeppe/optional_package_deformation_fails_to_build__mpir_h_not_found to u/dimpase/packages/deformat/no_mpir

[dimpase]

Changed commit from 9959a92 to dd68f33

[mkoeppe]

comment:11

I would strongly suggest to use more traditionally named release tags. If there is no version scheme, how about using the date.

[mkoeppe]

comment:12

Also, does not build for me on macos-homebrew:

[deformation-mpir_fix]         ^
[deformation-mpir_fix] nmod_mat_charpoly.c:9:6: error: redefinition of 'nmod_mat_charpoly'
[deformation-mpir_fix] void nmod_mat_charpoly(nmod_poly_t rop, const nmod_mat_t op)
[deformation-mpir_fix]      ^
[deformation-mpir_fix] /usr/local/include/flint/nmod_poly.h:1412:6: note: previous definition is here
[deformation-mpir_fix] void nmod_mat_charpoly(nmod_poly_t p, const nmod_mat_t M)
[deformation-mpir_fix]      ^
[deformation-mpir_fix] 1 error generated.

[dimpase]

comment:13

yes, the C code there is far from "normal", there are various ugly bits such as static functions implemented in .h files.
E.g. gcc 8.3 produces a slew of warnings. OK, it's something doable, to fix these.

[dimpase]

Work Issues: fix C code on clang

[dimpase]

comment:15

Do we assume that we have Flint 2.6 or newer? nmod_mat_charpoly appeared in Flint 2.6,
and we can either use it, or rename the one in deformation
(both ways work, but of course it's better to use one in Flint)

[mkoeppe]

comment:16

Yes, if we make #31525 (Wrap FLINT 2.6 functions, drop support for system FLINT < 2.6) a dependency of this ticket

[dimpase]

Dependencies: #31525

[dimpase]

comment:18

Unfortunately, some tests fail with Flint 2.6.3, while with Flint 2.5.2 everything passes.
https://github.com/dimpase/deformation/runs/2456263893

...
nmod_mat_charpoly... PASS
monotonic... PASS
make[1]: *** [../Makefile.subdirs:84: ../build/diagfrob/test/t-ell_curves_RUN] Aborted (core dumped)
ell_curves... make[1]: Leaving directory '/home/runner/work/deformation/deformation/diagfrob'
make: *** [Makefile:179: check] Error 2
Error: Process completed with exit code 2.

[dimpase]

comment:19

I found a workaround (by chance), it appears that the order the libraries are linked in is important, see dimpase/deformation#2

It likely points to a bug somewhere, though (valgrind shows trouble in some tests, although not in ones which fail), but, well...

[sagetrac-git]

Changed commit from dd68f33 to 79a7633

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

79a7633

update to 20210503, new location for releases

[sagetrac-git]

Changed commit from 79a7633 to b21456b

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

ff216bd	WIP
197696c	updated to the latest fix, using GMP
4822d1c	update to 20210503, new location for releases
b21456b	update checksum

[dimpase]

comment:22

OK, this also should work on macOS, and pass checks

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

44b1d0a

update upstream info

[sagetrac-git]

Changed commit from b21456b to 44b1d0a

[dimpase]

comment:24

the versions are now dates in format YYYYMMDD

[mkoeppe]

Reviewer: Matthias Koeppe

[mkoeppe]

comment:25

Builds OK now on macOS, thanks

[vbraun]

Changed branch from u/dimpase/packages/deformat/no_mpir to 44b1d0a