alpine linux: Add system package information / tox.ini, fix flint, giac, cvxopt

[mkoeppe]

To test: tox -e docker-alpine-standard

Depends on #33070
Depends on #33138

Upstream: Reported upstream. No feedback yet.

CC: @dimpase @slel @frederichan-IMJPRG @sagetrac-parisse @dkwo @tornaria @orlitzky

Component: porting

Author: Matthias Koeppe, Dima Pasechnik

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/33083

[mkoeppe]

Branch: u/mkoeppe/system_package_information___tox_ini___gh_actions_for_alpine_linux

[mkoeppe]

Commit: 1a49d24

[mkoeppe]

New commits:

1a49d24

tox.ini, build/bin/write-dockerfile.sh, build/bin/sage-print-system-package-command: Add alpine

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1 +1,2 @@
+To test: `tox -e docker-alpine-standard`
 

[sagetrac-git]

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

d1a9266

Add more alpine.txt

[sagetrac-git]

Changed commit from 1a49d24 to d1a9266

[mkoeppe]

comment:5

  [r-3.6.3]   ********************************************************************************
  [r-3.6.3]   /sage/build/bin/sage-dist-helpers: line 143: fmt: command not found
  [r-3.6.3]   ********************************************************************************

[sagetrac-git]

Changed commit from d1a9266 to 522c452

[sagetrac-git]

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

522c452

build/pkgs/_prereq/distros/alpine.txt: Add coreutils

[sagetrac-git]

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

f3e59a6

build/pkgs/{graphviz,qhull,r}/distros/alpine.txt: Add non-dev packages

[sagetrac-git]

Changed commit from 522c452 to f3e59a6

[mkoeppe]

comment:8

flint

In file included from /sage/local/var/tmp/sage/build/flint-2.7.1/src/thread_support.h:16,
                 from /sage/local/var/tmp/sage/build/flint-2.7.1/src/nmod_mat.h:35,
                 from /sage/local/var/tmp/sage/build/flint-2.7.1/src/nmod_poly.h:34,
                 from /sage/local/var/tmp/sage/build/flint-2.7.1/src/fmpz_poly.h:35,
                 from /sage/local/var/tmp/sage/build/flint-2.7.1/src/aprcl.h:18,
                 from config_gauss.c:12:
/sage/local/var/tmp/sage/build/flint-2.7.1/src/thread_pool.h:55:5: error: unknown type name 'cpu_set_t'
   55 |     cpu_set_t original_affinity;
      |     ^~~~~~~~~

giac:

In file included from History.cc:8:
first.h: In function 'float fgamma(float)':
first.h:546:39: error: 'gammaf' was not declared in this scope; did you mean 'tgammaf'?
  546 | inline float fgamma(float f1){ return gammaf(f1); } // or tgammaf(f1) on some versions of emscripten
      |                                       ^~~~~~
      |                                       tgammaf
make[5]: *** [Makefile:976: History.lo] Error 1

[dimpase]

comment:9

there is also mpfr-dev for mpfr.

[dimpase]

comment:10

see flintlib/flint#1054 for Flint error

Probably as a workaround on can put -D_GNU_SOURCE into CFLAGS.