add system packages info for R and others

[dimpase]

this is a followup to #29053 which missed packages mentioned on #28884, and also some gentoo, arch, fedora, debian packages

Depends on #29129

CC: @mkoeppe @kiwifb @orlitzky

Component: build

Author: Dima Pasechnik

Branch: 0f704d0

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/29273

[mkoeppe]

comment:1

See also #29129

[dimpase]

Branch: u/dimpase/packages/r_packages_in_distros

[dimpase]

Author: Dima Pasechnik

[dimpase]

New commits:

0fc301c	Add build/pkgs/{libgd|m4ri|ninja_build|perl_term_readline_gnu|yasm}/distros/*.txt - from repology
f7785ce	build/pkgs/fedora.txt: Add diffutils
6d2bbd8	build/pkgs/arch.txt: Add 'which'
0aa90c1	build/pkgs/debian.txt: Add ca-certificates
9e0acb5	data for R packages

[dimpase]

Commit: 9e0acb5

[dimpase]

Dependencies: #29129

[sagetrac-git]

Changed commit from 9e0acb5 to 9ebcd33

[sagetrac-git]

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

9ebcd33

gentoo R pkg

[sagetrac-git]

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

e22f974

libgd package in gentoo

[sagetrac-git]

Changed commit from 9ebcd33 to e22f974

[sagetrac-git]

Changed commit from e22f974 to 8de5981

[sagetrac-git]

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

8de5981

libgd and ninja packages in gentoo

[sagetrac-git]

Changed commit from 8de5981 to 9eff18b

[sagetrac-git]

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

9eff18b

libgd, symmetrica, ninja packages in gentoo

[sagetrac-git]

Changed commit from 9eff18b to fe0851f

[sagetrac-git]

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

fe0851f

r in conda

[sagetrac-git]

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

7e129ef

gentoo pkgs for givaro and pari

[sagetrac-git]

Changed commit from fe0851f to 7e129ef

[sagetrac-git]

Changed commit from 7e129ef to 095e0bf

[sagetrac-git]

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

3fcf987	Add build/pkgs/{libgd|m4ri|ninja_build|perl_term_readline_gnu|yasm}/distros/*.txt - from repology
d923e1f	build/pkgs/fedora.txt: Add diffutils
7f4f7cd	build/pkgs/arch.txt: Add 'which'
fa64cdb	build/pkgs/debian.txt: Add ca-certificates
d8e3a13	data for R packages
8dacd22	gentoo R pkg
0ed2cce	libgd, symmetrica, ninja packages in gentoo
82d0896	r in conda
74b4d8e	gentoo pkgs for givaro and pari
095e0bf	pkgs for planarity and tachyon on debian and gentoo

[dimpase]

comment:13

rebased over 9.1.beta6

[kiwifb]

comment:14

I am getting concerned that a rather unusual feature of gentoo may need additional description. The useflags. While packages in binary distro are built with all possible options [and when that is not possible either the best sets or variants of the package are offered] in Gentoo we leave the end user to choose a number of options by themselves. So not only do I want a package list, I want the option to go with it. Like for pari, we really want to use the gmp option (although I think it would just be slower in that case) and the doc option [not negotiable I even spent time making sure the doc was usable for cypari and sage when when it was part of it].

A list of useflags for Gentoo is at https://github.com/cschwan/sage-on-gentoo/blob/master/package.use/sage - some of the packages - pplpy, pynac and lcalc - are not in the main gentoo tree, only in the sage-on-gentoo overlay.

[dimpase]

comment:15

perhaps there should be an extra optional datapoint for each gentoo package, the needed useflags, and then the installation advice would be generated by combining these flags into one list somehow?

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

3103055

m4ri must use png on gentoo

[sagetrac-git]

Changed commit from 8ae9764 to 3103055

[dimpase]

comment:41

OK, I should stop fiddling with this. Gentoo stuff needs moar workz.

[vbraun]

comment:42

Merge conflict

[mkoeppe]

Changed branch from u/dimpase/packages/r_packages_in_distros to u/mkoeppe/packages/r_packages_in_distros

[sagetrac-git]

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

8ae9764	gsl and openblas libs
3103055	m4ri must use png on gentoo
1b48aa1	Merge tag '9.1.beta7' into t/29273/packages/r_packages_in_distros

[sagetrac-git]

Changed commit from 3103055 to 1b48aa1

[vbraun]

comment:46

Merge conflict

[sagetrac-git]

Changed commit from 1b48aa1 to 0f704d0

[sagetrac-git]

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

0fc301c	Add build/pkgs/{libgd|m4ri|ninja_build|perl_term_readline_gnu|yasm}/distros/*.txt - from repology
f7785ce	build/pkgs/fedora.txt: Add diffutils
6d2bbd8	build/pkgs/arch.txt: Add 'which'
0aa90c1	build/pkgs/debian.txt: Add ca-certificates
c49acdc	Merge tag '9.1.beta7' into t/29129/add_more_system_packages_to_build_pkgs_spkg_distros_
0f704d0	Merge branch 't/29129/add_more_system_packages_to_build_pkgs_spkg_distros_' into t/29273/packages/r_packages_in_distros

[vbraun]

Changed branch from u/mkoeppe/packages/r_packages_in_distros to 0f704d0

[dimpase]

Changed commit from 0f704d0 to none

[dimpase]

comment:50

a followup on #29352