Add some dependencies

[jdemeyer]

A more or less arbitrary list of packages for which I added a dependencies file.

CC: @sagetrac-tmonteil @mkoeppe @embray @fchapoton @jdemeyer @vbraun @tscrim

Component: packages: optional

Author: Jeroen Demeyer

Branch/Commit: 6aef10c

Reviewer: Thierry Monteil, Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/19295

[jdemeyer]

Branch: u/jdemeyer/add_some_dependencies

[jdemeyer]

Commit: 8bd7801

[jdemeyer]

New commits:

8bd7801

Add some missing dependencies

[sagetrac-git]

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

48e1694

Add a few more dependencies

[sagetrac-git]

Changed commit from 8bd7801 to 48e1694

[sagetrac-git]

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

b0eab92

Add dependencies for autotools

[sagetrac-git]

Changed commit from 48e1694 to b0eab92

[sagetrac-tmonteil]

comment:6

I am on it, but it takes time.

[sagetrac-tmonteil]

Attachment: autotools-20141105.log

[sagetrac-tmonteil]

Attachment: database_gap-4.7.8.log

Attachment: igraph-0.7.1.log

[sagetrac-tmonteil]

Attachment: libtheora-1.1.1.log

[sagetrac-tmonteil]

Attachment: normaliz-2.12.1.p0.log

[sagetrac-tmonteil]

Changed branch from u/jdemeyer/add_some_dependencies to u/tmonteil/add_some_dependencies

[sagetrac-tmonteil]

Reviewer: Thierry Monteil

[sagetrac-tmonteil]

comment:8

Here was my testing protocol:

For each package pkg, start from a Sage with only

    make distclean
    make base

Then do make $pkg and see what happens.

The things that made me crazy is that if some package do not have a dependencies file, then the build system starts to build every standard package, i didn't underdtood that... Because of that "feature", we have to ensure that all dependencies of a package that is tested has a (possibly trivial) dependency file, recursively, or we are not testing much. So, to be tested well, this ticket should depend on #19261.

Now about the packages involved in the ticket, i had problems with the following:

• autotools still creates a bug, but i do not know what is missing, see the attached log.

• database_gap: because of the last line in spkg-install script, sage -c "gap_reset_workspace()", it should depend on a working Sage installation. So i added SAGERUNTIME as a dependency. It is overkill ?

• igraph requires the libxml2 (which we are not shipping), see the attached log. Perhaps we should package it, or perhaps move it to expermiental ? I added some hints on SPKG.txt. Moreover, from https://github.com/igraph/igraph/blob/master/debian/control it seems that igraph would be happy with blas/lapack and glpk, so perhaps should we also add atlas and glpk as dependencies ?

• libtheora depends on libogg, see the attached log. I updated the dependency file.

• normaliz depends on boost_cropped, see the attached log. I updated the dependency file. Also, Singular appears in the dependencies, but i am not sure it is the case, to my understanding of the documentation, i am not sure, but it seems that Singular can use Normaliz, but the converse. Shall we remove singular from normaliz dependencies ?

• i added a # no dependencies for configure.

Also, only configure is a "base" package, while "make base" installs:

base: $(INST)/$(BZIP2) $(INST)/$(PATCH) $(INST)/$(PKGCONF)

Shall those 3 packages have "base" priority too ?

---

New commits:

ec50fed

#19295 review

[sagetrac-tmonteil]

Changed commit from b0eab92 to ec50fed

[jdemeyer]

comment:9

Replying to @sagetrac-tmonteil:

The things that made me crazy is that if some package do not have a dependencies file, then the build system starts to build every standard package, i didn't underdtood that...

That's the default for optional packages. It was chosen because it's reasonably safe. But after these tickets have been dealt with, we should probably make dependencies mandatory.

• autotools still creates a bug, but i do not know what is missing, see the attached log.

Are you sure that you tested this correctly? Because it seems from the log that ncurses wasn't installed. Note that I added the autotools dependency in an additional commit.

• database_gap: because of the last line in spkg-install script, sage -c "gap_reset_workspace()", it should depend on a working Sage installation. So i added SAGERUNTIME as a dependency. It is overkill ?

No overkill, it is correct.

• igraph requires the libxml2 (which we are not shipping), see the attached log.
  Perhaps we should package it, or perhaps move it to expermiental ?

Let's leave this for now.

it seems that igraph would be happy with blas/lapack and glpk, so perhaps should we also add atlas and glpk as dependencies ?

Well, igraph doesn't use them even if they are present. While igraph might be able to use those libraries, it doesn't do so by default. So no extra dependencies are needed.

• libtheora depends on libogg, see the attached log. I updated the dependency file.

Good.

• normaliz depends on boost_cropped, see the attached log. I updated the dependency file.

Good.

Shall we remove singular from normaliz dependencies ?

The spkg-install file for normaliz really installs things specifically for Singular, so I think we need the dependency.

• i added a # no dependencies for configure.

Well, configure isn't really a package... If you really want a dependencies file, it should perhaps say something like # not a real package.

base: $(INST)/$(BZIP2) $(INST)/$(PATCH) $(INST)/$(PKGCONF)

Shall those 3 packages have "base" priority too ?

No. Like I said, configure isn't a package, but these 3 are real packages.

[jdemeyer]

comment:10

Does this still need work?

[mkoeppe]

comment:11

Part of this (for latte_int, 4ti2) was duplicated in #20748.
What's up with this bigger patch?
(And what's up with all these tickets without followup?)

[embray]

comment:12

Well, I guess it will have to be rebased anyhow.

[mkoeppe]

comment:13

This patch adds lines of the form:

 $(INST)/$(SAGE_MP_LIBRARY) $(INST)/$(NTL) $(INST)/$(CDDLIB)

whereas #20748 added:

 $(MP_LIBRARY) ntl 4ti2 cddlib

What is the preferred way of writing these dependencies?
Is this documented?

[vbraun]

comment:16

This is a recent change, the new syntax is $(MP_LIBRARY) ntl 4ti2 cddlib

[jdemeyer]

comment:19

Replying to @mkoeppe:

What is the preferred way of writing these dependencies?
Is this documented?

http://doc.sagemath.org/html/en/developer/packaging.html#package-dependencies

[jdemeyer]

Changed branch from u/tmonteil/add_some_dependencies to u/jdemeyer/add_some_dependencies

[jdemeyer]

Changed commit from ec50fed to 6aef10c

[jdemeyer]

New commits:

6aef10c

Update to new style of dependencies

[mkoeppe]

Changed reviewer from Thierry Monteil to Thierry Monteil, Matthias Koeppe

[vbraun]

Changed branch from u/jdemeyer/add_some_dependencies to 6aef10c