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polymake 4.11 #36878

Merged
merged 5 commits into from
Jan 14, 2024
Merged

polymake 4.11 #36878

merged 5 commits into from
Jan 14, 2024

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mkoeppe
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@mkoeppe mkoeppe commented Dec 14, 2023 •
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Fixes #36023

📝 Checklist

  • The title is concise, informative, and self-explanatory.
  • The description explains in detail what this PR is about.
  • I have linked a relevant issue or discussion.
  • I have created tests covering the changes.
  • I have updated the documentation accordingly.

⌛ Dependencies

@mkoeppe mkoeppe self-assigned this Dec 14, 2023
@mkoeppe mkoeppe requested a review from dimpase December 19, 2023 20:27
@mkoeppe mkoeppe requested a review from tscrim December 28, 2023 05:57
@kwankyu
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kwankyu commented Jan 4, 2024

"CI Linux incremental" all failed. Is that related with this PR? Or rerunning the test will fix itself after rebase?

@mkoeppe
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mkoeppe commented Jan 4, 2024

It's because it was trying to install dummy packages perl_cpan_polymake_prereq, libxml2.

I think I fixed this recently in the workflows

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mkoeppe commented Jan 4, 2024

Rebased, let's see.

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kwankyu commented Jan 4, 2024

My system has polymake 4.11. So I ran make polymake, which failed

...
[perl_term_readline_gnu-1.35] Successfully installed perl_term_readline_gnu-1.35
[perl_term_readline_gnu-1.35] Deleting temporary build directory
[perl_term_readline_gnu-1.35] /Users/kwankyu/GitHub/sage-dev/local/var/tmp/sage/build/perl_term_readline_gnu-1.35
[perl_term_readline_gnu-1.35] Finished installing perl_term_readline_gnu-1.35
make --no-print-directory perl_cpan_polymake_prereq-SAGE_LOCAL-no-deps
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Note: perl_cpan_polymake_prereq is a dummy package that the Sage distribution uses
[perl_cpan_polymake_prereq-none] to provide information about equivalent system packages.
[perl_cpan_polymake_prereq-none] It cannot be installed using the Sage distribution.
[perl_cpan_polymake_prereq-none] Please install it manually, for example using the system packages
[perl_cpan_polymake_prereq-none] recommended at the end of a run of './configure'
[perl_cpan_polymake_prereq-none] See below for package-specific information.
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] perl_cpan_polymake_prereq: Represents all Perl packages that are prerequisites for polymake
[perl_cpan_polymake_prereq-none] ===========================================================================================
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Description
[perl_cpan_polymake_prereq-none] -----------
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] This script package represents all Perl packages that are prerequisites
[perl_cpan_polymake_prereq-none] for polymake.
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] License
[perl_cpan_polymake_prereq-none] -------
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Various free software licenses
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Type
[perl_cpan_polymake_prereq-none] ----
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] optional
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Dependencies
[perl_cpan_polymake_prereq-none] ------------
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Version Information
[perl_cpan_polymake_prereq-none] -------------------
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Equivalent System Packages
[perl_cpan_polymake_prereq-none] --------------------------
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] alpine:
[perl_cpan_polymake_prereq-none]     $ apk add perl-term-readkey perl-dev perl-file-slurp perl-json \
[perl_cpan_polymake_prereq-none]           perl-xml-writer perl-xml-libxslt
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] cpan:
[perl_cpan_polymake_prereq-none]     $ cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp JSON SVG \
[perl_cpan_polymake_prereq-none]           Term::ReadKey
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Debian/Ubuntu:
[perl_cpan_polymake_prereq-none]     $ sudo apt-get install libxml-libxslt-perl libxml-writer-perl libxml2-dev \
[perl_cpan_polymake_prereq-none]           libperl-dev libfile-slurp-perl libjson-perl libsvg-perl \
[perl_cpan_polymake_prereq-none]           libterm-readkey-perl libterm-readline-gnu-perl
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Fedora/Redhat/CentOS:
[perl_cpan_polymake_prereq-none]     $ sudo yum install perl-ExtUtils-Embed perl-File-Slurp perl-JSON \
[perl_cpan_polymake_prereq-none]           perl-Term-ReadLine-Gnu perl-TermReadKey perl-XML-Writer \
[perl_cpan_polymake_prereq-none]           perl-XML-LibXML perl-XML-LibXSLT
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] freebsd:
[perl_cpan_polymake_prereq-none]     $ sudo pkg install textproc/p5-XML-Writer textproc/p5-XML-LibXML \
[perl_cpan_polymake_prereq-none]           textproc/p5-XML-LibXSLT devel/p5-File-Slurp converters/p5-JSON \
[perl_cpan_polymake_prereq-none]           textproc/p5-SVG devel/p5-Term-ReadKey
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] gentoo:
[perl_cpan_polymake_prereq-none]     $ sudo emerge XML-Writer XML-LibXML XML-LibXSLT File-Slurp \
[perl_cpan_polymake_prereq-none]           dev-perl/Term-ReadLine-Gnu dev-perl/TermReadKey JSON SVG
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] void:
[perl_cpan_polymake_prereq-none]     $ sudo xbps-install perl-File-Slurp perl-JSON perl-SVG perl-Term-ReadKey \
[perl_cpan_polymake_prereq-none]           perl-XML-LibXML perl-XML-LibXSLT perl-XML-Writer
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] If the system package is installed, ./configure will check if it can be used.
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] 
[perl_cpan_polymake_prereq-none] Error: perl_cpan_polymake_prereq is a dummy package and 
[perl_cpan_polymake_prereq-none] cannot be installed using the Sage distribution.
make[2]: *** [perl_cpan_polymake_prereq-SAGE_LOCAL-no-deps] Error 1
make[1]: *** [/Users/kwankyu/GitHub/sage-dev/local/var/lib/sage/installed/perl_cpan_polymake_prereq-none] Error 2

@mkoeppe
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mkoeppe commented Jan 4, 2024

What does config.log say about perl_cpan_polymake_prereq?

@kwankyu
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kwankyu commented Jan 4, 2024 

## -------------------------------------------------------------------------- ##
## Checking whether SageMath should install SPKG perl_cpan_polymake_prereq... ##
## -------------------------------------------------------------------------- ##
configure:46263: checking for perl module XML::Writer
configure:46269: result: no
configure:46263: checking for perl module XML::LibXML
configure:46269: result: no
configure:46263: checking for perl module XML::LibXSLT
configure:46269: result: no
configure:46263: checking for perl module File::Slurp
configure:46269: result: no
configure:46263: checking for perl module JSON
configure:46269: result: no
configure:46263: checking for perl module SVG
configure:46269: result: no
configure:46263: checking for perl module Term::ReadKey
configure:46269: result: no
configure:46312: no suitable system package found for SPKG perl_cpan_polymake_prereq

@kwankyu
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kwankyu commented Jan 4, 2024 •
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So this is normal. I should first install "perl_cpan_polymake_prereq" by homebrew, or maybe it is not possible on mac.

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kwankyu commented Jan 4, 2024

After installing prerequisite perl modules, make polymake is making polymake 4.11 on my system.

Some observations:

  1. "CI Linux incremental" is still failing. But I think this is normal because optional dependencies (dummy packages: perl_cpan_polymake_prereq and libxml2) are missing.

  2. libxml2 is a dependency of perl_cpan_polymake_prereq. Hence I think libxml2 should be placed before perl_cpan_polymake_prereq in dependencies. But because they are all dummy packages, this point may be meaningless.

  3. lrslib is both in dependencies_optional and dependencies. Is this ok?

  4. perl_cpan_polymake_prereq is called a "script package" in SPKG.rst of polymake. Isn't this a "dummy package"?

@mkoeppe
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mkoeppe commented Jan 4, 2024

  • "CI Linux incremental" is still failing. But I think this is normal because optional dependencies (dummy packages: perl_cpan_polymake_prereq and libxml2) are missing.

You are right. We don't have a mechanism for that in the CI.

  • libxml2 is a dependency of perl_cpan_polymake_prereq. Hence I think libxml2 should be placed before perl_cpan_polymake_prereq in dependencies. But because they are all dummy packages, this point may be meaningless.

I don't think the order of the packages in our dependencies has any meaning.

I have made the other suggested changes.

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kwankyu commented Jan 4, 2024 •
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  • libxml2 is a dependency of perl_cpan_polymake_prereq. Hence I think libxml2 should be placed before perl_cpan_polymake_prereq in dependencies. But because they are all dummy packages, this point may be meaningless.

I don't think the order of the packages in our dependencies has any meaning.

Right. But the messages from ./configure are in the same order as the packages are listed in dependencies. So, following the messages, the user will try to install perl_cpan_polymake_prereq first and then libxml2. But in the end, the user is forced to install libxml2 first and then perl_cpan_polymake_prereq.

This is a trivial point. No action is required.

I have made the other suggested changes.

Thanks.

@mkoeppe
build/pkgs/polymake/dependencies: libxml2 is a dep of perl_cpan_polym…
dcbb426 
…ake_prereq, so list it first so that users can install them from left to right
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mkoeppe commented Jan 4, 2024

OK, thanks. Done

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Documentation preview for this PR (built with commit dcbb426; changes) is ready! 🎉

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It works well on mac, and perhaps on linux too 🤞

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mkoeppe commented Jan 4, 2024

Thank you!

vbraun pushed a commit to vbraun/sage that referenced this pull request Jan 5, 2024
sagemathgh-36878: polymake 4.11
bb87fb1 
    
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Fixes sagemath#36023

### 📝 Checklist

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- [ ] The title is concise, informative, and self-explanatory.
- [ ] The description explains in detail what this PR is about.
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- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on
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- sagemath#36930

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URL: sagemath#36878
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee
@vbraun vbraun merged commit 87a91d9 into sagemath:develop Jan 14, 2024
24 of 44 checks passed
@mkoeppe mkoeppe added this to the sage-10.3 milestone Jan 14, 2024
@mkoeppe mkoeppe deleted the polymake_4_11 branch February 16, 2024 03:12
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old Polymake incompatibility with system Perl 5.38 (Fedora 39) - update to polymake 4.11
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