Bug 1340513 - Review Request: gap-pkg-gbnp - Computing Gröbner bases of noncommutative polynomials
Summary: Review Request: gap-pkg-gbnp - Computing Gröbner bases of noncommutative poly...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Till Hofmann
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2016-05-27 16:08 UTC by Jerry James
Modified: 2016-07-18 18:27 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2016-07-18 18:27:58 UTC
Type: ---
Embargoed:
thofmann: fedora-review+


Attachments (Terms of Use)

Description Jerry James 2016-05-27 16:08:59 UTC
Spec URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp.spec
SRPM URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp-1.0.3-1.fc25.src.rpm
Fedora Account System Username: jjames
Description: GBNP provides GAP algorithms for computing Grobner bases of non-commutative polynomials with coefficients from a field implemented in GAP, and some variations, such as a weighted and truncated version and a tracing facility.

The word algorithm is interpreted loosely: in general one cannot expect such an algorithm to terminate, as it would imply solvability of the word problem for finitely presented (semi)groups.

Comment 1 Till Hofmann 2016-06-04 13:10:38 UTC
Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- Large documentation must go in a -doc subpackage. Large could be size
  (~1MB) or number of files.
  Note: Documentation size in /usr/share is 20480 bytes in 4 files, but there is
  documentation in /usr/lib/gap/pkg/gbnp/doc with 137 files and size 3.4MB.
  I know from the last review that gap handles documentation differently, but is
  it still possible to move those files to a doc package?
  You could also put all doc files in /usr/share and then symlink /usr/lib/gap/pkg/gbnp/doc.
- There are a lot of files in /usr/lib/gap/pkg/gbnp/doc that look like they
  shouldn't be packaged. Some of them are removed in %install, but all files
  in subfolders are still there. I suggest you replace rm -f in %install with
  some suitable find ... -delete
- [!]: Uses parallel make %{?_smp_mflags} macro.
  If for some reason you can't use %{?_smp_mflags}, please specify the reason in
  the Spec file.
- There are 81 test files packaged. Do they need to be in the package? If so,
  please specify the reason.
- Not sure if the TODO file should be packaged.
- Please convert the following files to utf8:
  gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/share/doc/gap-pkg-gbnp/TODO
  gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/lib/gap/pkg/gbnp/doc/gbnp_doc.tex
- spelling:
  gap-pkg-gbnp.noarch: W: spelling-error Summary(en_US) noncommutative -> non
  commutative, non-commutative, noncom mutative
  This should probably be non-commutative. All other spelling errors are okay.

not necessarily an issue:
- [?]: Development files must be in a -devel package
  I don't know enough about gap to be able to say which files are development
  files. Please move all development files to a -devel package if there are any.

not an issue:

- If (and only if) the source package includes the text of the license(s)
  in its own file, then that file, containing the text of the license(s)
  for the package is included in %license.
  Note: License file copyrightcomment is not marked as %license
  See:
  http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text
  --> that file is not actually a license file


===== MUST items =====

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[x]: License field in the package spec file matches the actual license.
     Note: There is no build directory. Running licensecheck on vanilla
     upstream sources. No licenses found. Please check the source files for
     licenses manually.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[?]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: Package is not known to require an ExcludeArch tag.
[!]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 20480 bytes in 4 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: Package requires other packages for directories it uses.
[x]: Package must own all directories that it creates.
[x]: Package does not own files or directories owned by other packages.
[x]: All build dependencies are listed in BuildRequires, except for any
     that are listed in the exceptions section of Packaging Guidelines.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package does not use a name that already exists.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

===== SHOULD items =====

Generic:
[!]: Uses parallel make %{?_smp_mflags} macro.
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[?]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[-]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[x]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: gap-pkg-gbnp-1.0.3-1.fc25.noarch.rpm
          gap-pkg-gbnp-1.0.3-1.fc25.src.rpm
gap-pkg-gbnp.noarch: W: spelling-error Summary(en_US) noncommutative -> non commutative, non-commutative, noncom mutative
gap-pkg-gbnp.noarch: W: spelling-error %description -l en_US solvability -> sociability, livability, solubility
gap-pkg-gbnp.noarch: W: only-non-binary-in-usr-lib
gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/share/doc/gap-pkg-gbnp/TODO
gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/lib/gap/pkg/gbnp/doc/gbnp_doc.tex
gap-pkg-gbnp.src: W: spelling-error Summary(en_US) noncommutative -> non commutative, non-commutative, noncom mutative
gap-pkg-gbnp.src: W: spelling-error %description -l en_US solvability -> sociability, livability, solubility
2 packages and 0 specfiles checked; 0 errors, 7 warnings.




Rpmlint (installed packages)
----------------------------
sh: /usr/bin/python: No such file or directory
gap-pkg-gbnp.noarch: W: spelling-error Summary(en_US) noncommutative -> non commutative, non-commutative, noncom mutative
gap-pkg-gbnp.noarch: W: spelling-error %description -l en_US solvability -> sociability, livability, solubility
gap-pkg-gbnp.noarch: W: only-non-binary-in-usr-lib
gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/lib/gap/pkg/gbnp/doc/gbnp_doc.tex
gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/share/doc/gap-pkg-gbnp/TODO
1 packages and 0 specfiles checked; 0 errors, 5 warnings.



Requires
--------
gap-pkg-gbnp (rpmlib, GLIBC filtered):
    /bin/sh
    gap-core



Provides
--------
gap-pkg-gbnp:
    gap-pkg-gbnp



Source checksums
----------------
http://mathdox.org/products/gbnp/GBNP-1.0.3.tar.gz :
  CHECKSUM(SHA256) this package     : efde746049eedd63159c5f7fed810f82b3929105402ef60fe5530f7496c93e06
  CHECKSUM(SHA256) upstream package : efde746049eedd63159c5f7fed810f82b3929105402ef60fe5530f7496c93e06


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Comment 2 Jerry James 2016-06-06 03:37:14 UTC
Thank you for the review, Till.

(In reply to Till Hofmann from comment #1)
> - Large documentation must go in a -doc subpackage. Large could be size
>   (~1MB) or number of files.
>   Note: Documentation size in /usr/share is 20480 bytes in 4 files, but
> there is
>   documentation in /usr/lib/gap/pkg/gbnp/doc with 137 files and size 3.4MB.
>   I know from the last review that gap handles documentation differently,
> but is
>   it still possible to move those files to a doc package?
>   You could also put all doc files in /usr/share and then symlink
> /usr/lib/gap/pkg/gbnp/doc.

I have put the documentation files into a -doc subpackage.

> - There are a lot of files in /usr/lib/gap/pkg/gbnp/doc that look like they
>   shouldn't be packaged. Some of them are removed in %install, but all files
>   in subfolders are still there. I suggest you replace rm -f in %install with
>   some suitable find ... -delete

I have more aggressively removed some of the files in the doc subdirectory.

> - [!]: Uses parallel make %{?_smp_mflags} macro.
>   If for some reason you can't use %{?_smp_mflags}, please specify the
> reason in
>   the Spec file.

I added it, but it won't do any good.  The only thing being built is the documentation, and that is an inherently sequential process.

> - There are 81 test files packaged. Do they need to be in the package? If so,
>   please specify the reason.

In addition to having a builtin documentation browser, GAP also has a builtin package testsuite.  For that to function properly, yes, the test files need to be packaged.  Probably very few GAP users run the test suite, but I want it to work for those that do run it.

> - Not sure if the TODO file should be packaged.

Agreed.  I have removed the TODO file.

> - Please convert the following files to utf8:
>   gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/share/doc/gap-pkg-gbnp/TODO
>   gap-pkg-gbnp.noarch: W: file-not-utf8
> /usr/lib/gap/pkg/gbnp/doc/gbnp_doc.tex

The TODO file is no longer packaged.  The other file is a TeX input file, which tells TeX that it is ISO8859-1, like so:

\usepackage[latin1]{inputenc}

Therefore converting the encoding is incorrect in this case.  Also, the HTML output is UTF-8.

> - spelling:
>   gap-pkg-gbnp.noarch: W: spelling-error Summary(en_US) noncommutative -> non
>   commutative, non-commutative, noncom mutative
>   This should probably be non-commutative. All other spelling errors are
> okay.

No, "noncommutative" is correct; see http://www.thefreedictionary.com/noncommutative for example.  The problem is that Fedora's default dictionary contains very few technical terms, which seems like a terrible idea, given that we use it to check descriptions of technical products.  I have found that the spell checking output of rpmlint is almost always wrong.

> not necessarily an issue:
> - [?]: Development files must be in a -devel package
>   I don't know enough about gap to be able to say which files are development
>   files. Please move all development files to a -devel package if there are
> any.

Hmmm.  You know, there really isn't a notion of a development file in GAP, although perhaps there should be.  In this package, the files are used for runtime (files ending in .g, .gd, or .gi), testing, or documentation.  Perhaps the testing files should be considered development files.  I will give that some thought.  Right now, the existing GAP packages bundle the testing files with the main package, for use by GAP's builtin test suite.  I will do some experiments to see if I can split the testing files out into separate packages without causing runtime problems.

New URLs:
Spec URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp.spec
SRPM URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp-1.0.3-2.fc25.src.rpm

Comment 3 Till Hofmann 2016-06-06 08:13:53 UTC
Thanks for your update.

(In reply to Jerry James from comment #2)
> Thank you for the review, Till.
> 
> (In reply to Till Hofmann from comment #1)
> > - Large documentation must go in a -doc subpackage. Large could be size
> >   (~1MB) or number of files.
> >   Note: Documentation size in /usr/share is 20480 bytes in 4 files, but
> > there is
> >   documentation in /usr/lib/gap/pkg/gbnp/doc with 137 files and size 3.4MB.
> >   I know from the last review that gap handles documentation differently,
> > but is
> >   it still possible to move those files to a doc package?
> >   You could also put all doc files in /usr/share and then symlink
> > /usr/lib/gap/pkg/gbnp/doc.
> 
> I have put the documentation files into a -doc subpackage

That looks good. I think the -doc package should own %{_gap_dir}/pkg/%{pkgname}/ because it doesn't depend on the main package and the directory should be owned even if you only install the doc package, see https://fedoraproject.org/wiki/Packaging:Guidelines?rd=Packaging/Guidelines#File_and_Directory_Ownership
> 
> > - There are a lot of files in /usr/lib/gap/pkg/gbnp/doc that look like they
> >   shouldn't be packaged. Some of them are removed in %install, but all files
> >   in subfolders are still there. I suggest you replace rm -f in %install with
> >   some suitable find ... -delete
> 
> I have more aggressively removed some of the files in the doc subdirectory.

I would still prefer using find over rm because it's more stable to future changes, but this is okay.
> 
> > - [!]: Uses parallel make %{?_smp_mflags} macro.
> >   If for some reason you can't use %{?_smp_mflags}, please specify the
> > reason in
> >   the Spec file.
> 
> I added it, but it won't do any good.  The only thing being built is the
> documentation, and that is an inherently sequential process.
I see, but as it doesn't break anything either, I think it's better this way.
> 
> > - There are 81 test files packaged. Do they need to be in the package? If so,
> >   please specify the reason.
> 
> In addition to having a builtin documentation browser, GAP also has a
> builtin package testsuite.  For that to function properly, yes, the test
> files need to be packaged.  Probably very few GAP users run the test suite,
> but I want it to work for those that do run it.

That makes sense. Can you please add an explanation to the Spec file? This is useful because other users know why those files are packaged, and it allows re-evaluation in the future.
> 
> > - Not sure if the TODO file should be packaged.
> 
> Agreed.  I have removed the TODO file.
> 
> > - Please convert the following files to utf8:
> >   gap-pkg-gbnp.noarch: W: file-not-utf8 /usr/share/doc/gap-pkg-gbnp/TODO
> >   gap-pkg-gbnp.noarch: W: file-not-utf8
> > /usr/lib/gap/pkg/gbnp/doc/gbnp_doc.tex
> 
> The TODO file is no longer packaged.  The other file is a TeX input file,
> which tells TeX that it is ISO8859-1, like so:
> 
> \usepackage[latin1]{inputenc}
> 
> Therefore converting the encoding is incorrect in this case.  Also, the HTML
> output is UTF-8.

OK. Why do package tex files in the first place?

> 
> > - spelling:
> >   gap-pkg-gbnp.noarch: W: spelling-error Summary(en_US) noncommutative -> non
> >   commutative, non-commutative, noncom mutative
> >   This should probably be non-commutative. All other spelling errors are
> > okay.
> 
> No, "noncommutative" is correct; see
> http://www.thefreedictionary.com/noncommutative for example.  The problem is
> that Fedora's default dictionary contains very few technical terms, which
> seems like a terrible idea, given that we use it to check descriptions of
> technical products.  I have found that the spell checking output of rpmlint
> is almost always wrong.

I see. I checked Merriam Webster and it didn't know "noncommutative", but if you say that is the correct term, this is fine with me.

> 
> > not necessarily an issue:
> > - [?]: Development files must be in a -devel package
> >   I don't know enough about gap to be able to say which files are development
> >   files. Please move all development files to a -devel package if there are
> > any.
> 
> Hmmm.  You know, there really isn't a notion of a development file in GAP,
> although perhaps there should be.  In this package, the files are used for
> runtime (files ending in .g, .gd, or .gi), testing, or documentation. 
> Perhaps the testing files should be considered development files.  I will
> give that some thought.  Right now, the existing GAP packages bundle the
> testing files with the main package, for use by GAP's builtin test suite.  I
> will do some experiments to see if I can split the testing files out into
> separate packages without causing runtime problems.

Sounds good.

> 
> New URLs:
> Spec URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp.spec
> SRPM URL:
> https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp-1.0.3-2.fc25.src.
> rpm


To summarize, please:
- fix ownership of %{_gap_dir}/pkg/%{pkgname}/ in the doc package,
- add an explanation about the test files to the Spec file,
- clarify why you need to package tex files

Comment 4 Jerry James 2016-07-01 21:53:44 UTC
Sorry for the delay.  Had a little too much going on there for a few weeks.

I have:
- fixed the directory ownership issue in the doc package
- added a comment about including the test files
- removed the TeX files from the binary package

New URLs:
Spec URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp.spec
SRPM URL: https://jjames.fedorapeople.org/gap-pkg-gbnp/gap-pkg-gbnp-1.0.3-3.fc25.src.rpm

Comment 5 Till Hofmann 2016-07-02 08:28:08 UTC
Approved. Thanks for packaging!

Comment 6 Gwyn Ciesla 2016-07-05 16:13:34 UTC
Package request has been approved: https://admin.fedoraproject.org/pkgdb/package/rpms/gap-pkg-gbnp

Comment 7 Fedora Update System 2016-07-06 03:39:01 UTC
gap-pkg-gbnp-1.0.3-3.fc24 has been submitted as an update to Fedora 24. https://bodhi.fedoraproject.org/updates/FEDORA-2016-3b2905f488

Comment 8 Fedora Update System 2016-07-10 16:01:17 UTC
gap-pkg-gbnp-1.0.3-3.fc24 has been pushed to the Fedora 24 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-3b2905f488

Comment 9 Fedora Update System 2016-07-18 18:27:56 UTC
gap-pkg-gbnp-1.0.3-3.fc24 has been pushed to the Fedora 24 stable repository. If problems still persist, please make note of it in this bug report.


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