[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #31 from Fedora Update System  ---
seqan2-2.4.0-0.4.20180103git8a875d.fc27 has been pushed to the Fedora 27 stable
repository. If problems still persist, please make note of it in this bug
report.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA
Last Closed||2018-01-26 12:56:00



--- Comment #30 from Fedora Update System  ---
seqan2-2.4.0-0.4.20180103git8a875d.fc26 has been pushed to the Fedora 26 stable
repository. If problems still persist, please make note of it in this bug
report.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #29 from Fedora Update System  ---
seqan2-2.4.0-0.4.20180103git8a875d.fc27 has been pushed to the Fedora 27
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-2018-136a004437

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955

Fedora Update System  changed:

   What|Removed |Added

 Status|MODIFIED|ON_QA



--- Comment #28 from Fedora Update System  ---
seqan2-2.4.0-0.4.20180103git8a875d.fc26 has been pushed to the Fedora 26
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-2018-d8c7f694e9

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #27 from Fedora Update System  ---
seqan2-2.4.0-0.4.20180103git8a875d.fc27 has been submitted as an update to
Fedora 27. https://bodhi.fedoraproject.org/updates/FEDORA-2018-136a004437

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #26 from Fedora Update System  ---
seqan2-2.4.0-0.4.20180103git8a875d.fc26 has been submitted as an update to
Fedora 26. https://bodhi.fedoraproject.org/updates/FEDORA-2018-d8c7f694e9

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #25 from Fedora Update System  ---
seqan2-2.4.0-0.3.20180103git8a875d.fc26 has been submitted as an update to
Fedora 26. https://bodhi.fedoraproject.org/updates/FEDORA-2018-ad26aa004e

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955

Fedora Update System  changed:

   What|Removed |Added

 Status|POST|MODIFIED



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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #24 from Fedora Update System  ---
seqan2-2.4.0-0.3.20180103git8a875d.fc27 has been submitted as an update to
Fedora 27. https://bodhi.fedoraproject.org/updates/FEDORA-2018-e1b5369a2c

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #23 from Gwyn Ciesla  ---
(fedrepo-req-admin):  The Pagure repository was created at
https://src.fedoraproject.org/rpms/seqan2

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955

Alec Leamas  changed:

   What|Removed |Added

 Status|ASSIGNED|POST
  Flags||fedora-review+



--- Comment #22 from Alec Leamas  ---
All looks good. Thanks for your work!

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #21 from Antonio Trande  ---
Everything should be okay now (without packaging release bump).

Spec URL: https://sagitter.fedorapeople.org/seqan2.spec
SRPM URL: 
https://sagitter.fedorapeople.org/seqan2-2.4.0-0.2.20180103git8a875d.fc27.src.rpm

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #20 from Alec Leamas  ---
Seems that almost everything from comment #12 is fixed. However:

- According to GL referenced in comment #9, bundled code must be removed 
  in %prep. However, the awesome font files are removed in %install 
  instead.
- One single license file apps/rabema/COPYING is missing a %license
  statement.

close, but no cigar...

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #19 from Antonio Trande  ---
Spec URL: https://sagitter.fedorapeople.org/seqan2.spec
SRPM URL: 
https://sagitter.fedorapeople.org/seqan2-2.4.0-0.2.20180103git8a875d.fc27.src.rpm

- plot.awk/ps2pswLinks.gawk installed in a private share datadir
- plot.awk/ps2pswLinks.gawk symliked in '_bindir'
- Renamed each single license file

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #18 from Alec Leamas  ---
Again, I think I understand your reasoning. That said, my position is that you
will need to copy all of them. There are a formal and a practical aspect of
this.

Formally, the GL reguires you to include all license files, no exceptions.

Practically, as an example look at e. g., /apps/seqcons2/LICENSE  and
/apps/bs_tools/LICENSE. These are both BSD (3-clause) and, as  I understand it,
you deem them as the same. However:

$ diff apps/seqcons2/LICENSE apps/bs_tools/LICENSE

< //  Seqcons2 - Compute consensus from sequences.
---
> // SeqAn - The Library for Sequence Analysis
4c4
< // Copyright (c) 2011-2015, Manuel Holtgrewe, FU Berlin
---
> // Copyright (c) 2006-2016, Knut Reinert, FU Berlin
15c15
< // * Neither the name of Manuel Holtgrewe or the FU Berlin nor the names
of
---
> // * Neither the name of Knut Reinert or the FU Berlin nor the names of
22c22
< // ARE DISCLAIMED. IN NO EVENT SHALL MANUEL HOLTGREWE OR THE FU BERLIN BE
LIABLE
---
> // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
31,32d30
< // ==
< // Author: Manuel Holtgrewe 


They are *not* the same. Excluding any of these actually means excluding the
copyright notice, the very point of the license file. Of course, we cannot do
that. Also note that the very condition of BSD code is that you must always
distribute the license together with the code. 

Sorry, but both from a formal and practical standpoint I cannot see any other
solution than distributing all these files.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #17 from Antonio Trande  ---
(In reply to Alec Leamas from comment #16)
> (In reply to Antonio Trande from comment #15)
> 
> > 
> > All LICENSE files are already included:
> > 
> > ## Renamed each single license file 
> > cp -p apps/rep_sep/LICENSE LGPLv3+.txt
> > cp -p apps/rabema/LICENSE GPLv3+.txt
> > cp -p LICENSE BSD.txt
> 
> Not really. I see:
> 
> $ cd BUILD
> $ find . -name LICENSE\* | wc -l
> 39
> 
> So, here is at least 39 license files. Looking at size, many are unique:
> 
> ls -l $(find . -iname LICENSE\* ) | awk '{print $5}' | sort | uniq | wc -l
> 30
> 

find . -name LICENSE | xargs licensecheck 
./apps/pair_align/LICENSE: LGPL (v3 or later)
./apps/sam2matrix/LICENSE: BSD (3 clause)
./apps/splazers/LICENSE: LGPL (v3)
./apps/razers3/LICENSE: UNKNOWN
./apps/snp_store/LICENSE: *No copyright* LGPL (v3)
./apps/dfi/LICENSE: UNKNOWN
./apps/fiona/LICENSE: UNKNOWN
./apps/yara/LICENSE: BSD (3 clause)
./apps/stellar/LICENSE: LGPL (v3)
./apps/alf/LICENSE: BSD (3 clause)
./apps/sgip/LICENSE: LGPL (v3)
./apps/seqcons2/LICENSE: BSD (3 clause)
./apps/bs_tools/LICENSE: BSD (3 clause)
./apps/fx_tools/LICENSE: BSD (3 clause)
./apps/searchjoin/LICENSE: BSD (3 clause)
./apps/tree_recon/LICENSE: LGPL (v3 or later)
./apps/insegt/LICENSE: BSD (3 clause)
./apps/param_chooser/LICENSE: LGPL (v3)
./apps/mason2/LICENSE: BSD (3 clause)
./apps/micro_razers/LICENSE: LGPL (v3)
./apps/gustaf/LICENSE: BSD (3 clause)
./apps/razers/LICENSE: UNKNOWN
./apps/seqan_tcoffee/LICENSE: LGPL (v3 or later)
./apps/ngs_roi/tool_shed/LICENSE: BSD (3 clause)
./apps/ngs_roi/LICENSE: BSD (3 clause)
./apps/ngs_roi/R/ngsroi/LICENSE: BSD (3 clause)
./apps/samcat/LICENSE: UNKNOWN
./apps/sak/LICENSE: LGPL (v3 or later)
./demos/LICENSE: BSD (3 clause)
./include/seqan/LICENSE: BSD (3 clause)
./util/cmake/ctd/LICENSE: BSD (3 clause)
./util/py_lib/seqan/LICENSE: BSD (3 clause)
./util/skel/app_template/LICENSE: BSD (3 clause)


> 
> > They're different licenses with same file name, here why i chose to rename
> > them.  There is not problem in my opinion.
> 
> GL at https://fedoraproject.org/wiki/Packaging:LicensingGuidelines says:
> 
> "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 must
> be included in %license."
> 
> I see no exceptions here. All of them should go into %license, >= 40 files. 

I don't want copy >= 40 files identical.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #16 from Alec Leamas  ---
(In reply to Antonio Trande from comment #15)

> 
> All LICENSE files are already included:
> 
> ## Renamed each single license file 
> cp -p apps/rep_sep/LICENSE LGPLv3+.txt
> cp -p apps/rabema/LICENSE GPLv3+.txt
> cp -p LICENSE BSD.txt

Not really. I see:

$ cd BUILD
$ find . -name LICENSE\* | wc -l
39

So, here is at least 39 license files. Looking at size, many are unique:

ls -l $(find . -iname LICENSE\* ) | awk '{print $5}' | sort | uniq | wc -l
30


> They're different licenses with same file name, here why i chose to rename
> them.  There is not problem in my opinion.

GL at https://fedoraproject.org/wiki/Packaging:LicensingGuidelines says:

"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 must be
included in %license."

I see no exceptions here. All of them should go into %license, >= 40 files. 

> 'plot.awk' and 'ps2pswLinks.gawk' are used as input files by other seqan
> scripts; see 'roi_plot_9.sh' script.
> 
> To be used, 'roi_plot_9.sh' needs them inside /usr/bin.

That still doesn't make them to binaries, for sure. They should be 444, and
such files does not belong in /usr/bin. I think I'd move them to
/usr/share/seqan2 and either patch the scripts using them or add a symlink to
/usr/bin (a symlink  is OK).

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #15 from Antonio Trande  ---
(In reply to Alec Leamas from comment #14)
> (In reply to Antonio Trande from comment #13)
> > (In reply to Alec Leamas from comment #12)
> > > Hi!
> 
> > > ===
> > > - 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 LICENSE is not marked as %license
> > >   See:
> > >   http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text
> > 
> > It is as GPLv3+, BSD and LGPLv3+
> 
> Yes, no doubt. But the GL doesn't really seem to care - they just require
> that these files should be included, full stop. You'll need include all of
> them. I agree this is a mess, but GL being what they are I see no
> alternative. Debian has a better system here, and IIRC there has been Fedora
> discussions on hardlinking these files. But I'm not aware of any conclusion.

All LICENSE files are already included:

## Renamed each single license file 
cp -p apps/rep_sep/LICENSE LGPLv3+.txt
cp -p apps/rabema/LICENSE GPLv3+.txt
cp -p LICENSE BSD.txt

They're different licenses with same file name, here why i chose to rename
them.  There is not problem in my opinion.

>  
> > > - The scripts /usr/bin/plot.awk and /usr/bin/ps2pswLinks.gawk are
> > >   executable but has no shebang. Looking at them, it seems that they are
> > >   no scripts, should be 444 and thus live somewhere else (/usr/share?)
> > > 
> > 
> > Here i don't know how manage these files. Let me check.
> 
> I would just have made them 444 and moved them to /usr/share/seqan2 in
> %install, checking references and add a note to README.fedora

'plot.awk' and 'ps2pswLinks.gawk' are used as input files by other seqan
scripts; see 'roi_plot_9.sh' script.

To be used, 'roi_plot_9.sh' needs them inside /usr/bin.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955

Antonio Trande  changed:

   What|Removed |Added

 Blocks||1331187




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1331187
[Bug 1331187] seqan badly needs an update
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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #14 from Alec Leamas  ---

(In reply to Antonio Trande from comment #13)
> (In reply to Alec Leamas from comment #12)
> > Hi!

> > ===
> > - 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 LICENSE is not marked as %license
> >   See:
> >   http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text
> 
> It is as GPLv3+, BSD and LGPLv3+

Yes, no doubt. But the GL doesn't really seem to care - they just require that
these files should be included, full stop. You'll need include all of them. I
agree this is a mess, but GL being what they are I see no alternative. Debian
has a better system here, and IIRC there has been Fedora discussions on
hardlinking these files. But I'm not aware of any conclusion.

> > - The devel package has no R: %{name}%{?_isa} = %{version}-%{release}
> >   (GL reference in comment #9)
> 
> Devel sub-package does not need 'seqan'. They're independant. 

OK, this is nothing like usual. Are you sure -devel is the proper name? That
said, this is C++ and you can do a lot in headers. If you are sure you can do
useful things with -devel without the base package, then you're certainly
right. 

That said, it looks weird.

> > - The scripts /usr/bin/plot.awk and /usr/bin/ps2pswLinks.gawk are
> >   executable but has no shebang. Looking at them, it seems that they are
> >   no scripts, should be 444 and thus live somewhere else (/usr/share?)
> > 
> 
> Here i don't know how manage these files. Let me check.

I would just have made them 444 and moved them to /usr/share/seqan2 in
%install, checking references and add a note to README.fedora

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #13 from Antonio Trande  ---
(In reply to Alec Leamas from comment #12)
> Hi!
> 
> Things begin to take shape... with issues below fix I'm ready to approve
> 
> 
> Package Review
> ==
> 
> Legend:
> [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> 
> 
> Issues:
> ===
> - 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 LICENSE is not marked as %license
>   See:
>   http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text

It is as GPLv3+, BSD and LGPLv3+

> - The devel package has no R: %{name}%{?_isa} = %{version}-%{release}
>   (GL reference in comment #9)

Devel sub-package does not need 'seqan'. They're independant. 

> - The scripts /usr/bin/plot.awk and /usr/bin/ps2pswLinks.gawk are
>   executable but has no shebang. Looking at them, it seems that they are
>   no scripts, should be 444 and thus live somewhere else (/usr/share?)
> 

Here i don't know how manage these files. Let me check.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #12 from Alec Leamas  ---
Hi!

Things begin to take shape... with issues below fix I'm ready to approve


Package Review
==

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


Issues:
===
- 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 LICENSE is not marked as %license
  See:
  http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text
- License: contains a typo (and and)
- According to GL referenced in comment #9, bundled code must be removed 
  in %prep. However, the awesome font files are removed in %install 
  instead.
- The iostream  header files mentioned in comment #10  are bundled, and
  thus needs a Provides(...).
- The devel package has no R: %{name}%{?_isa} = %{version}-%{release}
  (GL reference in comment #9)
- The scripts /usr/bin/plot.awk and /usr/bin/ps2pswLinks.gawk are
  executable but has no shebang. Looking at them, it seems that they are
  no scripts, should be 444 and thus live somewhere else (/usr/share?)


= MUST items =

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.

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: Checking patched sources after %prep for licenses. Licenses
 found: "Apache (v2.0)", "MIT/X11 (BSD like) GPL (v3 or later)", "SIL
 (v1.1)", "GPL (v3 or later)", "Unknown or generated", "*No copyright*
 LGPL (v3)", "MIT/X11 (BSD like)", "MIT/X11 (BSD like) BSD (3 clause)",
 "*No copyright* CC0 (v5)", "BSL (v1.0) BSD (3 clause)", "zlib/libpng",
 "BSD (unspecified)", "LGPL (v3 or later)", "GPL (v3)", "*No copyright*
 CC0", "*No copyright* BSD (unspecified)", "BSD (3 clause)", "BSD (2
 clause)", "MIT/X11 (BSD like) Apache (v2.0)", "*No copyright* BSD (3
 clause)", "LGPL (v3)". 3263 files have unknown license. Detailed
 output of licensecheck in
 /home/mk/tmp/FedoraReview/1531955-seqan2/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[x]: If the package is under multiple licenses, the licensing breakdown
 must be documented in the spec.
[x]: %build honors applicable compiler flags or justifies otherwise.
[!]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[x]: 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.
[x]: 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]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
 (~1MB) or number of files.
 Note: Documentation size is 61440 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]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
 beginning of %install.
[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

[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #11 from Antonio Trande  ---
(In reply to Alec Leamas from comment #10)
> Some follow-up from another box:
> 
> The bundled headers are iostream_bgzf.h, iostream_bzip2.h,
> iostream_bzip2_impl.h,  iostream_zip.h and iostream_zip_impl.h. I assume
> this is bundled code from
> https://www.codeproject.com/Articles/4457/zipstream-bzip-stream-iostream-
> wrappers-for-the-zl
> 
> As for licensing,  yy bad gut feeling about a single license is actually
> perfectly right. Reading the reference I see this: "If your package contains
> files which are under multiple, distinct, and independent licenses, then the
> spec must reflect this by using "and" as a separator"

It's right too; above all when you use different *incompatible* licenses.


Spec URL: https://sagitter.fedorapeople.org/seqan2.spec
SRPM URL: 
https://sagitter.fedorapeople.org/seqan2-2.4.0-0.1.20180103git8a875d.fc27.src.rpm

- Pre-released as seqan-2.4.0
- Add gcc-c++ BR
- Remove unnecessary R files
- Unbundle font-awesome
- Apps/libraries licensing commented

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #10 from Alec Leamas  ---
Some follow-up from another box:

The bundled headers are iostream_bgzf.h, iostream_bzip2.h,
iostream_bzip2_impl.h,  iostream_zip.h and iostream_zip_impl.h. I assume this
is bundled code from
https://www.codeproject.com/Articles/4457/zipstream-bzip-stream-iostream-wrappers-for-the-zl

As for licensing,  yy bad gut feeling about a single license is actually
perfectly right. Reading the reference I see this: "If your package contains
files which are under multiple, distinct, and independent licenses, then the
spec must reflect this by using "and" as a separator"

So, even if I understand your way of reasoning, a single license is not
applicable here. You need to declare all licenses present in the code using
AND. Removing unused stuff such as the SIL-licensed font in %prep could
simplify this.

Also note the GL on break-down: "In addition, the package must contain a
comment explaining the multiple licensing breakdown". Which is what I have been
trying to explain.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #9 from Alec Leamas  ---
(In reply to Antonio Trande from comment #8)

> > - seqan2 obsoletes seqan without providing seqan.
> 
> It's not needed. seqan2 and seqan must coexist for now.

Well, if they should coexist the Obsoletes: is obsolete(sic!). Perhaps you just
should drop that?

> > - seqan2-devel does not depend on seqan2 = %{version}-%{release}.
> 
> Why?

https://fedoraproject.org/wiki/Packaging:Guidelines#Requiring_Base_Package

> > - A binary zip file is present in the examples package.

No comment on this?

> > - Several bundled files/directories in util/py_lib/seqan/dox/tpl/lib and
> >   include/seqan/stream. Please either remove these in %prep and/or bundle
> >   properly using Provides: bundled(...)
> 
> I have already said why it's not needed. 

GL says something else: Bundled libraries must be treated as such:

https://fedoraproject.org/wiki/Packaging:Guidelines#Bundling_and_Duplication_of_system_libraries

Not bundled code must be removed in %prep:

https://fedoraproject.org/wiki/Bundled_Libraries?rd=Packaging:Bundled_Libraries#Treatment_of_Bundled_Libraries

> And why 'include/seqan/stream'?

Some of those headers carry specific licenses and comes from other projects. I
don't have the code at my current box, and the srpm link is broken (could you
please fix?) so I don't have the details. That said, several headers are
definitely bundled code.

> > - The License field comment does not match the actual file licenses in the
> >   sources. My proposal: Remove in %prep, add a text document describing 
> >   the licensing situation.
> 
> https://bugzilla.redhat.com/show_bug.cgi?id=1531955#c4

This is not about the overall License: tag, it's about the comment. That said, 
note that the GL strongly recommends using an AND type of licensing in cases
like this

https://fedoraproject.org/wiki/Packaging:LicensingGuidelines#Multiple_Licensing_Scenarios

But either way, a clarification of what code has what license is needed, even
if  you choose to go for a common license. 

I might wan't to refer to fedora-devel before using a common license, though.
My gut feeling somewhat bad.

> > - There are tests available. Why are these not run?
> 
> Tests are performed in %check.

Indeed, my bad. Sorry for the noise.

> > - The pkg-config file is not shipped with the -devel package for no obvious
> > reason.
> > - Likewise for seqan-config.cmake.
> > 
> 
> Why? Is it indispensable?

That's certainly subjective. But using my version of common sense, if upstream
makes efforts to create .pc and cmake macro files we need a compelling reason
to *not* include them. After all, they save a lot of work for those who use the
package.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #8 from Antonio Trande  ---
(In reply to Alec Leamas from comment #6)
> Here comes the full list of issues I see after making a full review:
> 
> - seqan2 obsoletes seqan without providing seqan.

It's not needed. seqan2 and seqan must coexist for now.

> - seqan2-devel does not depend on seqan2 = %{version}-%{release}.

Why?

> - A binary zip file is present in the examples package.
> - Several bundled files/directories in util/py_lib/seqan/dox/tpl/lib and
>   include/seqan/stream. Please either remove these in %prep and/or bundle
>   properly using Provides: bundled(...)

I have already said why it's not needed. And why 'include/seqan/stream'?

> - The License field comment does not match the actual file licenses in the
>   sources. My proposal: Remove in %prep, add a text document describing 
>   the licensing situation.

https://bugzilla.redhat.com/show_bug.cgi?id=1531955#c4

> - There are tests available. Why are these not run?

Tests are performed in %check.

> - The pkg-config file is not shipped with the -devel package for no obvious
> reason.
> - Likewise for seqan-config.cmake.
> 

Why? Is it indispensable?

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #7 from Alec Leamas  ---
Oops... there is more:
- There is no BR against gcc, gcc-c++ or clang [1].
- Note that this being a library might need also a similar Requires: [1]


[1] https://fedoraproject.org/wiki/Packaging:C_and_C%2B%2B

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #6 from Alec Leamas  ---
Here comes the full list of issues I see after making a full review:

- seqan2 obsoletes seqan without providing seqan.
- seqan2-devel does not depend on seqan2 = %{version}-%{release}.
- A binary zip file is present in the examples package.
- Several bundled files/directories in util/py_lib/seqan/dox/tpl/lib and
  include/seqan/stream. Please either remove these in %prep and/or bundle
  properly using Provides: bundled(...)
- The License field comment does not match the actual file licenses in the
  sources. My proposal: Remove in %prep, add a text document describing 
  the licensing situation.
- ps2pswLinks.gawk and plot.awk in /usr/bin are executable but have no
  shebang.
- There are tests available. Why are these not run?
- The pkg-config file is not shipped with the -devel package for no obvious
reason.
- Likewise for seqan-config.cmake.

Thoughts?

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #5 from Alec Leamas  ---
(In reply to Antonio Trande from comment #4)

> It's a false problem. Those files are not involved during the compilation
> neither packed in the binary rpms.

Does this also apply to the bundled headers in include/seqan/stream? In any
case they should then be removed in %prep, right? [1]

> Many apps are released under BSD, others under LGPv3+ and GPLv3+. These
> licenses are compatible among them, therefore the resultant binary rpm can
> be licensed under a single collective license (GPLv3+).

I have no overall problem with that conclusion. However, a statement describing
the grounds for it is required  - that is, the actual license for the different
files. This is a bit convoluted as of now, but would become clearer after
removing unused stuff in %prep.

[1]
https://fedoraproject.org/wiki/Bundled_Libraries?rd=Packaging:Bundled_Libraries

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #4 from Antonio Trande  ---
(In reply to Alec Leamas from comment #3)
> At a glance, here are bundling issues. The library
> util/py_lib/seqan/dox/tpl/lib includes several bundled libraries whih needs
> to be dealt with. In particular, shouldn't the bundled font be unbundled
> even under current, somewhat relaxed rules?

It's a false problem. Those files are not involved during the compilation
neither packed in the binary rpms.

> 
> Also the license situation is somewhat more complicated than what could be
> expressed in a few comments. I suggest that you run fedora-review and use
> the license-check.txt file created, review it and use it as license
> clarification.
> 
> This is just some initial findings.  seqan2 is quite a large package, and I
> expect there is more. Please take a stab at this for now.

Many apps are released under BSD, others under LGPv3+ and GPLv3+. These
licenses are compatible among them, therefore the resultant binary rpm can be
licensed under a single collective license (GPLv3+).


Spec URL: https://sagitter.fedorapeople.org/seqan2.spec
SRPM URL: 
https://sagitter.fedorapeople.org/seqan2-2.3.2-3.20180103git8a875d.fc27.src.rpm

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #3 from Alec Leamas  ---
At a glance, here are bundling issues. The library
util/py_lib/seqan/dox/tpl/lib includes several bundled libraries whih needs to
be dealt with. In particular, shouldn't the bundled font be unbundled even
under current, somewhat relaxed rules?

Also the license situation is somewhat more complicated than what could be
expressed in a few comments. I suggest that you run fedora-review and use the
license-check.txt file created, review it and use it as license clarification.

This is just some initial findings.  seqan2 is quite a large package, and I
expect there is more. Please take a stab at this for now.

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955

Alec Leamas  changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 CC||leamas.a...@gmail.com
   Assignee|nob...@fedoraproject.org|leamas.a...@gmail.com
 Whiteboard||mailto:nobody@fedoraproject
   ||.org



--- Comment #2 from Alec Leamas  ---
Taking this one

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[Bug 1531955] Review Request: seqan2 - C++ library of efficient algorithms and data structures

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1531955



--- Comment #1 from Antonio Trande  ---
Relevant upstream bug regarding SeqAn and OpenMS:
https://github.com/OpenMS/OpenMS/issues/1313#issuecomment-291078025

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