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Re: [MoM] mmseqs2



Hello Andreas,

Now with the newest version of Lintian which was pushed a week ago, I
still do not see any of the output you are getting. In fact, I am seeing
this:


I: mmseqs2: spelling-error-in-binary usr/bin/mmseqs alteratives alternatives
I: mmseqs2: spelling-error-in-binary usr/bin/mmseqs Dont Don't
I: mmseqs2: spelling-error-in-binary usr/bin/mmseqs seperated separated
I: mmseqs2: spelling-error-in-binary ... use --no-tag-display-limit to
see all (or pipe to a file/program)
I: mmseqs2: description-synopsis-might-not-be-phrased-properly "ultra
fast and sensitive protein search and clustering."
I: mmseqs2: possible-documentation-but-no-doc-base-registration

This is what I have been working with the whole time, so my judgement
was that it was fairly complete.

Right now I just ran lintian as is, as before I was specifying the
specific deb package using a manual invoke of the command, and now I get
what you are getting. So I guess I was doing it wrong the whole time :(

Lesson learned, thanks!

Shayan Doust

On 20/07/2019 17:40, Andreas Tille wrote:
> On Sat, Jul 20, 2019 at 03:00:56PM +0100, Shayan Doust wrote:
>>
>>> Did you push everything (git push --all && git push --tags)? Repackaging
>>> should have left commits in 'upstream' and 'pristine-tar' branches, as
>>> well as new tags. Without them my build process fail. Other than that
>>> seems fine.
>>
>> How about now? Also, in pristine-tar branch, there are two sets of delta
>> and id files. Should the old one (without +ds) be removed?
> 
> If you really want to do the work to clean up that's OK but I usually do
> not mind to much.  Except of some extra bytes it does not really harm
> (except if really huge data files might have been removed from some
> source - than it makes sense).
>  
>>> I'd expect 'licensecheck' to be able of doing this, but haven't
>>> checked it yet.
>>
>> Unfortunately I haven't had much luck with licensecheck, especially when
>> detecting the type of license used within some src files in the
>> directory. It either ends up blank or displays a FIXME output.
> 
> As I said: That's the boring part of packaging ...
>  
>>> I will be on vacation for a month starting on Monday, but I will stay
>>> on-line most of the time. Most probably I won't have access to my
>>> Debian building machine.
>>
>> Ok.
> 
> DebConf is usually for work on Debian tasks - so I should be available
> the next week.
> 
> For the moment I see:
> 
> 
> I: mmseqs2 source: wildcard-matches-nothing-in-dep5-copyright lib/cadode/* (paragraph at line 17)
> N: 
> N:    The wildcard that was specified matches no file in the source tree. This
> N:    either indicates that you should fix the wildcard so that it matches the
> N:    intended file or that you can remove the wildcard. Notice that in
> N:    contrast to shell globs, the "*" (star or asterisk) matches slashes and
> N:    leading dots.
> N:    
> N:    Refer to
> N:    https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ for
> N:    details.
> N:    
> N:    Severity: minor, Certainty: possible
> N:    
> N:    Check: source-copyright, Type: source
> N: 
> I: mmseqs2 source: wildcard-matches-nothing-in-dep5-copyright lib/kseq2/* (paragraph at line 21)
> I: mmseqs2 source: unused-file-paragraph-in-dep5-copyright paragraph at line 17
> N: 
> N:    The Files paragraph in debian/copyright appears to be superfluous as it
> N:    is does not match any files.
> N:    
> N:    You should be able to safely remove it.
> N:    
> N:    This can also be caused by incorrect relative ordering of paragraphs.
> N:    
> N:    Refer to
> N:    https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ for
> N:    details.
> N:    
> N:    Severity: minor, Certainty: possible
> N:    
> N:    Check: source-copyright, Type: source
> N: 
> I: mmseqs2 source: unused-file-paragraph-in-dep5-copyright paragraph at line 21
> 
> I just fixed
> 
>   I: mmseqs2 source: out-of-date-standards-version 4.3.0 (released 2018-12-23) (current is 4.4.0)
> 
> and
> 
>   W: mmseqs2 source: debian-watch-file-should-mangle-version line 5
> 
> as well as
> 
>   I: mmseqs2: description-synopsis-might-not-be-phrased-properly "ultra fast and sensitive protein search and clustering."
> 
> 
> If you manage to hunt down the lintian issues in d/copyright I could
> upload.
> 
> Kind regards
> 
>           Andreas.
> 

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