[Bug 490723] Review Request: R-IRanges - Low-level containers for storing sets of integer ranges
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Sun Mar 22 10:05:37 UTC 2009
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https://bugzilla.redhat.com/show_bug.cgi?id=490723
--- Comment #5 from Pierre-YvesChibon <pingou at pingoured.fr> 2009-03-22 06:05:24 EDT ---
> ! The package license corresponds to the license as mentioned in the
> DESCRIPTION file and in the website, however several source files
> contain the statement:
>
> * This file is copyright 2002 Jim Kent, but license is hereby
> * granted for all use - public, private or commercial. */
>
> which is not the same as "Artistic licence 2.0". Needs some
> consultation with upstream.
I will ask upstream for clarification
> ! Specfile is written in legible English and uses macro consitently,
> however:
>
> The Source and URL fields uses the macro %{BioC} with is not defined
> anywhere. The urls point to the right location if this macro is
> assumed to be an empty string, so techncally they are correct, but
> it is a source of confusion. Suggestion - remove the macros.
The macro is defined (line 2 of the file), however the %define should be
changed to %global according to the newly approved guidelines.
> The comment that says "#i368 arch" should probaly read something
> like "#architecture dependent package", because that I think is what
> you really mean.
That comment is generated by R2spec, it can be changed/ignored/removed
(I will change R2spec to this)
> ! Package compiles, but there are warnings that should be fixed:
>
> IntervalTree.c:48: warning: missing braces around initializer
> memalloc.c:293: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
> memalloc.c:293: warning: format '%d' expects type 'int', but argument 3 has type 'size_t'
>
> The "... may be used uninitialized" warnings might be harmless (or
> not, ...)
> I have no idea if these warnings are harmful or not:
>
> Creating a generic for "cbind" in package "IRanges"
> (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level))
> Creating a generic for "rbind" in package "IRanges"
> (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level))
I will point these warning to upstream.
> ! %check is present and check pass, but
>
> Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...11,12c11
> < rbind,
> < sapply
> ---
> > rbind
>
> It test still says "OK", but it looks "strange".
This is just the output of the test run
> ! No package owns the package's main directory /usr/lib64/R/library/IRanges
Oups, I will change this
> Ideally both main and devel should own the main directory in order
> to avoid orphaned directories after package removal, but at least
> main must own it.
I do not agree. Since -devel has the main package has a requirement, only the
main need to own the directory.
> ! Since the -devel package does not include a .pc file it should not
> require pkgconfig (or is there some other reason for this?)
Will be fixed
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