[Bug 490721] Review Request: R-Biostrings - String objects representing biological sequences

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https://bugzilla.redhat.com/show_bug.cgi?id=490721


Mattias Ellert <mattias.ellert at fysast.uu.se> changed:

           What    |Removed                     |Added
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         AssignedTo|nobody at fedoraproject.org    |mattias.ellert at fysast.uu.se
               Flag|                            |fedora-review?




--- Comment #1 from Mattias Ellert <mattias.ellert at fysast.uu.se>  2009-03-25 14:33:11 EDT ---
Fedora review R-Biostrings-2.10.21-1.fc10.src.rpm (2009-03-25)

* OK
! Needs attention

* rpmlint output

R-Biostrings.x86_64: W: one-line-command-in-%post
/usr/lib/rpm/R-make-search-index.sh
R-Biostrings.x86_64: W: one-line-command-in-%postun
/usr/lib/rpm/R-make-search-index.sh
R-Biostrings-devel.x86_64: W: only-non-binary-in-usr-lib
R-Biostrings-devel.x86_64: W: no-documentation
4 packages and 1 specfiles checked; 0 errors, 4 warnings.

  The one-line-command warnings are standard for R packages
  The no-documentation warning for devel is OK (documentation is in main)
  The only-non-binary-in-usr-lib devel for devel can be ignored
    (the previous rpmlint version listed this one as an error)

* Package is named according to R packaging guidlines

* Package follows R packaging guidelines

* The package is licensed under a Fedora approved license (Artistic 2.0)

* The package license corresponds to the license mentioned in the
  DESCRIPTION file, no conflicting license statements are present in
  the package's source files.

  (There is a different license [LGPL] mentioned in the Biostrings1
  subdirectory, but no files from this subdirectory are packaged or
  used during the build.)

* License text not included in the package (OK since the stated
  licence does not require it).

! Specfile is written in legible English and uses macros consitently,
  however:

  The URL field uses the macro %{BioC} with is not defined anywhere.
  The url 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. [Sorry for putting this comment in the R-IRanges
  review, where it didn't belong (as you rightly pointed out) - the
  intention was to put it in this review.]

  The comment that says "#i368 arch" should probaly read something
  like "#architecture dependent package", because that I think is what
  you really mean.

  The NEWS file might belong in %doc

* Sources match upstream and are the latest version:

  59e67acb017722ace830721d2edcb3de  Biostrings_2.10.21.tar.gz
  59e67acb017722ace830721d2edcb3de  SRPM/Biostrings_2.10.21.tar.gz

! Package compiles, but there are some warnings

  The warnings from the C code are all of types that usually can be ignored.
  There are some warnings from R that I can not judge:

Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XString" no definition for class:
"AsIs"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XStringSet" no definition for class:
"AsIs"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "BStringViews" no definition for class:
"file"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "PDict" no definition for class: "AsIs"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "eq" no definition for class:
"BioString"

  Are these benign or an indication of missing BuildRequires?

* BuildRequires look sane (but see comment on the previous point)

* %check is present, but disabled with the comment:

  # Ask for R-BSgenome which cannot build without R-Biostring

  Disabling the test in this case is OK, since you otherwise would
  have a chicken and egg problem. Changing "Ask" to "Asks" in the
  comment would be better grammar, and saying "Requires" instead might
  be even better, but that is just details that are not really
  significant.

* The package owns the directories it creates

* No duplicate files

* %files has %defattrs, and permissions are sane.

* %clean clears %buildroot

* Package contains code

* Headers are in -devel

! Since the -devel package does not include a .pc file it should not
  require pkgconfig

* -devel requires main with fully qualified version

* Package doesn't own other's directories

* %install clears %buildroot

* Installed filenames are valid UTF8 (even valid ASCII)

* Package builds in mock (Fedora 10)

* Scriptlets are sane

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