[Bug 490722] New: Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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Summary: Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

https://bugzilla.redhat.com/show_bug.cgi?id=490722

Summary: Review Request: R-BSgenome - Infrastructure for
                    Biostrings-based genome data packages
           Product: Fedora
           Version: rawhide
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: medium
          Priority: medium
         Component: Package Review
        AssignedTo: [e-mail]
        ReportedBy: [e-mail]
         QAContact: [e-mail]
                CC: [e-mail], [e-mail]
   Estimated Hours: 0.0
    Classification: Fedora

Spec URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome.spec
SRPM URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome-1.10.5-1.fc10.src.rpm
Description: 
Infrastructure shared by all the Biostrings-based genome data packages

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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https://bugzilla.redhat.com/show_bug.cgi?id=490722

Pierre-YvesChibon  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
         Depends on|                            |490721

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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Mattias Ellert  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |[e-mail]

--- Comment #1 from Mattias Ellert   2009-03-25 22:27:59 EDT ---
Package does not build due to missing BuildRequires:

Error: package 'Biostrings' required by 'BSgenome' could not be found
Execution halted
ERROR: lazy loading failed for package 'BSgenome'

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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--- Comment #2 from Pierre-YvesChibon   2009-04-01 05:15:36 EDT ---
arf there is a missing BR on R-Biostrings

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #3 from Pierre-YvesChibon   2009-04-01 05:21:08 EDT ---
Updated:
Spec URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome.spec
SRPM URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome-1.10.5-2.fc10.src.rpm

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #4 from Mattias Ellert   2009-04-03 05:16:45 EDT ---
see bug 490721 comment 3

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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Mattias Ellert  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED
                 CC|[e-mail] |
         AssignedTo|[e-mail]    |[e-mail]
               Flag|                            |fedora-review?

--- Comment #5 from Mattias Ellert   2009-05-11 07:42:53 EDT ---
Fedora review R-BSgenome-1.10.5-1.fc10.src.rpm (2009-05-11)

* OK
! Needs attention

* rpmlint output

R-BSgenome.noarch: W: one-line-command-in-%post
/usr/lib/rpm/R-make-search-index.sh
R-BSgenome.noarch: W: one-line-command-in-%postun
/usr/lib/rpm/R-make-search-index.sh
2 packages and 1 specfiles checked; 0 errors, 2 warnings.

The one-line-command warnings are standard for R packages

* Package is named according to R packaging guidelines

* Package follows R packaging guidelines

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

* The license matches what is written in the DESCRIPTION file
  No license/copyright statements that contradict this was found

* 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

* Source matches upstream

9e9f8793065e5c49c07240c6cdcade9c  BSgenome_1.10.5.tar.gz
  9e9f8793065e5c49c07240c6cdcade9c  SRPM/BSgenome_1.10.5.tar.gz

! However it is not the latest version (1.12.0 is available for BioC 2.4)

* Package compiles in mock (Fedora 10)

! BuildRequires and Requires look sane, but

Is the "Requires: R-biobase" appropriate? It is not listed as a
  Depends or Imports on the package web site. (It will be dragged in
  as a dependency of the R-Biostrings package which is a direct
  dependency)

* %check is present, but disabled with the comment - which makes sense.

* The package owns the directories it creates

* No duplicate files

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

* %clean clears %buildroot

* Package contains permissable content

* Package doesn't own other's directories

* %install clears %buildroot

* Installed filenames are valid UTF8 (even valid ASCII)

* Scriptlets are sane

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #6 from Pierre-YvesChibon   2009-05-18 11:09:30 EDT ---
(In reply to comment #5)
> Fedora review R-BSgenome-1.10.5-1.fc10.src.rpm (2009-05-11)
> ! However it is not the latest version (1.12.0 is available for BioC 2.4)
> ! BuildRequires and Requires look sane, but
>
> Is the "Requires: R-biobase" appropriate? It is not listed as a
>   Depends or Imports on the package web site. (It will be dragged in
>   as a dependency of the R-Biostrings package which is a direct
>   dependency)

Corrected in :
Spec URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome.spec
SRPM URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome-1.12.0-1.fc10.src.rpm

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

Mattias Ellert  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
               Flag|fedora-review?              |fedora-review+

--- Comment #7 from Mattias Ellert   2009-05-18 17:25:55 EDT ---
There is one tiny issue left - which I should have noted earlier:

According to https://fedoraproject.org/wiki/Packaging/R#Documentation_files the
NAMESPACE file should not be marked %doc.

I trust you can fix that before importing the package to cvs.

Package approved.

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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comments should be made in the comments box of this bug.

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Pierre-YvesChibon  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
               Flag|                            |fedora-cvs?

--- Comment #8 from Pierre-YvesChibon   2009-05-18 17:55:15 EDT ---
Thanks for the review (once again :-) ), I will fix the %doc before importing

New Package CVS Request
=======================
Package Name: R-BSgenome
Short Description: Infrastructure shared by all the Biostrings-based genome
data packages 
Owners: pingou
Branches: F-10 F-11
InitialCC:

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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comments should be made in the comments box of this bug.

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Kevin Fenzi  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
               Flag|fedora-cvs?                 |fedora-cvs+

--- Comment #9 from Kevin Fenzi   2009-05-18 19:43:44 EDT ---
cvs done.

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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https://bugzilla.redhat.com/show_bug.cgi?id=490722

Bug 490722 depends on bug 490721, which changed state.

Bug 490721 Summary: Review Request: R-Biostrings - String objects representing biological sequences
https://bugzilla.redhat.com/show_bug.cgi?id=490721

What    |Old Value                   |New Value
----------------------------------------------------------------------------
             Status|ASSIGNED                    |CLOSED
         Resolution|                            |NEXTRELEASE

--- Comment #10 from Fedora Update System   2009-05-28 03:23:46 EDT ---
R-BSgenome-1.12.0-2.fc10 has been submitted as an update for Fedora 10.
http://admin.fedoraproject.org/updates/R-BSgenome-1.12.0-2.fc10

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #11 from Fedora Update System   2009-05-28 03:23:51 EDT ---
R-BSgenome-1.12.0-2.fc11 has been submitted as an update for Fedora 11.
http://admin.fedoraproject.org/updates/R-BSgenome-1.12.0-2.fc11

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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comments should be made in the comments box of this bug.

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Fedora Update System  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |ON_QA

--- Comment #12 from Fedora Update System   2009-05-29 22:29:23 EDT ---
R-BSgenome-1.12.0-2.fc10 has been pushed to the Fedora 10 testing repository. 
If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update R-BSgenome'.  You can provide
feedback for this update here:
http://admin.fedoraproject.org/updates/F10/FEDORA-2009-5661

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #13 from Fedora Update System   2009-05-29 22:35:44 EDT ---
R-BSgenome-1.12.0-2.fc11 has been pushed to the Fedora 11 testing repository. 
If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update R-BSgenome'.  You can provide
feedback for this update here:
http://admin.fedoraproject.org/updates/F11/FEDORA-2009-5694

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #14 from Fedora Update System   2009-06-16 11:40:09 EDT ---
R-Biobase-2.4.1-1.fc10,R-RUnit-0.4.22-1.fc10,R-IRanges-1.2.3-1.fc10,R-BSgenome-1.12.2-1.fc10,R-BufferedMatrixMethods-1.8.0-3.fc10,R-Biostrings-2.12.6-1.fc10
has been submitted as an update for Fedora 10.
http://admin.fedoraproject.org/updates/R-Biobase-2.4.1-1.fc10,R-RUnit-0.4.22...

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #15 from Fedora Update System   2009-06-16 11:41:17 EDT ---
R-Biobase-2.4.1-1.fc11,R-RUnit-0.4.22-1.fc11,R-IRanges-1.2.3-1.fc11,R-BSgenome-1.12.2-1.fc11,R-BufferedMatrixMethods-1.8.0-3.fc11,R-Biostrings-2.12.6-1.fc11
has been submitted as an update for Fedora 11.
http://admin.fedoraproject.org/updates/R-Biobase-2.4.1-1.fc11,R-RUnit-0.4.22...

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #16 from Fedora Update System   2009-06-18 07:40:44 EDT ---
R-Biobase-2.4.1-1.fc10, R-RUnit-0.4.22-1.fc10, R-IRanges-1.2.3-1.fc10,
R-BSgenome-1.12.2-1.fc10, R-BufferedMatrixMethods-1.8.0-3.fc10,
R-Biostrings-2.12.6-1.fc10 has been pushed to the Fedora 10 testing repository.
 If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update R-Biobase R-RUnit R-IRanges
R-BSgenome R-BufferedMatrixMethods R-Biostrings'.  You can provide feedback for
this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-6530

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #17 from Fedora Update System   2009-06-18 07:58:59 EDT ---
R-Biobase-2.4.1-1.fc11, R-RUnit-0.4.22-1.fc11, R-IRanges-1.2.3-1.fc11,
R-BSgenome-1.12.2-1.fc11, R-BufferedMatrixMethods-1.8.0-3.fc11,
R-Biostrings-2.12.6-1.fc11 has been pushed to the Fedora 11 testing repository.
 If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update R-Biobase R-RUnit R-IRanges
R-BSgenome R-BufferedMatrixMethods R-Biostrings'.  You can provide feedback for
this update here: http://admin.fedoraproject.org/updates/F11/FEDORA-2009-6673

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #18 from Fedora Update System   2009-07-02 01:49:17 EDT ---
R-Biobase-2.4.1-1.fc10, R-RUnit-0.4.22-1.fc10, R-IRanges-1.2.3-1.fc10,
R-BSgenome-1.12.2-1.fc10, R-BufferedMatrixMethods-1.8.0-3.fc10,
R-Biostrings-2.12.6-1.fc10 has been pushed to the Fedora 10 stable repository. 
If problems still persist, please make note of it in this bug report.

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

Fedora Update System  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ON_QA                       |CLOSED
   Fixed In Version|                            |2.4.1-1.fc10
         Resolution|                            |ERRATA

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

--- Comment #19 from Fedora Update System   2009-07-02 01:50:27 EDT ---
R-Biobase-2.4.1-1.fc11, R-RUnit-0.4.22-1.fc11, R-IRanges-1.2.3-1.fc11,
R-BSgenome-1.12.2-1.fc11, R-BufferedMatrixMethods-1.8.0-3.fc11,
R-Biostrings-2.12.6-1.fc11 has been pushed to the Fedora 11 stable repository. 
If problems still persist, please make note of it in this bug report.

[Bug 490722] Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=490722

Fedora Update System  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
   Fixed In Version|2.4.1-1.fc10                |2.4.1-1.fc11