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Bug 902383

Summary: science: obsolete hashes used in Manifest
Product: Gentoo Linux Reporter: Michał Górny <mgorny>
Component: OverlaysAssignee: Gentoo Science Related Packages <sci>
Status: RESOLVED FIXED    
Severity: normal CC: andrewammerlaan
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 902221    

Description Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2023-03-20 06:22:22 UTC
The Manifest files in this repository are using obsolete hashes RMD160 or WHIRLPOOL.  Please update to newer Manifest hashes to avoid problems with newer package managers.  For more information, see the tracker blocked by this bug.
Comment 1 Andrew Nowa Ammerlaan gentoo-dev 2023-03-20 07:58:54 UTC
Those packages are fetch-restricted. Only someone with access to the software can regenerate the manifest files. For this reason these packges have already been masked.

Someone with access needs to step up and fix these ebuilds, otherwise they will have to be removed. Here's the list:

dev-lang/pgi
sci-biology/signalp
sci-biology/tmhmm
sci-chemistry/ligplot+
sci-chemistry/nmrview
sci-chemistry/rosetta-tools
Comment 2 Larry the Git Cow gentoo-dev 2023-04-25 11:28:16 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f11cdaea2f9c040e9eef4e7552ffda13016eedb

commit 1f11cdaea2f9c040e9eef4e7552ffda13016eedb
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2023-04-25 11:27:47 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2023-04-25 11:27:59 +0000

    sci-chemistry/rosetta-tools: treeclean
    
    Closes: https://bugs.gentoo.org/902383
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 profiles/package.mask                              |  4 ---
 sci-chemistry/rosetta-tools/Manifest               |  1 -
 sci-chemistry/rosetta-tools/metadata.xml           | 11 --------
 .../rosetta-tools/rosetta-tools-3.0.ebuild         | 29 ----------------------
 4 files changed, 45 deletions(-)

Additionally, it has been referenced in the following commit(s):

https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c236b098be9ef80615f681b063eb4247189e851

commit 1c236b098be9ef80615f681b063eb4247189e851
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2023-04-25 11:27:08 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2023-04-25 11:27:08 +0000

    sci-chemistry/nmrview: treeclean
    
    Bug: https://bugs.gentoo.org/902383
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 profiles/package.mask                         |  1 -
 sci-chemistry/nmrview/Manifest                |  2 -
 sci-chemistry/nmrview/files/README.Gentoo     | 17 --------
 sci-chemistry/nmrview/files/nmrview.sh        |  6 ---
 sci-chemistry/nmrview/files/nmrview.sh-r1     |  6 ---
 sci-chemistry/nmrview/metadata.xml            | 12 ------
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild | 57 ---------------------------
 7 files changed, 101 deletions(-)

https://gitweb.gentoo.org/proj/sci.git/commit/?id=99bb0d558f8f42fd8a39f3341213e379eabf7a79

commit 99bb0d558f8f42fd8a39f3341213e379eabf7a79
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2023-04-25 11:26:36 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2023-04-25 11:26:36 +0000

    sci-chemistry/ligplot+: treeclean
    
    Bug: https://bugs.gentoo.org/902383
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 profiles/package.mask                      |  1 -
 sci-chemistry/ligplot+/Manifest            |  1 -
 sci-chemistry/ligplot+/ligplot+-1.4.ebuild | 42 ------------------------------
 sci-chemistry/ligplot+/metadata.xml        |  8 ------
 4 files changed, 52 deletions(-)

https://gitweb.gentoo.org/proj/sci.git/commit/?id=0ceb993976976439639c7414d3e2aa2be5bb64de

commit 0ceb993976976439639c7414d3e2aa2be5bb64de
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2023-04-25 11:26:06 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2023-04-25 11:26:06 +0000

    sci-biology/tmhmm: treeclean
    
    Bug: https://bugs.gentoo.org/902383
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 profiles/package.mask               |  1 -
 sci-biology/tmhmm/Manifest          |  1 -
 sci-biology/tmhmm/metadata.xml      |  8 --------
 sci-biology/tmhmm/tmhmm-2.0c.ebuild | 39 -------------------------------------
 4 files changed, 49 deletions(-)

https://gitweb.gentoo.org/proj/sci.git/commit/?id=df1b752e2d45731e3ed75840ec6b2e04e314bd64

commit df1b752e2d45731e3ed75840ec6b2e04e314bd64
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2023-04-25 11:25:25 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2023-04-25 11:25:25 +0000

    sci-biology/signalp: treeclean
    
    Bug: https://bugs.gentoo.org/902383
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 profiles/package.mask                  |  1 -
 sci-biology/signalp/Manifest           |  1 -
 sci-biology/signalp/metadata.xml       |  8 ------
 sci-biology/signalp/signalp-3.0.ebuild | 46 ----------------------------------
 4 files changed, 56 deletions(-)

https://gitweb.gentoo.org/proj/sci.git/commit/?id=a60ef457ab7c7039a22d9dd04268748bd5e35c8f

commit a60ef457ab7c7039a22d9dd04268748bd5e35c8f
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2023-04-25 11:24:28 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2023-04-25 11:24:28 +0000

    dev-lang/pgi: treeclean
    
    Bug: https://bugs.gentoo.org/902383
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 dev-lang/pgi/Manifest                      |   1 -
 dev-lang/pgi/files/pgi-13.5-glibc.patch    |  31 ---------
 dev-lang/pgi/files/pgi-13.5-terminal.patch |  39 -----------
 dev-lang/pgi/metadata.xml                  |  15 -----
 dev-lang/pgi/pgi-13.5.ebuild               | 105 -----------------------------
 profiles/package.mask                      |   1 -
 6 files changed, 192 deletions(-)