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Bug 911646

Summary: sci-chemistry/mdtraj-1.9.7 - Error compiling Cython file:
Product: Gentoo Linux Reporter: Toralf Förster <toralf>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Status: RESOLVED OBSOLETE    
Severity: normal CC: mgorny, treecleaner
Priority: Normal Keywords: PMASKED
Version: unspecified   
Hardware: All   
OS: Linux   
See Also: https://github.com/mdtraj/mdtraj/issues/1800
https://github.com/mdtraj/mdtraj/pull/1801
Whiteboard:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 897934    
Attachments: emerge-info.txt
emerge-history.txt
environment
etc.clang.tar.xz
etc.portage.tar.xz
sci-chemistry:mdtraj-1.9.7:20230803-080753.log
temp.tar.xz

Description Toralf Förster gentoo-dev 2023-08-03 08:09:59 UTC 
WARNING  Overriding pythran description with argspec information for: numpy.random.uniform
WARNING  Overriding pythran description with argspec information for: numpy.random.weibull
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

Error compiling Cython file:
------------------------------------------------------------
...

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_plasma-20230731-184110

  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10
 [2] x86_64-pc-linux-gnu-13 *
clang/llvm (if any):
clang version 16.0.6
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/16/bin
Configuration file: /etc/clang/clang.cfg
/usr/lib/llvm/16
16.0.6
Python 3.11.4
Available Ruby profiles:
  [1]   ruby31 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.71.0 *
The following VMs are available for generation-2:
1)	Eclipse Temurin JDK 11.0.19_p7 [openjdk-bin-11]
*)	Eclipse Temurin JDK 17.0.7_p7 [openjdk-bin-17]
3)	Eclipse Temurin JDK 8.372_p07 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8 
  [2]   openjdk-bin-11 
  [3]   openjdk-bin-17  system-vm

php cli (if any):
go version go1.20.6 linux/amd64

  HEAD of ::gentoo
commit f8097d1a7eb0388264657f953093d19fd1259e27
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Thu Aug 3 07:01:41 2023 +0000

    2023-08-03 07:01:41 UTC

emerge -qpvO sci-chemistry/mdtraj
[ebuild  N    ] sci-chemistry/mdtraj-1.9.7  USE="-test" PYTHON_TARGETS="python3_11 -python3_10"
Comment 1 Toralf Förster gentoo-dev 2023-08-03 08:10:00 UTC 
Created attachment 866917 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2023-08-03 08:10:02 UTC 
Created attachment 866918 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2023-08-03 08:10:03 UTC 
Created attachment 866919 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2023-08-03 08:10:04 UTC 
Created attachment 866920 [details]
etc.clang.tar.xz
Comment 5 Toralf Förster gentoo-dev 2023-08-03 08:10:04 UTC 
Created attachment 866921 [details]
etc.portage.tar.xz
Comment 6 Toralf Förster gentoo-dev 2023-08-03 08:10:05 UTC 
Created attachment 866922 [details]
sci-chemistry:mdtraj-1.9.7:20230803-080753.log
Comment 7 Toralf Förster gentoo-dev 2023-08-03 08:10:06 UTC 
Created attachment 866923 [details]
temp.tar.xz
Comment 8 Larry the Git Cow gentoo-dev 2023-08-13 01:09:56 UTC 
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bd539f89b5aa658654fd717864e6210913d05942

commit bd539f89b5aa658654fd717864e6210913d05942
Author:     Sam James <sam@gentoo.org>
AuthorDate: 2023-08-13 00:51:37 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2023-08-13 00:51:37 +0000

    sci-chemistry/mdtraj: depend on <cython-3
    
    Bug: https://bugs.gentoo.org/911646
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)
Comment 9 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2024-02-28 13:49:20 UTC 
No reply for half a year, no revdeps.
Comment 10 Larry the Git Cow gentoo-dev 2024-03-10 16:37:04 UTC 
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0ac23a5da73e80d5424ab2830cae3eec5b42c2f8

commit 0ac23a5da73e80d5424ab2830cae3eec5b42c2f8
Author:     Michał Górny <mgorny@gentoo.org>
AuthorDate: 2024-03-10 16:17:08 +0000
Commit:     Michał Górny <mgorny@gentoo.org>
CommitDate: 2024-03-10 16:36:52 +0000

    package.mask: Last rite dev-python/astunparse, sci-chemistry/mdtraj
    
    Bug: https://bugs.gentoo.org/911646
    Signed-off-by: Michał Górny <mgorny@gentoo.org>

 profiles/package.mask | 13 +++++++++++++
 1 file changed, 13 insertions(+)
Comment 11 Larry the Git Cow gentoo-dev 2024-04-13 14:45:54 UTC 
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2b1667bc65dcbdcc00c565f1c31976d2c631992a

commit 2b1667bc65dcbdcc00c565f1c31976d2c631992a
Author:     Michał Górny <mgorny@gentoo.org>
AuthorDate: 2024-04-13 14:35:28 +0000
Commit:     Michał Górny <mgorny@gentoo.org>
CommitDate: 2024-04-13 14:36:51 +0000

    dev-python/astunparse: Remove last-rited pkg
    
    Bug: https://bugs.gentoo.org/911646
    Signed-off-by: Michał Górny <mgorny@gentoo.org>

 dev-python/astunparse/Manifest                     |  1 -
 dev-python/astunparse/astunparse-1.6.3-r1.ebuild   | 39 ------------
 .../astunparse/files/astunparse-1.6.2-tests.patch  | 23 -------
 .../astunparse/files/astunparse-1.6.3-py39.patch   | 74 ----------------------
 .../files/astunparse-1.6.3-test-py311.patch        | 26 --------
 dev-python/astunparse/metadata.xml                 | 16 -----
 profiles/package.mask                              |  1 -
 7 files changed, 180 deletions(-)

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8e78e2bf9ed815575f8c00157166095423e14681

commit 8e78e2bf9ed815575f8c00157166095423e14681
Author:     Michał Górny <mgorny@gentoo.org>
AuthorDate: 2024-04-13 14:32:16 +0000
Commit:     Michał Górny <mgorny@gentoo.org>
CommitDate: 2024-04-13 14:33:01 +0000

    sci-chemistry/mdtraj: Remove last-rited pkg
    
    Bug: https://bugs.gentoo.org/911646
    Signed-off-by: Michał Górny <mgorny@gentoo.org>

 profiles/package.mask                              |  2 -
 sci-chemistry/mdtraj/Manifest                      |  1 -
 .../mdtraj/files/mdtraj-1.9.7-python311.patch      | 16 -------
 sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild           | 49 ----------------------
 sci-chemistry/mdtraj/metadata.xml                  | 12 ------
 5 files changed, 80 deletions(-)