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Bug 881783 - sci-biology/bedtools-2.30.0 - src/.../version.cpp: fatal error: version_git.h: No such file or directory
Summary: sci-biology/bedtools-2.30.0 - src/.../version.cpp: fatal error: version_git.h...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2022-11-18 09:42 UTC by Toralf Förster
Modified: 2024-04-25 09:38 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,19.95 KB, text/plain)
2022-11-18 09:42 UTC, Toralf Förster
Details
emerge-history.txt.bz2 (emerge-history.txt.bz2,77.28 KB, application/x-bzip)
2022-11-18 09:42 UTC, Toralf Förster
Details
environment (environment,92.80 KB, text/plain)
2022-11-18 09:42 UTC, Toralf Förster
Details
etc.clang.tar.bz2 (etc.clang.tar.bz2,703 bytes, application/x-bzip)
2022-11-18 09:42 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,36.07 KB, application/x-bzip)
2022-11-18 09:42 UTC, Toralf Förster
Details
sci-biology:bedtools-2.30.0:20221118-050050.log (sci-biology:bedtools-2.30.0:20221118-050050.log,57.70 KB, text/plain)
2022-11-18 09:42 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,25.36 KB, application/x-bzip)
2022-11-18 09:42 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2022-11-18 09:42:39 UTC
too long lines were shrinked:

  * compiling src/utils/FileRecordTools/Records/RecordList.cpp
x86_64-pc-linux-gnu-g++ -Wall -std=c++11 -pipe -march=native -fno-diagnostics-color -O2 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile 
  * compiling src/utils/version/version.cpp
x86_64-pc-linux-gnu-g++ -Wall -std=c++11 -pipe -march=native -fno-diagnostics-color -O2 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile 
src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file or directory
    2 | #include "version_git.h"
      |          ^~~~~~~~~~~~~~~

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_plasma-j4-20221114-040020

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

GNUMAKEFLAGS="$GNUMAKEFLAGS --shuffle"
gcc-config -l:
 [1] x86_64-pc-linux-gnu-11
 [2] x86_64-pc-linux-gnu-12 *
clang/llvm (if any):
clang version 15.0.5
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/15/bin
Configuration file: /etc/clang/clang.cfg
/usr/lib/llvm/15
15.0.5
Python 3.10.8
Available Rust versions:
  [1]   rust-bin-1.65.0
  [2]   rust-1.65.0 *
The following VMs are available for generation-2:
1)	OpenJDK 11.0.17_p8 [openjdk-11]
2)	Eclipse Temurin JDK 11.0.17_p8 [openjdk-bin-11]
*)	Eclipse Temurin JDK 17.0.5_p8 [openjdk-bin-17]
4)	Eclipse Temurin JDK 8.352_p08 [openjdk-bin-8]
5)	Eclipse Temurin JRE 17.0.5_p8 [openjdk-jre-bin-17]
Available Java Virtual Machines:
  [1]   openjdk-11 
  [2]   openjdk-bin-8 
  [3]   openjdk-bin-11 
  [4]   openjdk-bin-17  system-vm
  [5]   openjdk-jre-bin-17 

The Glorious Glasgow Haskell Compilation System, version 8.10.6
php cli (if any):

  HEAD of ::gentoo
commit 3ceed0db2ae822fc06f5b2b746cf36f43c2fb361
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Fri Nov 18 04:31:52 2022 +0000

    2022-11-18 04:31:51 UTC

emerge -qpvO sci-biology/bedtools
[ebuild  N    ] sci-biology/bedtools-2.30.0  USE="-test"
Comment 1 Toralf Förster gentoo-dev 2022-11-18 09:42:40 UTC
Created attachment 833291 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2022-11-18 09:42:41 UTC
Created attachment 833293 [details]
emerge-history.txt.bz2
Comment 3 Toralf Förster gentoo-dev 2022-11-18 09:42:43 UTC
Created attachment 833295 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2022-11-18 09:42:44 UTC
Created attachment 833297 [details]
etc.clang.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2022-11-18 09:42:45 UTC
Created attachment 833299 [details]
etc.portage.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2022-11-18 09:42:46 UTC
Created attachment 833301 [details]
sci-biology:bedtools-2.30.0:20221118-050050.log
Comment 7 Toralf Förster gentoo-dev 2022-11-18 09:42:47 UTC
Created attachment 833303 [details]
temp.tar.bz2
Comment 8 Larry the Git Cow gentoo-dev 2024-04-25 09:38:01 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6659d55f12a3e8b75dbf9545cac23f37ca00bd58

commit 6659d55f12a3e8b75dbf9545cac23f37ca00bd58
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2024-04-25 09:37:47 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2024-04-25 09:37:47 +0000

    sci-biology/bedtools: add 2.31.1
    
    Bug: https://bugs.gentoo.org/881783
    Bug: https://bugs.gentoo.org/907971
    Bug: https://bugs.gentoo.org/929751
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/bedtools/Manifest                      |   1 +
 sci-biology/bedtools/bedtools-2.31.1.ebuild        |  49 ++++++
 .../files/bedtools-2.31.1-buildsystem.patch        |  84 ++++++++++
 .../bedtools/files/bedtools-2.31.1-includes.patch  | 178 +++++++++++++++++++++
 .../bedtools/files/bedtools-2.31.1-python.patch    |  40 +++++
 5 files changed, 352 insertions(+)