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Bug 895860 - sci-biology/bedtools-2.30.0 - src/.../ParseTools.h: error: uint32_t was not declared in this scope
Summary: sci-biology/bedtools-2.30.0 - src/.../ParseTools.h: error: uint32_t was not d...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: gcc-13
  Show dependency tree
 
Reported: 2023-02-22 09:00 UTC by Toralf Förster
Modified: 2023-04-18 10:04 UTC (History)
0 users

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


Attachments
emerge-info.txt (emerge-info.txt,19.11 KB, text/plain)
2023-02-22 09:00 UTC, Toralf Förster
Details
emerge-history.txt.bz2 (emerge-history.txt.bz2,69.36 KB, application/x-bzip)
2023-02-22 09:00 UTC, Toralf Förster
Details
environment (environment,90.38 KB, text/plain)
2023-02-22 09:00 UTC, Toralf Förster
Details
etc.clang.tar.bz2 (etc.clang.tar.bz2,838 bytes, application/x-bzip)
2023-02-22 09:00 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,37.59 KB, application/x-bzip)
2023-02-22 09:00 UTC, Toralf Förster
Details
sci-biology:bedtools-2.30.0:20230222-082931.log.bz2 (sci-biology:bedtools-2.30.0:20230222-082931.log.bz2,8.29 KB, application/x-bzip)
2023-02-22 09:00 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,30.03 KB, application/x-bzip)
2023-02-22 09:00 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2023-02-22 09:00:27 UTC
too long lines were shrinked:

   16 | class NoPosPlusRecord : public Record {
      |       ^~~~~~~~~~~~~~~
  * compiling src/utils/general/CompressionTools.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 
In file included from src/utils/general/ParseTools.cpp:1:
src/utils/general/ParseTools.h: In function 'void int2str(U, T&, bool)':
src/utils/general/ParseTools.h:55:9: error: 'uint32_t' was not declared in this scope
   55 |         uint32_t n;
      |         ^~~~~~~~

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no_multilib-j4-20230218-230029

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-13 *
clang/llvm (if any):
clang version 15.0.7
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
15.0.7
Python 3.10.10
Available Rust versions:
  [1]   rust-1.67.1 *
The following VMs are available for generation-2:
1)	Eclipse Temurin JDK 11.0.18_p10 [openjdk-bin-11]
*)	Eclipse Temurin JDK 17.0.6_p10 [openjdk-bin-17]
3)	Eclipse Temurin JDK 8.362_p09 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8 
  [2]   openjdk-bin-11 
  [3]   openjdk-bin-17  system-vm

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli (if any):

  HEAD of ::gentoo
commit f86fa8f9ffe61663407dff34bbc41fddc56379b6
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Wed Feb 22 08:02:04 2023 +0000

    2023-02-22 08:02:03 UTC

emerge -qpvO sci-biology/bedtools
[ebuild  N    ] sci-biology/bedtools-2.30.0  USE="-test"
Comment 1 Toralf Förster gentoo-dev 2023-02-22 09:00:28 UTC
Created attachment 853850 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2023-02-22 09:00:30 UTC
Created attachment 853852 [details]
emerge-history.txt.bz2
Comment 3 Toralf Förster gentoo-dev 2023-02-22 09:00:31 UTC
Created attachment 853854 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2023-02-22 09:00:32 UTC
Created attachment 853856 [details]
etc.clang.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2023-02-22 09:00:33 UTC
Created attachment 853858 [details]
etc.portage.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2023-02-22 09:00:34 UTC
Created attachment 853860 [details]
sci-biology:bedtools-2.30.0:20230222-082931.log.bz2
Comment 7 Toralf Förster gentoo-dev 2023-02-22 09:00:35 UTC
Created attachment 853862 [details]
temp.tar.bz2
Comment 8 Larry the Git Cow gentoo-dev 2023-04-18 10:04:44 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e

commit 0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2023-04-18 10:04:37 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2023-04-18 10:04:37 +0000

    sci-biology/bedtools: fix gcc 13 build
    
    Closes: https://bugs.gentoo.org/895860
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/bedtools/bedtools-2.30.0.ebuild        |  1 +
 .../bedtools/files/bedtools-2.30.0-gcc13.patch     | 25 ++++++++++++++++++++++
 2 files changed, 26 insertions(+)