| Summary: | sci-biology/bedtools-2.30.0 - src/.../version.cpp: fatal error: version_git.h: No such file or directory | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | CONFIRMED --- | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
emerge-info.txt
emerge-history.txt.bz2 environment etc.clang.tar.bz2 etc.portage.tar.bz2 sci-biology:bedtools-2.30.0:20221118-050050.log temp.tar.bz2 |
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Created attachment 833291 [details]
emerge-info.txt
Created attachment 833293 [details]
emerge-history.txt.bz2
Created attachment 833295 [details]
environment
Created attachment 833297 [details]
etc.clang.tar.bz2
Created attachment 833299 [details]
etc.portage.tar.bz2
Created attachment 833301 [details]
sci-biology:bedtools-2.30.0:20221118-050050.log
Created attachment 833303 [details]
temp.tar.bz2
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(+) |
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"