| Summary: | sci-biology/kallisto-0.43.1 - /.../MinCollector.cpp: error: numeric_limits is not a member of std (maybe gcc-11 related) | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | |||
| Bug Blocks: | 732706 | ||
| Attachments: |
emerge-info.txt
emerge-history.txt environment etc.portage.tar.bz2 logs.tar.bz2 sci-biology:kallisto-0.43.1:20210505-190312.log temp.tar.bz2 |
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Created attachment 706224 [details]
emerge-info.txt
Created attachment 706227 [details]
emerge-history.txt
Created attachment 706230 [details]
environment
Created attachment 706233 [details]
etc.portage.tar.bz2
Created attachment 706236 [details]
logs.tar.bz2
Created attachment 706239 [details]
sci-biology:kallisto-0.43.1:20210505-190312.log
Created attachment 706242 [details]
temp.tar.bz2
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06fc538689feab7fb91e62f619cfdc213074e8e3 commit 06fc538689feab7fb91e62f619cfdc213074e8e3 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-05-08 14:14:57 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-05-08 14:14:57 +0000 sci-biology/kallisto: Remove old 0.43.1 Closes: https://bugs.gentoo.org/696504 Closes: https://bugs.gentoo.org/708658 Closes: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/kallisto/Manifest | 1 - sci-biology/kallisto/kallisto-0.43.1.ebuild | 25 ------------------------- 2 files changed, 26 deletions(-) Additionally, it has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5c94901047b60e7e21d38dea38be43e2d5f7a816 commit 5c94901047b60e7e21d38dea38be43e2d5f7a816 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-05-08 14:14:54 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-05-08 14:14:54 +0000 sci-biology/kallisto: Bump to 0.46.2 Bug: https://bugs.gentoo.org/696504 Bug: https://bugs.gentoo.org/708658 Bug: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/kallisto/Manifest | 1 + .../kallisto/files/kallisto-0.46.2-catch2.patch | 38 ++++++ .../kallisto/files/kallisto-0.46.2-cmake.patch | 149 +++++++++++++++++++++ .../kallisto/files/kallisto-0.46.2-gcc11.patch | 21 +++ .../kallisto/files/kallisto-0.46.2-htslib.patch | 52 +++++++ sci-biology/kallisto/kallisto-0.46.2.ebuild | 64 +++++++++ 6 files changed, 325 insertions(+) |
/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp: In member function ‘std::vector<int> MinCollector::intersectECs(std::vector<std::pair<KmerEntry, int> >&) const’: /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp:194:21: error: ‘numeric_limits’ is not a member of ‘std’ 194 | int minpos = std::numeric_limits<int>::max(); | ^~~~~~~~~~~~~~ /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp:194:36: error: expected primary-expression before ‘int’ 194 | int minpos = std::numeric_limits<int>::max(); ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_no-multilib-20210423-202814 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-7.3.1 [2] x86_64-pc-linux-gnu-8.3.1 [3] x86_64-pc-linux-gnu-11.1.0 * clang version 12.0.0 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/12/bin /usr/lib/llvm/12 12.0.0 Python 3.8.10 Available Ruby profiles: [1] ruby26 (with Rubygems) [2] ruby30 (with Rubygems) * Available Rust versions: [1] rust-bin-1.51.0 * The Glorious Glasgow Haskell Compilation System, version 8.10.4 [1] php7.3 * [2] php7.4 [3] php8.0 timestamp(s) of HEAD at this tinderbox image: /var/db/repos/gentoo Wed May 5 18:50:23 UTC 2021 emerge -qpvO sci-biology/kallisto [ebuild N ] sci-biology/kallisto-0.43.1