| Summary: | sci-biology/velvet-1.2.10 - src/readSet.c: error: assignment to gzFile {aka struct gzFile_s } from incompatible pointer type AutoFile [-Wincompatible- | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | Keywords: | PullRequest |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| See Also: | https://github.com/gentoo/gentoo/pull/35993 | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | |||
| Bug Blocks: | 870412 | ||
| Attachments: |
emerge-info.txt
emerge-history.txt.xz environment etc.clang.tar.xz etc.portage.tar.xz qlist-info.txt.xz sci-biology:velvet-1.2.10:20231204-073620.log temp.tar.xz |
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Created attachment 877118 [details]
emerge-info.txt
Created attachment 877119 [details]
emerge-history.txt.xz
Created attachment 877120 [details]
environment
Created attachment 877121 [details]
etc.clang.tar.xz
Created attachment 877122 [details]
etc.portage.tar.xz
Created attachment 877123 [details]
qlist-info.txt.xz
Created attachment 877124 [details]
sci-biology:velvet-1.2.10:20231204-073620.log
Created attachment 877125 [details]
temp.tar.xz
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d11fa811ea39d044575471f7c4006bab88e23bfe commit d11fa811ea39d044575471f7c4006bab88e23bfe Author: NHOrus <jy6x2b32pie9@yahoo.com> AuthorDate: 2024-03-29 20:44:26 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2024-05-08 10:43:28 +0000 sci-biology/velvet: Fix incompatible pointer types in 1.2.10 * C99 porting. Split multi-assignments of NULLs into multiple lines * Also added dependencies on OpenMP if USE=openmp is enabled [sam: Formatting tweaks to commit msg.] Closes: https://bugs.gentoo.org/919223 Signed-off-by: NHOrus <jy6x2b32pie9@yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/35993 Signed-off-by: Sam James <sam@gentoo.org> .../velvet-1.2.10-incompatible-pointers.patch | 27 ++++++++++++++++++++++ sci-biology/velvet/velvet-1.2.10.ebuild | 13 +++++++++-- 2 files changed, 38 insertions(+), 2 deletions(-) |
too long lines were shrinked: | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function readFastXFile: src/readSet.c:641:21: error: assignment to gzFile {aka struct gzFile_s *} from incompatible pointer type AutoFile * [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_no_multilib-20231127-152538 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-10 [2] x86_64-pc-linux-gnu-14 * clang/llvm (if any): clang version 17.0.6 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/17/bin Configuration file: /etc/clang/x86_64-pc-linux-gnu-clang.cfg /usr/lib/llvm/17 17.0.6 Python 3.11.6 Available Rust versions: [1] rust-bin-1.73.0 * The following VMs are available for generation-2: 1) OpenJDK 17.0.8.1_p1 [openjdk-17] 2) OpenJDK 21.0.1_p12 [openjdk-21] 3) OpenJDK 8.382_p05 [openjdk-8] 4) Eclipse Temurin JDK 17.0.8.1_p1 [openjdk-bin-17] *) Eclipse Temurin JDK 21.0.1_p12 [openjdk-bin-21] Available Java Virtual Machines: [1] openjdk-8 [2] openjdk-17 [3] openjdk-21 [4] openjdk-bin-17 [5] openjdk-bin-21 system-vm The Glorious Glasgow Haskell Compilation System, version 9.2.8 php cli (if any): go version go1.21.4 linux/amd64 HEAD of ::gentoo commit dcde4ece3c2c958a47ff40c295a86e6630b7dc8c Author: Repository mirror & CI <repomirrorci@gentoo.org> Date: Mon Dec 4 07:02:00 2023 +0000 2023-12-04 07:01:59 UTC emerge -qpvO sci-biology/velvet [ebuild N ] sci-biology/velvet-1.2.10 USE="openmp -doc"