Bug 919223 – sci-biology/velvet-1.2.10 - src/readSet.c: error: assignment to gzFile {aka struct gzFile_s } from incompatible pointer type AutoFile [-Wincompatible-

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Toralf Förster 2023-12-04 20:15:53 UTC]

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 <[e-mail]>
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"

[Comment 1 Toralf Förster 2023-12-04 20:15:53 UTC]

Created attachment 877118 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2023-12-04 20:15:55 UTC]

Created attachment 877119 [details]
emerge-history.txt.xz

[Comment 3 Toralf Förster 2023-12-04 20:15:56 UTC]

Created attachment 877120 [details]
environment

[Comment 4 Toralf Förster 2023-12-04 20:15:57 UTC]

Created attachment 877121 [details]
etc.clang.tar.xz

[Comment 5 Toralf Förster 2023-12-04 20:15:58 UTC]

Created attachment 877122 [details]
etc.portage.tar.xz

[Comment 6 Toralf Förster 2023-12-04 20:16:00 UTC]

Created attachment 877123 [details]
qlist-info.txt.xz

[Comment 7 Toralf Förster 2023-12-04 20:16:01 UTC]

Created attachment 877124 [details]
sci-biology:velvet-1.2.10:20231204-073620.log

[Comment 8 Toralf Förster 2023-12-04 20:16:01 UTC]

Created attachment 877125 [details]
temp.tar.xz