Bug 941102 – sci-biology/dialign-tx-1.0.2-r2 - [libtool] [gcc-15] museq.c: error: type of simple_aligner does not match original declaration [-Werror=lto-type-mismatch]

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Toralf Förster 2024-10-07 08:39:53 UTC]

make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source'
make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source'
rm -f ./museq
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -o ./museq \
./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o  \
-pipe -Wall -lm 
museq.c:58:13: error: type of simple_aligner does not match original declaration [-Werror=lto-type-mismatch]
   58 | extern int  simple_aligner(struct seq_col *scol, struct diag_col *dcol,
      |             ^

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 23.0_hardened-20241003-135501

  UNMASKED:
  /etc/portage/package.unmask/60gcc:<sys-devel/gcc-15.0.9999:15
    Requested by sam

  The attached etc.portage.tar.xz has all details.
  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-15 *
clang/llvm (if any):
clang version 19.1.1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/19/bin
Configuration file: /etc/clang/x86_64-pc-linux-gnu-clang.cfg
/usr/lib/llvm/19
19.1.1
Python 3.12.7
Available Ruby profiles:
  [1]   ruby32 (with Rubygems)
  [2]   ruby33 (with Rubygems) *
Available Rust versions:
  [1]   rust-bin-1.81.0 *
The following VMs are available for generation-2:
*)	Eclipse Temurin JDK 21.0.4_p7 [openjdk-bin-21]
Available Java Virtual Machines:
  [1]   openjdk-bin-21  system-vm

The Glorious Glasgow Haskell Compilation System, version 9.2.8
php cli (if any):
  [1]   php8.3 *
go version go1.23.1 linux/amd64

  HEAD of ::gentoo
commit f43ea290d28ccce3546e4192765c972f2e4dc4a8
Author: Repository mirror & CI <[e-mail]>
Date:   Sun Oct 6 20:03:19 2024 +0000

    2024-10-06 20:03:18 UTC

emerge -qpvO =sci-biology/dialign-tx-1.0.2-r2
[ebuild  N    ] sci-biology/dialign-tx-1.0.2-r2

[Comment 1 Toralf Förster 2024-10-07 08:39:54 UTC]

Created attachment 905034 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2024-10-07 08:39:56 UTC]

Created attachment 905035 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2024-10-07 08:39:57 UTC]

Created attachment 905036 [details]
environment

[Comment 4 Toralf Förster 2024-10-07 08:39:58 UTC]

Created attachment 905037 [details]
etc.clang.tar.xz

[Comment 5 Toralf Förster 2024-10-07 08:39:59 UTC]

Created attachment 905038 [details]
etc.portage.tar.xz

[Comment 6 Toralf Förster 2024-10-07 08:40:00 UTC]

Created attachment 905039 [details]
qlist-info.txt.xz

[Comment 7 Toralf Förster 2024-10-07 08:40:01 UTC]

Created attachment 905040 [details]
sci-biology:dialign-tx-1.0.2-r2:20241006-221256.log

[Comment 8 Toralf Förster 2024-10-07 08:40:02 UTC]

Created attachment 905041 [details]
temp.tar.xz