Bug 716110 – sci-biology/shrimp-2.2.3 : mergesam/mergesam.h: error: int32_t does not name a type

• Status: RESOLVED OBSOLETE
• Product: Gentoo Linux

[Description Toralf Förster 2020-04-04 07:33:08 UTC]

x86_64-gentoo-linux-musl-g++ -O3 -pipe -march=native -fopenmp -O3 -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=missing_git_version -c -o mergesam/sam_reader.o mergesam/sam_reader.c
In file included from mergesam/sam_reader.c:6:
mergesam/mergesam.h:47:2: error: int32_t does not name a type
   47 |  int32_t max_alignments;
      |  ^~~~~~~
mergesam/mergesam.h:48:2: error: int32_t does not name a type

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0_musl_hardened-20200328-201618

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

gcc-config -l:
 [1] x86_64-gentoo-linux-musl-9.3.0 *
clang version 10.0.0 
Target: x86_64-gentoo-linux-musl
Thread model: posix
InstalledDir: /usr/lib/llvm/10/bin
/usr/lib/llvm/10
10.0.0
Available Python interpreters, in order of preference:
  [1]   python3.8
  [2]   python3.7
  [3]   python3.6
  [4]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.42.0 *
Available Java Virtual Machines:
  (none found)


timestamp of HEAD at this tinderbox image:
/var/db/repos/gentoo	Sat Apr  4 01:37:47 UTC 2020
/var/db/repos/musl	Thu Apr  2 19:02:24 UTC 2020

emerge -qpvO sci-biology/shrimp
[ebuild  N    ] sci-biology/shrimp-2.2.3  USE="-custom-cflags" CPU_FLAGS_X86="sse2" PYTHON_SINGLE_TARGET="python2_7"

[Comment 1 Toralf Förster 2020-04-04 07:33:12 UTC]

Created attachment 629678 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-04-04 07:33:16 UTC]

Created attachment 629680 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-04-04 07:33:19 UTC]

Created attachment 629682 [details]
environment

[Comment 4 Toralf Förster 2020-04-04 07:33:22 UTC]

Created attachment 629684 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-04-04 07:33:25 UTC]

Created attachment 629686 [details]
sci-biology:shrimp-2.2.3:20200404-021658.log

[Comment 6 Toralf Förster 2020-04-04 07:33:28 UTC]

Created attachment 629688 [details]
temp.tbz2

[Comment 7 Michael 'veremitz' Everitt 2020-04-26 23:54:34 UTC]

Upstream should consider using portable POSIX-compatible integer types as
defined in
https://pubs.opengroup.org/onlinepubs/009695399/basedefs/stdint.h.html .

[Comment 8 Michał Górny 2020-10-09 07:36:48 UTC]

Package removed.