Bug 712504 – sci-biology/emboss-6.6.0-r2 : embossversion.c: error: _USE_FORTIFY_LEVEL undeclared (first use in this function)

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Toralf Förster 2020-03-14 15:11:58 UTC]

x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../ajax/core  -I../ajax/acd -I../ajax/ajaxdb -I../ajax/core -I../ajax/ensembl -I../ajax/graphics  -I../nucleus  -DNO_AUTH -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -I/usr/include/plplot  -O2 -pipe -march=native -fno-common -falign-functions=32:25:16  -O2 -c -o embossversion.o embossversion.c
embossversion.c: In function main:
embossversion.c:418:47: error: __USE_FORTIFY_LEVEL undeclared (first use in this function)
  418 |  ajFmtPrintF(outfile, _FORTIFY_SOURCE %d\n, __USE_FORTIFY_LEVEL);
      |                                               ^~~~~~~~~~~~~~~~~~~
embossversion.c:418:47: note: each undeclared identifier is reported only once for each function it appears in

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0_musl-20200311-204810

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

gcc-config -l:
 [1] x86_64-gentoo-linux-musl-9.2.0 *
 [2] 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-1.41.1 *

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Sat, 14 Mar 2020 12:39:55 +0000
emerge -qpvO sci-biology/emboss
[ebuild  N    ] sci-biology/emboss-6.6.0-r1  USE="-X -minimal -mysql -pdf -png -postgres -static-libs"

[Comment 1 Toralf Förster 2020-03-14 15:12:01 UTC]

Created attachment 618962 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-03-14 15:12:04 UTC]

Created attachment 618964 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-03-14 15:12:07 UTC]

Created attachment 618966 [details]
environment

[Comment 4 Toralf Förster 2020-03-14 15:12:10 UTC]

Created attachment 618968 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-03-14 15:12:12 UTC]

Created attachment 618970 [details]
logs.tbz2

[Comment 6 Toralf Förster 2020-03-14 15:12:15 UTC]

Created attachment 618972 [details]
sci-biology:emboss-6.6.0-r1:20200314-144454.log

[Comment 7 Toralf Förster 2020-03-14 15:12:18 UTC]

Created attachment 618974 [details]
temp.tbz2

[Comment 8 Toralf Förster 2020-03-16 16:12:49 UTC]

The first attempt to tinderbox a musl image failed at all.

I'll mass close therefore all filed bug reports of the last days related to this tinderbox image.

Please feel free to re-open if you think that the bug is real in musl and not fixed by the musl overlay.

[Comment 9 Agostino Sarubbo 2022-09-26 09:13:46 UTC]

tinderbox_musl has reproduced this issue with version 6.6.0-r2 - Updating summary.