Bug 755566 – [science overlay] sci-biology/miranda-3.3a : fails to build with -fno-common or gcc-10

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2020-11-19 16:53:57 UTC]

x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/    -O2 -pipe -march=native -fno-diagnostics-color  -c thermo.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/    -O2 -pipe -march=native -fno-diagnostics-color  -c utils.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/    -O2 -pipe -march=native -fno-diagnostics-color  -c ExpString.c
x86_64-pc-linux-gnu-gcc  -O2 -pipe -march=native -fno-diagnostics-color   -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o miranda  miranda.o output.o scan.o seqio.o swat.o pairs.o thermo.o utils.o ExpString.o ../RNAlib/libRNA.a -lm -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no-multilib-libressl_science-20201116-220441

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10.2.0 *
/usr/lib/llvm/11
11.0.0
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.9 (fallback)
  [3]   python3.8 (fallback)
  [4]   python2.7 (fallback)
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.272_p10 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.8.4

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Thu Nov 19 02:35:38 PM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/miranda
[ebuild  N    ] sci-biology/miranda-3.3a

[Comment 1 Toralf Förster 2020-11-19 16:53:59 UTC]

Created attachment 673165 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-11-19 16:54:00 UTC]

Created attachment 673168 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-11-19 16:54:01 UTC]

Created attachment 673171 [details]
environment

[Comment 4 Toralf Förster 2020-11-19 16:54:03 UTC]

Created attachment 673174 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-11-19 16:54:04 UTC]

Created attachment 673177 [details]
logs.tbz2

[Comment 6 Toralf Förster 2020-11-19 16:54:05 UTC]

Created attachment 673180 [details]
sci-biology:miranda-3.3a:20201119-153055.log

[Comment 7 Toralf Förster 2020-11-19 16:54:06 UTC]

Created attachment 673183 [details]
temp.tbz2

[Comment 8 Larry the Git Cow 2021-02-20 23:26:07 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/proj/sci.git/commit/?id=db54d87b772d63b32065d310116ca6396bbc2b2b

commit db54d87b772d63b32065d310116ca6396bbc2b2b
Author:     Jakov Smolic <[e-mail]>
AuthorDate: 2021-02-20 21:10:43 +0000
Commit:     Jakov Smolic <[e-mail]>
CommitDate: 2021-02-20 21:57:41 +0000

    sci-biology/miranda: Port to EAPI 7
    
    Closes: https://bugs.gentoo.org/755566
    Signed-off-by: Jakov Smolic <[e-mail]>

 sci-biology/miranda/miranda-3.3a.ebuild | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)