Bug 755470 – [science overlay] sci-mathematics/cipi-1.0 : /.../ld: CMakeFiles/.../main.o: undefined reference to symbol pthread_condattr_setclock@@GLIBC_2.3.3

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Toralf Förster 2020-11-19 08:24:22 UTC]

cd /var/tmp/portage/sci-mathematics/cipi-1.0/work/cipi-1.0/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cipi.dir/link.txt --verbose=1
/usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -rdynamic CMakeFiles/cipi.dir/main.o CMakeFiles/cipi.dir/functions.o CMakeFiles/cipi.dir/ConfigFile.o CMakeFiles/cipi.dir/Marginal.o CMakeFiles/cipi.dir/Marginals.o -o cipi  -lboost_thread-mt 
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/cipi.dir/main.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: *** [src/CMakeFiles/cipi.dir/build.make:163: src/cipi] Error 1

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

  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 07:05:42 AM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-mathematics/cipi
[ebuild  N    ] sci-mathematics/cipi-1.0  USE="-doc"

[Comment 1 Toralf Förster 2020-11-19 08:24:23 UTC]

Created attachment 672802 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-11-19 08:24:24 UTC]

Created attachment 672805 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-11-19 08:24:26 UTC]

Created attachment 672808 [details]
environment

[Comment 4 Toralf Förster 2020-11-19 08:24:27 UTC]

Created attachment 672811 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-11-19 08:24:28 UTC]

Created attachment 672814 [details]
logs.tbz2

[Comment 6 Toralf Förster 2020-11-19 08:24:30 UTC]

Created attachment 672817 [details]
sci-mathematics:cipi-1.0:20201119-080125.log

[Comment 7 Toralf Förster 2020-11-19 08:24:31 UTC]

Created attachment 672820 [details]
temp.tbz2

[Comment 8 Lucas Mitrak 2021-08-05 19:06:51 UTC]

Created attachment 730476 [details]
emerge.log

[Comment 9 Lucas Mitrak 2021-08-05 19:07:24 UTC]

Created attachment 730479 [details]
emerge-history.txt

[Comment 10 Lucas Mitrak 2021-08-05 19:07:45 UTC]

Created attachment 730482 [details]
emerge-info.txt

[Comment 11 Lucas Mitrak 2021-08-05 19:07:57 UTC]

Created attachment 730485 [details]
etc/portage

[Comment 12 Lucas Mitrak 2021-08-05 19:08:38 UTC]

Created attachment 730488 [details]
ebuildtester emerge log

[Comment 13 Lucas Mitrak 2021-08-05 19:10:23 UTC]

I was able to reproduce this bug by using the previous ebuild. Attached are my logs. The commit 754ffafbd840e580a30c67163f5ac4b725bbf88c [1] fixed it.
[1] https://github.com/gentoo/sci/commit/754ffafbd840e580a30c67163f5ac4b725bbf88c

[Comment 14 Lucas Mitrak 2021-08-05 19:10:36 UTC]

Therefore this bug can be closed as resolved.