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Bug 707240

Summary: sci-libs/sundials-5.0.0 : fails to build with -fno-common or gcc-10
Product: Gentoo Linux Reporter: Toralf Förster <toralf>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Status: RESOLVED FIXED    
Severity: normal CC: mjo
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
URL: https://github.com/LLNL/sundials/issues/43
Whiteboard:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 705764, 762907    
Attachments: emerge-info.txt
CMakeCache.txt
emerge-history.txt
environment
etc.portage.tbz2
logs.tbz2
sci-libs:sundials-5.0.0:20200129-125558.log
temp.tbz2

Description Toralf Förster gentoo-dev 2020-01-29 18:11:06 UTC
cd /var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0_build/examples/arkode/F77_serial && /usr/bin/x86_64-pc-linux-gnu-gfortran  -I/var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0/include -I/var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0_build/include  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common   -o CMakeFiles/fark_diurnal_kry_bp.dir/fark_diurnal_kry_bp.f.o -c /var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0/examples/arkode/F77_serial/fark_diurnal_kry_bp.f
[ 83%] Linking Fortran executable fark_diurnal_kry_bp
cd /var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0_build/examples/arkode/F77_serial && /usr/bin/cmake -E cmake_link_script CMakeFiles/fark_diurnal_kry_bp.dir/link.txt --verbose=1
/usr/bin/x86_64-pc-linux-gnu-gfortran  -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common CMakeFiles/fark_diurnal_kry_bp.dir/fark_diurnal_kry_bp.f.o  -o fark_diurnal_kry_bp  -Wl,-rpath,/var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0_build/src/arkode:/var/tmp/portage/sci-libs/sundials-5.0.0/work/sundials-5.0.0_build/src/nvector/serial ../../../src/arkode/fcmix/libsundials_farkode.a ../../../src/arkode/libsundials_arkode.so.4.0.0 ../../../src/nvector/serial/libsundials_fnvecserial.so.5.0.0 ../../../src/nvector/serial/libsundials_nvecserial.so.5.0.0 -lm /usr/lib64/librt.so -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../../../src/arkode/fcmix/libsundials_farkode.a(fsunlinsol_spgmr.c.o):(.bss+0x18): multiple definition of `F2C_IDA_linsol'; ../../../src/arkode/fcmix/libsundials_farkode.a(fsunlinsol_band.c.o):(.bss+0x18): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../../../src/arkode/fcmix/libsundials_farkode.a(fsunlinsol_spgmr.c.o):(.bss+0x8): multiple definition of `F2C_ARKODE_linsol'; ../../../src/arkode/fcmix/libsundials_farkode.a(fsunlinsol_band.c.o):(.bss+0x8): first defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_gnome_systemd-libressl-20200125-150902

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

  Please see the tracker bug for details.

gcc-config -l:
 [1] x86_64-pc-linux-gnu-9.2.0 *

clang:
clang version 9.0.1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/9/bin
llvm:
9.0.1
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-1.40.0 *
java-config:
The following VMs are available for generation-2:
*)	IcedTea JDK 3.14.0 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Wed, 29 Jan 2020 11:46:22 +0000

emerge -qpvO sci-libs/sundials
[ebuild  N    ] sci-libs/sundials-5.0.0  USE="cxx fortran openmp -doc -examples -hypre -lapack -mpi -sparse -static-libs -superlumt -threads"
Comment 1 Toralf Förster gentoo-dev 2020-01-29 18:11:08 UTC
Created attachment 608122 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-29 18:11:11 UTC
Created attachment 608124 [details]
CMakeCache.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-29 18:11:15 UTC
Created attachment 608126 [details]
emerge-history.txt
Comment 4 Toralf Förster gentoo-dev 2020-01-29 18:11:18 UTC
Created attachment 608128 [details]
environment
Comment 5 Toralf Förster gentoo-dev 2020-01-29 18:11:22 UTC
Created attachment 608130 [details]
etc.portage.tbz2
Comment 6 Toralf Förster gentoo-dev 2020-01-29 18:11:26 UTC
Created attachment 608132 [details]
logs.tbz2
Comment 7 Toralf Förster gentoo-dev 2020-01-29 18:11:29 UTC
Created attachment 608134 [details]
sci-libs:sundials-5.0.0:20200129-125558.log
Comment 8 Toralf Förster gentoo-dev 2020-01-29 18:11:33 UTC
Created attachment 608136 [details]
temp.tbz2
Comment 9 Andreas K. Hüttel archtester gentoo-dev 2021-01-01 15:45:58 UTC
Is this fixed in other versions?
Comment 10 Toralf Förster gentoo-dev 2021-01-01 16:47:40 UTC
(In reply to Andreas K. Hüttel from comment #9)
> Is this fixed in other versions?

no:

tinderbox@mr-fox ~ $ grep sci-libs/sundials tb/data/ALREADY_CATCHED 
sci-libs/sundials-5.2.0 : fails to build with -fno-common or gcc-10
sci-libs/sundials-5.1.0 : fails to build with -fno-common or gcc-10
Comment 11 Larry the Git Cow gentoo-dev 2021-02-27 05:16:19 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ef3b07820955e5152f355d9fd294028aa73e203d

commit ef3b07820955e5152f355d9fd294028aa73e203d
Author:     Sam James <sam@gentoo.org>
AuthorDate: 2021-02-27 05:14:40 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2021-02-27 05:15:51 +0000

    sci-libs/sundials: fix gcc 10 build
    
    Closes: https://bugs.gentoo.org/707240
    Package-Manager: Portage-3.0.15, Repoman-3.0.2
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-libs/sundials/sundials-5.2.0.ebuild | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)