Bug 710088

Summary:	sci-geosciences/gmt-5.4.4 : fails to build with -fno-common or gcc-10
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Sci-geo Project <sci-geosciences>
Status:	RESOLVED FIXED
Severity:	normal	CC:	sam
Priority:	Normal	Keywords:	PATCH
Version:	unspecified
Hardware:	All
OS:	Linux
URL:	https://github.com/GenericMappingTools/gmt/pull/2511
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	705764, 762907
Attachments:	emerge-info.txt emerge-history.txt environment etc.portage.tbz2 logs.tbz2 sci-geosciences:gmt-5.4.4:20200218-051014.log temp.tbz2

Description Toralf Förster gentoo-dev

2020-02-18 18:54:16 UTC

FAILED: src/plugins/supplements.so 
: && /usr/bin/x86_64-pc-linux-gnu-gcc -fPIC -std=gnu99 -O2 -pipe -march=native -fno-common -fopenmp  -Wl,-O1 -Wl,--as-needed -shared  -o src/plugins/supplements.so src/CMakeFiles/supplib.dir/gmt_supplements_module.c.o src/CMakeFiles/supplib.dir/gshhg/gshhg.c.o src/CMakeFiles/supplib.dir/img/img2grd.c.o src/CMakeFiles/supplib.dir/meca/utilmeca.c.o src/CMakeFiles/supplib.dir/meca/sacio.c.o src/CMakeFiles/supplib.dir/meca/psmeca.c.o src/CMakeFiles/supplib.dir/meca/pspolar.c.o src/CMakeFiles/supplib.dir/meca/psvelo.c.o src/CMakeFiles/supplib.dir/meca/pscoupe.c.o src/CMakeFiles/supplib.dir/meca/pssac.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77_functions.c.o src/CMakeFiles/supplib.dir/mgd77/cm4_functions.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77convert.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77header.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77info.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77list.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77magref.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77manage.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77path.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77sniffer.c.o src/CMakeFiles/supplib.dir/mgd77/mgd77track.c.o src/CMakeFiles/supplib.dir/misc/dimfilter.c.o src/CMakeFiles/supplib.dir/potential/okbfuns.c.o src/CMakeFiles/supplib.dir/potential/grdredpol.c.o src/CMakeFiles/supplib.dir/potential/gmtgravmag3d.c.o src/CMakeFiles/supplib.dir/potential/gmtflexure.c.o src/CMakeFiles/supplib.dir/potential/gravfft.c.o src/CMakeFiles/supplib.dir/potential/gpsgridder.c.o src/CMakeFiles/supplib.dir/potential/grdflexure.c.o src/CMakeFiles/supplib.dir/potential/grdgravmag3d.c.o src/CMakeFiles/supplib.dir/potential/grdseamount.c.o src/CMakeFiles/supplib.dir/potential/talwani2d.c.o src/CMakeFiles/supplib.dir/potential/talwani3d.c.o src/CMakeFiles/supplib.dir/segy/segy_io.c.o src/CMakeFiles/supplib.dir/segy/segy2grd.c.o src/CMakeFiles/supplib.dir/segy/pssegy.c.o src/CMakeFiles/supplib.dir/segy/pssegyz.c.o src/CMakeFiles/supplib.dir/spotter/libspotter.c.o src/CMakeFiles/supplib.dir/spotter/backtracker.c.o src/CMakeFiles/supplib.dir/spotter/gmtpmodeler.c.o src/CMakeFiles/supplib.dir/spotter/grdpmodeler.c.o src/CMakeFiles/supplib.dir/spotter/grdrotater.c.o src/CMakeFiles/supplib.dir/spotter/grdspotter.c.o src/CMakeFiles/supplib.dir/spotter/hotspotter.c.o src/CMakeFiles/supplib.dir/spotter/originator.c.o src/CMakeFiles/supplib.dir/spotter/rotconverter.c.o src/CMakeFiles/supplib.dir/spotter/rotsmoother.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_init.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_put.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_get.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_binlist.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_datalist.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_cross.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_list.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_report.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_solve.c.o src/CMakeFiles/supplib.dir/x2sys/x2sys_merge.c.o  -Wl,-rpath,/var/tmp/portage/sci-geosciences/gmt-5.4.4/work/gmt-5.4.4_build/src:  src/libgmt.so.5.4.4  src/libpostscriptlight.so.5.4.4  -ldl  -lm  -lz  -lnetcdf  -lcurl  -lgdal  -lpcre  -lfftw3f  -ldl  -lm && :
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/CMakeFiles/supplib.dir/potential/gmtgravmag3d.c.o:(.bss+0x8): multiple definition of `okabe_mag_param'; src/CMakeFiles/supplib.dir/potential/okbfuns.c.o:(.bss+0x8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/CMakeFiles/supplib.dir/potential/gmtgravmag3d.c.o:(.bss+0x0): multiple definition of `okabe_mag_var'; src/CMakeFiles/supplib.dir/potential/okbfuns.c.o:(.bss+0x0): first defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_plasma_systemd-20200216-164747

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

  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]   python3.6
  [3]   python3.7 (fallback)
  [4]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *

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
ghc:
The Glorious Glasgow Haskell Compilation System, version 8.0.2

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Tue, 18 Feb 2020 03:37:42 +0000

emerge -qpvO sci-geosciences/gmt
[ebuild  N    ] sci-geosciences/gmt-5.4.4  USE="fftw gdal openmp pcre -doc -examples -gmttria -htmldoc -lapack -pcre2 -threads -tutorial"

Comment 1 Toralf Förster gentoo-dev

2020-02-18 18:54:19 UTC

Created attachment 614290 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2020-02-18 18:54:22 UTC

Created attachment 614292 [details]
emerge-history.txt

Comment 3 Toralf Förster gentoo-dev

2020-02-18 18:54:24 UTC

Created attachment 614294 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2020-02-18 18:54:27 UTC

Created attachment 614296 [details]
etc.portage.tbz2

Comment 5 Toralf Förster gentoo-dev

2020-02-18 18:54:30 UTC

Created attachment 614298 [details]
logs.tbz2

Comment 6 Toralf Förster gentoo-dev

2020-02-18 18:54:33 UTC

Created attachment 614300 [details]
sci-geosciences:gmt-5.4.4:20200218-051014.log

Comment 7 Toralf Förster gentoo-dev

2020-02-18 18:54:36 UTC

Created attachment 614302 [details]
temp.tbz2

Comment 8 Sam James archtester

2020-11-01 00:43:59 UTC

Bump probably better.

Comment 9 Larry the Git Cow gentoo-dev

2021-03-03 17:40:34 UTC

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

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=581973a7c1aff3201ff85b07b7004f53156ce7d0

commit 581973a7c1aff3201ff85b07b7004f53156ce7d0
Author:     Jakov Smolic <jakov.smolic@sartura.hr>
AuthorDate: 2021-03-02 20:08:06 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2021-03-03 16:51:47 +0000

    sci-geosciences/gmt: Apply gcc-10 workaround
    
    * Fix undeclared sys_siglist issue. Thanks to hangglider@gmx.de for providing the patch.
    
    Thanks-to: hangglider@gmx.de
    Closes: https://bugs.gentoo.org/738224
    Closes: https://bugs.gentoo.org/710088
    Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr>
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-geosciences/gmt/files/gmt-5.4.4-sighandler.patch | 14 ++++++++++++++
 sci-geosciences/gmt/gmt-5.4.4.ebuild                 |  7 ++++++-
 2 files changed, 20 insertions(+), 1 deletion(-)