Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 828677 - sci-libs/netcdf-4.8.1-r1 - /.../hdf5debug.c: fatal error: execinfo.h: No such file or directory
Summary: sci-libs/netcdf-4.8.1-r1 - /.../hdf5debug.c: fatal error: execinfo.h: No such...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords: PullRequest
Depends on:
Blocks: musl-porting 856418
  Show dependency tree
 
Reported: 2021-12-10 09:31 UTC by Toralf Förster
Modified: 2022-07-15 12:49 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,14.32 KB, text/plain)
2021-12-10 09:31 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,19.79 KB, text/plain)
2021-12-10 09:31 UTC, Toralf Förster
Details
environment (environment,89.22 KB, text/plain)
2021-12-10 09:31 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,29.37 KB, application/x-bzip)
2021-12-10 09:31 UTC, Toralf Förster
Details
logs.tar.bz2 (logs.tar.bz2,8.39 KB, application/x-bzip)
2021-12-10 09:31 UTC, Toralf Förster
Details
sci-libs:netcdf-4.7.4:20211209-230820.log (sci-libs:netcdf-4.7.4:20211209-230820.log,47.08 KB, text/plain)
2021-12-10 09:31 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,25.62 KB, application/x-bzip)
2021-12-10 09:31 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2021-12-10 09:31:47 UTC
too long lines were shrinked:

[45/145] /usr/bin/x86_64-gentoo-linux-musl-gcc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/include -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/oc2 -I/var/tmp/port
[46/145] /usr/bin/x86_64-gentoo-linux-musl-gcc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/include -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/oc2 -I/var/tmp/port
FAILED: libhdf5/CMakeFiles/netcdfhdf5.dir/hdf5debug.c.o 
/usr/bin/x86_64-gentoo-linux-musl-gcc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/include -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/oc2 -I/var/tmp/portage/sci-l
/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/libhdf5/hdf5debug.c:9:10: fatal error: execinfo.h: No such file or directory
    9 | #include <execinfo.h>
      |          ^~~~~~~~~~~~
compilation terminated.
[47/145] /usr/bin/x86_64-gentoo-linux-musl-gcc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/include -I/var/tmp/portage/sci-libs/netcdf-4.7.4/work/netcdf-c-4.7.4/oc2 -I/var/tmp/port

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

  This is an stable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0_musl_hardened-j4_stable-20211209-194823

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

gcc-config -l:
 [1] x86_64-gentoo-linux-musl-11.2.0 *
Python 3.9.9
Available Rust versions:
  [1]   rust-bin-1.56.1 *
php cli:

  HEAD of ::gentoo
commit 405da333b415c85be2ec5eb9b347a5e2ed74de71
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Thu Dec 9 22:22:06 2021 +0000

    2021-12-09 22:22:02 UTC

emerge -qpvO sci-libs/netcdf
[ebuild  N    ] sci-libs/netcdf-4.7.4  USE="dap examples hdf5 -doc -hdf -mpi -szip -test -tools"
Comment 1 Toralf Förster gentoo-dev 2021-12-10 09:31:48 UTC
Created attachment 757937 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2021-12-10 09:31:49 UTC
Created attachment 757938 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2021-12-10 09:31:50 UTC
Created attachment 757939 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2021-12-10 09:31:52 UTC
Created attachment 757940 [details]
etc.portage.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2021-12-10 09:31:53 UTC
Created attachment 757941 [details]
logs.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2021-12-10 09:31:54 UTC
Created attachment 757942 [details]
sci-libs:netcdf-4.7.4:20211209-230820.log
Comment 7 Toralf Förster gentoo-dev 2021-12-10 09:31:55 UTC
Created attachment 757943 [details]
temp.tar.bz2
Comment 8 Agostino Sarubbo gentoo-dev 2022-01-15 08:46:30 UTC
tinderbox_musl has reproduced this issue with version 4.8.1-r1 - Updating summary.
Comment 9 Larry the Git Cow gentoo-dev 2022-07-15 12:49:25 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=400a204bea4aa72d51a0ef53260743c9f7ee0310

commit 400a204bea4aa72d51a0ef53260743c9f7ee0310
Author:     brahmajit das <brahmajit.xyz@gmail.com>
AuthorDate: 2022-07-15 10:13:20 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2022-07-15 12:46:42 +0000

    sci-libs/netcdf: Fix musl missing execinfo.h check
    
    Check if execinfo.h is present before including the header. The check is
    preset in other parts of the souce code, here it was only being checked if
    it's WIN32 or CYGIWIN before including execinfo.h as a result build was
    failing on musl.
    
    Closes: https://bugs.gentoo.org/828677
    
    Signed-off-by: brahmajit das <brahmajit.xyz@gmail.com>
    Closes: https://github.com/gentoo/gentoo/pull/26284
    Signed-off-by: Sam James <sam@gentoo.org>

 .../files/netcdf-4.9.0-fix-musl-execinfo_h.patch   | 46 ++++++++++++++++++++++
 sci-libs/netcdf/netcdf-4.9.0.ebuild                |  1 +
 2 files changed, 47 insertions(+)