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Bug 905181 - sci-visualization/gwyddion-2.61 with sci-libs/hdf5-1.14 - hdf5file.c: fatal error: hdf5_hl.h: No such file or directory
Summary: sci-visualization/gwyddion-2.61 with sci-libs/hdf5-1.14 - hdf5file.c: fatal e...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Andreas K. Hüttel
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2023-04-27 18:14 UTC by Toralf Förster
Modified: 2023-04-29 16:18 UTC (History)
1 user (show)

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


Attachments
emerge-info.txt (emerge-info.txt,19.36 KB, text/plain)
2023-04-27 18:14 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,239.61 KB, text/plain)
2023-04-27 18:14 UTC, Toralf Förster
Details
environment (environment,80.08 KB, text/plain)
2023-04-27 18:14 UTC, Toralf Förster
Details
etc.clang.tar.bz2 (etc.clang.tar.bz2,706 bytes, application/x-bzip)
2023-04-27 18:14 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,46.75 KB, application/x-bzip)
2023-04-27 18:14 UTC, Toralf Förster
Details
logs.tar.bz2 (logs.tar.bz2,16.46 KB, application/x-bzip)
2023-04-27 18:14 UTC, Toralf Förster
Details
sci-visualization:gwyddion-2.61:20230427-121914.log.bz2 (sci-visualization:gwyddion-2.61:20230427-121914.log.bz2,14.90 KB, application/x-bzip)
2023-04-27 18:14 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,38.87 KB, application/x-bzip)
2023-04-27 18:14 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2023-04-27 18:14:02 UTC
too long lines were shrinked:

/bin/sh ../../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../..  -I../.. -DG_LOG_DOMAIN=\"Module\"  -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror=implicit-function-declaration -Werror=return-type -Wno-system-headers -Wno-pointer-sign -Wno-fo
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../.. -DG_LOG_DOMAIN=\"Module\" -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror=implicit-function-declaration -Werror=return-type -Wno-system-headers -Wno-pointer-sign -Wno-format-zero-length -Wdeclaration-a
/bin/sh ../../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../..  -I../.. -DG_LOG_DOMAIN=\"Module\"  -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror=implicit-function-declaration -Werror=return-type -Wno-system-headers -Wno-pointer-sign -Wno-fo
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../.. -DG_LOG_DOMAIN=\"Module\" -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror=implicit-function-declaration -Werror=return-type -Wno-system-headers -Wno-pointer-sign -Wno-format-zero-length -Wdeclaration-a
/bin/sh ../../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../..  -I../.. -DG_LOG_DOMAIN=\"Module\"  -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror=implicit-function-declaration -Werror=return-type -Wno-system-headers -Wno-pointer-sign -Wno-fo
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../.. -DG_LOG_DOMAIN=\"Module\" -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror=implicit-function-declaration -Werror=return-type -Wno-system-headers -Wno-pointer-sign -Wno-format-zero-length -Wdeclaration-a
hdf5file.c:47:10: fatal error: hdf5_hl.h: No such file or directory
   47 | #include <hdf5_hl.h>
      |          ^~~~~~~~~~~

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 23.0_desktop_gnome_systemd-j4-20230423-174504

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-13 *
clang/llvm (if any):
clang version 16.0.2
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/16/bin
Configuration file: /etc/clang/clang.cfg
/usr/lib/llvm/16
16.0.2
Python 3.10.11
Available Ruby profiles:
  [1]   ruby30 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.69.0 *
The following VMs are available for generation-2:
1)	Eclipse Temurin JDK 11.0.18_p10 [openjdk-bin-11]
*)	Eclipse Temurin JDK 17.0.6_p10 [openjdk-bin-17]
3)	Eclipse Temurin JDK 8.362_p09 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8 
  [2]   openjdk-bin-11 
  [3]   openjdk-bin-17  system-vm

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli (if any):
go version go1.20.3 linux/amd64

  HEAD of ::gentoo
commit 4934c79ba4faae21ce05bc407eef7802231a294b
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Thu Apr 27 11:34:01 2023 +0000

    2023-04-27 11:34:00 UTC

emerge -qpvO sci-visualization/gwyddion
[ebuild  N    ] sci-visualization/gwyddion-2.61  USE="X bzip2 hdf5 nls zlib -doc -fits -jansson -openexr -openmp -perl -ruby -sourceview -unique -xml"
Comment 1 Toralf Förster gentoo-dev 2023-04-27 18:14:03 UTC
Created attachment 860844 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2023-04-27 18:14:04 UTC
Created attachment 860845 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2023-04-27 18:14:05 UTC
Created attachment 860846 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2023-04-27 18:14:06 UTC
Created attachment 860847 [details]
etc.clang.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2023-04-27 18:14:07 UTC
Created attachment 860848 [details]
etc.portage.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2023-04-27 18:14:08 UTC
Created attachment 860849 [details]
logs.tar.bz2
Comment 7 Toralf Förster gentoo-dev 2023-04-27 18:14:09 UTC
Created attachment 860850 [details]
sci-visualization:gwyddion-2.61:20230427-121914.log.bz2
Comment 8 Toralf Förster gentoo-dev 2023-04-27 18:14:10 UTC
Created attachment 860851 [details]
temp.tar.bz2
Comment 9 Larry the Git Cow gentoo-dev 2023-04-29 16:18:50 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0c31c7063e987697406f439f566b7b98834ad84d

commit 0c31c7063e987697406f439f566b7b98834ad84d
Author:     Andreas K. Hüttel <dilfridge@gentoo.org>
AuthorDate: 2023-04-29 16:18:17 +0000
Commit:     Andreas K. Hüttel <dilfridge@gentoo.org>
CommitDate: 2023-04-29 16:18:40 +0000

    sci-visualization/gwyddion: require hdf5 with high-level tools
    
    Closes: https://bugs.gentoo.org/905181
    Signed-off-by: Andreas K. Hüttel <dilfridge@gentoo.org>

 sci-visualization/gwyddion/gwyddion-2.61.ebuild | 2 +-
 sci-visualization/gwyddion/gwyddion-2.62.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)