mbox series

[bug#77287,v2,0/8] Update default hdf5 to 1.14

Message ID cover.1743240092.git.andreas@enge.fr
Headers
Series Update default hdf5 to 1.14 |

Message

Andreas Enge March 29, 2025, 9:21 a.m. UTC 
  Hello,

here is an updated patch series, mostly for reference.

The main patch is "gnu: hdf5: Make hdf@1.14 the default version.".
The first patches correspond to packages that compiled neither with the
previous, nor with the current hdf5; I have opened separate issues for
removing them. If you want to test and apply them, then all first-level
dependencies of hdf5 still build.

Up to there, the hdf-java package is still at version 1.10. I did not
manage to update it easily, the final patch is there just for reference.
In fact the Makefile.am and Makefile.in files that are supposed to be
modified in a phase have disappeared, and there is only a CMakeLists.txt
file remaining. If someone else could work on this, it would be much
appreciated.

If not, I think that the "Make hdf5@1.14 the default version." patch can
be pushed as is, leaving hdf-java at the 1.10 version (the package has
no dependencies). (I just notice that there is a "5" missing in the
commit message, I will correct this immediately.)

Andreas Enge (8):
  gnu: Remove h5check.
  gnu: Remove shogun.
  gnu: Remove atlas.
  gnu: Remove variant-tools.
  gnu: Remove mia.
  gnu: Remove itk-snap.
  gnu: hdf5: Make hdf@1.14 the default version.
  gnu: hdf-java: Update to 1.14.3.

 gnu/packages/bioinformatics.scm   |  41 +------
 gnu/packages/cran.scm             |   2 +-
 gnu/packages/image-processing.scm | 187 ------------------------------
 gnu/packages/image.scm            |   2 +-
 gnu/packages/machine-learning.scm | 148 -----------------------
 gnu/packages/maths.scm            | 167 ++------------------------
 6 files changed, 11 insertions(+), 536 deletions(-)


base-commit: c31662f7294b194663bc521358b01c3a7d7e4e27

Comments

David Elsing March 30, 2025, 2:45 p.m. UTC | #1 
Hello,

Andreas Enge <andreas@enge.fr> writes:

> Up to there, the hdf-java package is still at version 1.10. I did not
> manage to update it easily, the final patch is there just for reference.
> In fact the Makefile.am and Makefile.in files that are supposed to be
> modified in a phase have disappeared, and there is only a CMakeLists.txt
> file remaining. If someone else could work on this, it would be much
> appreciated.

When adjusting the versions in the 'unbundle phase, the build succeeds:
https://issues.guix.gnu.org/77385

Cheers,
David
Andreas Enge March 31, 2025, 8:35 a.m. UTC | #2 
Am Sun, Mar 30, 2025 at 02:45:17PM +0000 schrieb David Elsing:
> When adjusting the versions in the 'unbundle phase, the build succeeds:
> https://issues.guix.gnu.org/77385

Ah, excellent, thanks a lot for your help! I have pushed your patch as
well as my patch updating hdf5, which makes all direct dependencies of
hdf5 build except for those that also did not build before.

So I am closing this, and will wait for the 1 month period until
(probably) removing the non-building dependencies; if you want to
comment on them, I have opened specific issues for each of them.

Andreas