diff mbox series

[bug#77287,v2,7/8] gnu: hdf5: Make hdf@1.14 the default version.

Message ID ecd728a9f49a24891291ab27983ac909f5e98a1b.1743240092.git.andreas@enge.fr
State New
Headers
Series Update default hdf5 to 1.14 |

Commit Message

Andreas Enge March 29, 2025, 9:21 a.m. UTC 
  This replaces all inputs hdf5@1.10 by hdf5@1.14 unless explicitly
specified otherwise.

* gnu/packages/maths.scm (hdf5-1.14): Rename to...
(hdf5): ...this, which was previously defined as hdf5-1.10.
(hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names.
(hdf-java)[inputs]: Keep hdf5-1.10.
* gnu/packages/bioinformatics.scm (fast5, ncbi-vdb),
gnu/packages/cran.scm (r-h5), gnu/packages/image.scm (vigra)[inputs]:
Keep hdf5-1.10.

Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485
---
 gnu/packages/bioinformatics.scm |  4 ++--
 gnu/packages/cran.scm           |  2 +-
 gnu/packages/image.scm          |  2 +-
 gnu/packages/maths.scm          | 16 ++++++----------
 4 files changed, 10 insertions(+), 14 deletions(-)
diff mbox series

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e8b585e495..8fd7789028 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7941,7 +7941,7 @@  (define-public fast5
           (add-after 'unpack 'chdir
             (lambda _
               (chdir "python"))))))
-    (inputs (list hdf5))
+    (inputs (list hdf5-1.10))
     (propagated-inputs
      (list python-dateutil))
     (native-inputs
@@ -11349,7 +11349,7 @@  (define-public ncbi-vdb
                 (install-file "libs/kfg/default.kfg" target)
                 (install-file "libs/kfg/certs.kfg" target)))))))
     (inputs
-     (list file hdf5 java-ngs libxml2 ngs-sdk ))
+     (list file hdf5-1.10 java-ngs libxml2 ngs-sdk ))
     (native-inputs (list perl))
     ;; NCBI-VDB requires SSE capability.
     (supported-systems '("i686-linux" "x86_64-linux"))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8522eb07a5..4e96d70849 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14934,7 +14934,7 @@  (define-public r-h5
          "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
     (build-system r-build-system)
     (inputs
-     (list zlib hdf5))
+     (list zlib hdf5-1.10))
     (native-inputs
      (list r-knitr r-testthat which))
     (propagated-inputs
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 89e7ef83e6..83b694b409 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -1389,7 +1389,7 @@  (define-public vigra
       `(("boost" ,boost)
         ("fftw" ,fftw)
         ("fftwf" ,fftwf)
-        ("hdf5" ,hdf5)
+        ("hdf5" ,hdf5-1.10)
         ("ilmbase" ,ilmbase) ; propagated by openexr, but needed explicitly
                              ; to create a configure-flag
         ("libjpeg" ,libjpeg-turbo)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 017abecc00..f851937a7c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1834,7 +1834,7 @@  (define-public hdf5-1.10
         (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00"))
        (patches (search-patches "hdf5-config-date.patch"))))))
 
-(define-public hdf5-1.14
+(define-public hdf5
   (package
     (inherit hdf5-1.8)
     (version "1.14.3")
@@ -1872,10 +1872,6 @@  (define-public hdf5-1.14
                   (("@UNAME_INFO@")
                    "Linux"))))))))))
 
-(define-public hdf5
-  ;; Default version of HDF5.
-  hdf5-1.10)
-
 ;; Keep this in sync with the current hdf5 package.
 (define-public hdf-java
   (package
@@ -1963,7 +1959,7 @@  (define-public hdf-java
            java-slf4j-simple))
     (inputs
      (list hdf4
-           hdf5
+           hdf5-1.10
            java-slf4j-api
            libjpeg-turbo
            zlib))
@@ -2041,7 +2037,7 @@  (define-public hdf-eos5
      (list autoconf automake gfortran libtool))
     (build-system gnu-build-system)
     (inputs
-     (list hdf5-1.14 zlib gctp))
+     (list hdf5 zlib gctp))
     (arguments
      (list
       #:configure-flags ''("--enable-install-include" "--enable-shared"
@@ -2076,13 +2072,13 @@  (define-public hdf-eos5
     (license (license:non-copyleft home-page))))
 
 (define-public hdf5-parallel-openmpi
-  (package/inherit hdf5-1.14                      ;use the latest
+  (package/inherit hdf5
     (name "hdf5-parallel-openmpi")
     (inputs
      `(("mpi" ,openmpi)
        ,@(package-inputs hdf5)))
     (arguments
-     (substitute-keyword-arguments (package-arguments hdf5-1.14)
+     (substitute-keyword-arguments (package-arguments hdf5)
        ((#:configure-flags flags)
         #~(cons "--enable-parallel"
                 (delete "--enable-cxx"
@@ -10481,7 +10477,7 @@  (define-public scilab
                   curl
                   fftw
                   gettext-minimal
-                  hdf5-1.14
+                  hdf5
                   libarchive
                   libx11
                   libxml2