02/03: gnu: hdf5@1.10: Update to 1.10.5.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit 94fea21b214a9111c5c8155bfebdad13114df95f
Author: Ludovic Courtès <address@hidden>
Date:   Fri Dec 13 13:44:51 2019 +0100

    gnu: hdf5@1.10: Update to 1.10.5.
    
    * gnu/packages/maths.scm (hdf5-1.10): Update to 1.10.5.  Remove
    "hdf5-mpi-deprecations.patch".
    * gnu/packages/patches/hdf5-mpi-deprecations.patch: Remove.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                     |  1 -
 gnu/packages/maths.scm                           |  7 ++-
 gnu/packages/patches/hdf5-mpi-deprecations.patch | 61 ------------------------
 3 files changed, 3 insertions(+), 66 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 7f87152..32b2c14 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -969,7 +969,6 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/hdf4-shared-fortran.patch               \
   %D%/packages/patches/hdf4-tirpc.patch                        \
   %D%/packages/patches/hdf5-config-date.patch                  \
-  %D%/packages/patches/hdf5-mpi-deprecations.patch             \
   %D%/packages/patches/hdf5-1.8-mpi-deprecations.patch         \
   %D%/packages/patches/hdf-eos2-build-shared.patch             \
   %D%/packages/patches/hdf-eos2-remove-gctp.patch              \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8364d52..0ed61ad 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -925,7 +925,7 @@ extremely large and complex data collections.")
 
 (define-public hdf5-1.10
   (package (inherit hdf5)
-    (version "1.10.4")
+    (version "1.10.5")
     (source
      (origin
       (method url-fetch)
@@ -939,9 +939,8 @@ extremely large and complex data collections.")
                                        (take (string-split version #\.) 2))
                                 "/src/hdf5-" version ".tar.bz2")))
       (sha256
-       (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
-      (patches (search-patches "hdf5-config-date.patch"
-                               "hdf5-mpi-deprecations.patch"))))))
+       (base32 "0i3g6v521vigzbx8wpd32ibsiiw92r65ca3qdbn0d8fj8f4fmmk8"))
+      (patches (search-patches "hdf5-config-date.patch"))))))
 
 (define-public hdf-java
   (package
diff --git a/gnu/packages/patches/hdf5-mpi-deprecations.patch 
b/gnu/packages/patches/hdf5-mpi-deprecations.patch
deleted file mode 100644
index eb5d1cb..0000000
--- a/gnu/packages/patches/hdf5-mpi-deprecations.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- a/src/H5.c
-+++ b/src/H5.c
-@@ -138,7 +138,7 @@
-         if (mpi_initialized && !mpi_finalized) {
-             int key_val;
- 
--            if(MPI_SUCCESS != (mpi_code = 
MPI_Comm_create_keyval(MPI_NULL_COPY_FN, 
-+            if(MPI_SUCCESS != (mpi_code = 
MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, 
-                                                                  
(MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, 
-                                                                  &key_val, 
NULL)))
-                 HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", 
mpi_code)
---- hdf5-1.10.4/testpar/t_cache.c
-+++ hdf5-1.10.4/testpar/t_cache.c
-@@ -1217,20 +1217,20 @@
-     struct mssg_t sample; /* used to compute displacements */
- 
-     /* setup the displacements array */
--    if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) ||
--         ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) {
-+    if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) ||
-+         ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) {
- 
-         nerrors++;
-         success = FALSE;
-         if ( verbose ) {
--            HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n",
-+            HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n",
-                       world_mpi_rank, FUNC);
-         }
- 
-@@ -1245,14 +1245,14 @@
- 
-     if ( success ) {
- 
--        result = MPI_Type_struct(9, block_len, displs, mpi_types, 
&mpi_mssg_t);
-+        result = MPI_Type_create_struct(9, block_len, displs, mpi_types, 
&mpi_mssg_t);
- 
-         if ( result != MPI_SUCCESS ) {
- 
-             nerrors++;
-             success = FALSE;
-             if ( verbose ) {
--                HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n",
-+                HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call 
failed.\n",
-                           world_mpi_rank, FUNC);
-             }
-         }