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branch master updated: gnu: hdf5: Update to 1.8.22.
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guix-commits |
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branch master updated: gnu: hdf5: Update to 1.8.22. |
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Date: |
Mon, 08 Feb 2021 14:26:20 -0500 |
This is an automated email from the git hooks/post-receive script.
bavier pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 8effdd1 gnu: hdf5: Update to 1.8.22.
8effdd1 is described below
commit 8effdd19691576a79aa4a1e26263b251376e25e5
Author: Eric Bavier <bavier@member.fsf.org>
AuthorDate: Mon Feb 8 13:16:17 2021 -0600
gnu: hdf5: Update to 1.8.22.
Fixes CVE-2018-14033, CVE-2018-11206, CVE-2018-13870, CVE-2018-13869, and
CVE-2018-17435
* gnu/packages/maths.scm (hdf5-1.8): Update to 1.8.22.
* gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch: Delete upstreamed
patch.
* gnu/local/mk (dist_patch_DATA): Remove it.
---
gnu/local.mk | 1 -
gnu/packages/maths.scm | 9 +-
.../patches/hdf5-1.8-mpi-deprecations.patch | 169 ---------------------
3 files changed, 4 insertions(+), 175 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index ae64a48..e515ab6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1156,7 +1156,6 @@ 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/hdf5-1.8-mpi-deprecations.patch \
%D%/packages/patches/hdf-eos2-build-shared.patch \
%D%/packages/patches/hdf-eos2-remove-gctp.patch \
%D%/packages/patches/hdf-eos2-fortrantests.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index eff1480..b572f8d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge
<andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier
<bavier@posteo.net>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Eric Bavier
<bavier@posteo.net>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus
<rekado@elephly.net>
@@ -1077,7 +1077,7 @@ incompatible with HDF5.")
(define-public hdf5-1.8
(package
(name "hdf5")
- (version "1.8.21")
+ (version "1.8.22")
(source
(origin
(method url-fetch)
@@ -1092,9 +1092,8 @@ incompatible with HDF5.")
(string-append major minor)))
"/src/hdf5-" version ".tar.bz2")))
(sha256
- (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
- (patches (search-patches "hdf5-config-date.patch"
- "hdf5-1.8-mpi-deprecations.patch"))))
+ (base32 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8"))
+ (patches (search-patches "hdf5-config-date.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
diff --git a/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
b/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
deleted file mode 100644
index 29242dc..0000000
--- a/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
+++ /dev/null
@@ -1,169 +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)
---- hdf5-1.8.19/testpar/t_cache.c
-+++ hdf5-1.8.19/testpar/t_cache.c
-@@ -1187,20 +1187,20 @@
- 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, fcn_name);
- }
-
-@@ -1215,14 +1215,14 @@
-
- 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, fcn_name);
- }
- }
---- hdf5-1.8.19/testpar/t_mpi.c
-+++ hdf5-1.8.19/testpar/t_mpi.c
-@@ -279,7 +279,7 @@
- printf("Skipped GB file range test "
- "because MPI_Offset cannot support it\n");
- }else{
-- buf = HDmalloc(MB);
-+ buf = (char *)HDmalloc(MB);
- VRFY((buf!=NULL), "malloc succeed");
-
- /* open a new file. Remove it first in case it exists. */
-@@ -624,7 +624,7 @@
- and this platform.
-
- 1. Details for the test:
--1) Create two derived datatypes with MPI_Type_hindexed:
-+1) Create two derived datatypes with MPI_Type_create_hindexed:
- datatype1:
- count = 1, blocklens = 1, offsets = 0,
- base type = MPI_BYTE(essentially a char)
-@@ -633,7 +633,7 @@
- base type = MPI_BYTE
-
- 2) Using these two derived datatypes,
-- Build another derived datatype with MPI_Type_struct:
-+ Build another derived datatype with MPI_Type_create_struct:
- advtype: derived from datatype1 and datatype2
- advtype:
- count = 2, blocklens[0] = 1, blocklens[1]=1,
-@@ -676,10 +676,9 @@
- int mpi_err_strlen;
- int mpi_err;
- int i;
-- int nerrors = 0; /* number of errors */
- MPI_Datatype etype,filetype;
- MPI_Datatype adv_filetype,bas_filetype[2];
-- MPI_Datatype etypenew, filetypenew;
-+ MPI_Datatype filetypenew;
- MPI_Offset disp;
- MPI_Status Status;
- MPI_Aint adv_disp[2];
-@@ -715,7 +714,7 @@
- blocklens[0] = 1;
- offsets[0] = 0;
-
-- if((mpi_err=
MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype))
-+ if((mpi_err=
MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype))
- != MPI_SUCCESS){
- MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
- printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str);
-@@ -731,7 +730,7 @@
- count = 1;
- blocklens[0]=1;
- offsets[0] = 1;
-- if((mpi_err=
MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew))
-+ if((mpi_err=
MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew))
- != MPI_SUCCESS){
- MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
- printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str);
-@@ -752,10 +751,10 @@
- bas_filetype[0] = filetype;
- bas_filetype[1] = filetypenew;
-
-- if((mpi_err=
MPI_Type_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype))
-+ if((mpi_err=
MPI_Type_create_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype))
- != MPI_SUCCESS){
- MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
-- printf("MPI_Type_struct failed (%s)\n", mpi_err_str);
-+ printf("MPI_Type_create_struct failed (%s)\n", mpi_err_str);
- return 1;
- }
- if((mpi_err=MPI_Type_commit(&adv_filetype))!=MPI_SUCCESS){
-@@ -842,7 +841,7 @@
- processes are needed.
-
- 1. Details for the test:
--1) Create one derived datatype with MPI_Type_hindexed:
-+1) Create one derived datatype with MPI_Type_create_hindexed:
-
- 2) Choosing at least two processes to contribute none for IO with
- the buf size inside MPI_Write_at_all to 0.
-@@ -898,7 +897,7 @@
- offsets[1] = (mpi_size+mpi_rank)*count;
-
- if(count !=0) {
-- if((mpi_err = MPI_Type_hindexed(2,
-+ if((mpi_err = MPI_Type_create_hindexed(2,
- blocklens,
- offsets,
- etype,
-@@ -914,7 +913,7 @@
- return 1;
- } /* end if */
-
-- if((mpi_err = MPI_Type_hindexed(2,
-+ if((mpi_err = MPI_Type_create_hindexed(2,
- blocklens,
- offsets,
- etype,
-@@ -1098,7 +1097,7 @@
- * calls. By then, MPI calls may not work.
- */
- if (H5dont_atexit() < 0){
-- printf("Failed to turn off atexit processing. Continue.\n", mpi_rank);
-+ printf("Failed to turn off atexit processing. Continue.\n");
- };
- H5open();
- if (parse_options(argc, argv) != 0){
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