Unverified Commit e05cc32b authored by Jan Kotanski's avatar Jan Kotanski
Browse files

add patches

parent 90d04e69
Index: hdf5/java/src/jni/h5pFCPLImp.c
From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
Date: Thu, 19 Sep 2019 19:39:22 +0200
Subject: fix-HDFFV-10745
===================================================================
--- hdf5.orig/java/src/jni/h5pFCPLImp.c
+++ hdf5/java/src/jni/h5pFCPLImp.c
---
java/src/jni/h5pFCPLImp.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/java/src/jni/h5pFCPLImp.c b/java/src/jni/h5pFCPLImp.c
index 34ac065..cc7c264 100644
--- a/java/src/jni/h5pFCPLImp.c
+++ b/java/src/jni/h5pFCPLImp.c
@@ -240,7 +240,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1sym_1k
done:
......
Package: libhdf5-100
Version: 1.10.0-patch1+docs-3
Tags: upstream patch
User: debian-sparc@lists.debian.org
Usertags: sparc64
X-Debbugs-Cc: debian-sparc@lists.debian.org, Ghislain Vaillant <ghisvail@gmail.com>
Control: affects -1 src:h5py
From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
Date: Thu, 19 Sep 2019 19:39:22 +0200
Subject: fix-unaligned-accesses
Hi,
Currently libhdf5-100 performs unaligned memory accesses on sparc64 in
......@@ -38,10 +34,15 @@ free to forward this patch upstream if you deem it acceptable.
Regards,
James
Index: hdf5/config/cmake/ConversionTests.c
===================================================================
--- hdf5.orig/config/cmake/ConversionTests.c
+++ hdf5/config/cmake/ConversionTests.c
---
config/cmake/ConversionTests.c | 8 +++----
src/H5Tvlen.c | 47 ++++++++++++++++++++++++++++++++++--------
2 files changed, 42 insertions(+), 13 deletions(-)
diff --git a/config/cmake/ConversionTests.c b/config/cmake/ConversionTests.c
index 6d597a0..cc071b5 100644
--- a/config/cmake/ConversionTests.c
+++ b/config/cmake/ConversionTests.c
@@ -259,13 +259,13 @@ main ()
char *chp = "beefs";
......@@ -68,11 +69,11 @@ Index: hdf5/config/cmake/ConversionTests.c
if (vlp2->len != vl.len || vlp2->p != vl.p) {
free (vlp);
return 1;
Index: hdf5/src/H5Tvlen.c
===================================================================
--- hdf5.orig/src/H5Tvlen.c
+++ hdf5/src/H5Tvlen.c
@@ -1044,35 +1044,64 @@ H5T_vlen_reclaim_recurse(void *elem, con
diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index ba31cd1..7bbf451 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -1044,35 +1044,64 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
case H5T_VLEN:
/* Recurse on the VL information if it's VL, compound, enum or array, then free VL sequence */
if(dt->shared->u.vlen.type == H5T_VLEN_SEQUENCE) {
......
Description: avoid the issue of PATH_MAX not being available on Hurd.
Call realpath() the POSIX way, with NULL as second parameter so that
the returned string is dynamically allocated. This way there is no
more need for the strdup() call.
Author: Gilles Filippini <pini@debian.org>
Bug-Debian: http://bugs.debian.org/627896
Bug: HDFFV-9209
Index: hdf5/src/H5Fint.c
From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
Date: Thu, 19 Sep 2019 19:39:22 +0200
Subject: path_max
===================================================================
--- hdf5.orig/src/H5Fint.c
+++ hdf5/src/H5Fint.c
@@ -2282,10 +2282,6 @@ H5F_build_actual_name(const H5F_t *f, co
---
src/H5Fint.c | 18 +-----------------
1 file changed, 1 insertion(+), 17 deletions(-)
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 253ec3c..f8193f6 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -2282,10 +2282,6 @@ H5F_build_actual_name(const H5F_t *f, const H5P_genplist_t *fapl, const char *na
char **actual_name/*out*/)
{
hid_t new_fapl_id = -1; /* ID for duplicated FAPL */
......@@ -20,7 +22,7 @@ Index: hdf5/src/H5Fint.c
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -2319,10 +2315,6 @@ H5F_build_actual_name(const H5F_t *f, co
@@ -2319,10 +2315,6 @@ H5F_build_actual_name(const H5F_t *f, const H5P_genplist_t *fapl, const char *na
h5_stat_t fst; /* Stat info from fstat() call */
hbool_t want_posix_fd; /* Flag for retrieving file descriptor from VFD */
......@@ -31,7 +33,7 @@ Index: hdf5/src/H5Fint.c
/* Perform a sanity check that the file or link wasn't switched
* between when we opened it and when we called lstat(). This is
* according to the security best practices for lstat() documented
@@ -2357,12 +2349,8 @@ H5F_build_actual_name(const H5F_t *f, co
@@ -2357,12 +2349,8 @@ H5F_build_actual_name(const H5F_t *f, const H5P_genplist_t *fapl, const char *na
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL, "files' st_ino or st_dev fields changed!")
/* Get the resolved path for the file name */
......
Description: remove check on patch version
hopefully changes in that number always are compatible.
Without this every bugfix update would require a full transition as it will
abort when the version does not match exactly.
The version check will be executed with compile time values on every file
access see e.g. H5F_ACC_RDONLY in src/H5Fpublic.h
Author: Julian Taylor <jtaylor@ubuntu.com>
Bug-Debian: http://bugs.debian.org/693610
Index: hdf5/src/H5.c
From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
Date: Thu, 19 Sep 2019 19:39:22 +0200
Subject: relax-version-check
===================================================================
--- hdf5.orig/src/H5.c
+++ hdf5/src/H5.c
@@ -751,8 +751,7 @@ H5check_version(unsigned majnum, unsigne
---
src/H5.c | 3 +--
test/testcheck_version.sh.in | 17 +++++++++++++----
2 files changed, 14 insertions(+), 6 deletions(-)
diff --git a/src/H5.c b/src/H5.c
index 5e342ff..064e58d 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -751,8 +751,7 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
disable_version_check = (unsigned int)HDstrtol (s, NULL, 0);
}
......@@ -20,10 +22,10 @@ Index: hdf5/src/H5.c
switch (disable_version_check) {
case 0:
HDfprintf(stderr, "%s%s", version_mismatch_warning,
Index: hdf5/test/testcheck_version.sh.in
===================================================================
--- hdf5.orig/test/testcheck_version.sh.in
+++ hdf5/test/testcheck_version.sh.in
diff --git a/test/testcheck_version.sh.in b/test/testcheck_version.sh.in
index a5641f5..0e5ad0a 100644
--- a/test/testcheck_version.sh.in
+++ b/test/testcheck_version.sh.in
@@ -152,8 +152,12 @@ TESTING() {
esac
case "$h5DisableVersion" in
......
Index: hdf5/configure.ac
From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
Date: Thu, 19 Sep 2019 19:39:22 +0200
Subject: reproducibility
===================================================================
--- hdf5.orig/configure.ac
+++ hdf5/configure.ac
---
configure.ac | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/configure.ac b/configure.ac
index 4ac4a5b..2b7fc24 100644
--- a/configure.ac
+++ b/configure.ac
@@ -170,7 +170,7 @@ AC_MSG_RESULT([done])
## Save system information for the library settings file.
##
......@@ -11,7 +20,7 @@ Index: hdf5/configure.ac
## ----------------------------------------------------------------------
## Some platforms have broken basename, and/or xargs programs. Check
@@ -3004,10 +3004,10 @@ H5_VERSION="`cut -d' ' -f3 $srcdir/READM
@@ -3004,10 +3004,10 @@ H5_VERSION="`cut -d' ' -f3 $srcdir/README.txt | head -1`"
AC_SUBST([H5_VERSION])
## Configuration date
......
Description: force the ullong conversion anywhere.
Author: Sylvestre Ledru <sylvestre.ledru@scilab-enterprises.com>
Index: hdf5/src/H5Tconv.c
From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
Date: Thu, 19 Sep 2019 19:39:22 +0200
Subject: ullong_force
===================================================================
--- hdf5.orig/src/H5Tconv.c
+++ hdf5/src/H5Tconv.c
@@ -7548,7 +7548,6 @@ H5T__conv_ullong_double (hid_t src_id, h
---
src/H5Tconv.c | 2 --
1 file changed, 2 deletions(-)
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index 803a6da..d4928ad 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -7548,7 +7548,6 @@ H5T__conv_ullong_double (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
*
*-------------------------------------------------------------------------
*/
......@@ -12,7 +19,7 @@ Index: hdf5/src/H5Tconv.c
herr_t
H5T__conv_ullong_ldouble (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nelmts, size_t buf_stride, size_t H5_ATTR_UNUSED bkg_stride,
@@ -7556,7 +7555,6 @@ H5T__conv_ullong_ldouble (hid_t src_id,
@@ -7556,7 +7555,6 @@ H5T__conv_ullong_ldouble (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
{
H5T_CONV_xF(ULLONG, LDOUBLE, unsigned long long, long double, -, -);
}
......
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