add patches

debian/patches/fix-HDFFV-10745.patch

-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:

debian/patches/fix-unaligned-accesses.patch

-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) {

debian/patches/path_max.diff

-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 */

debian/patches/relax-version-check.patch

-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

debian/patches/reproducibility.patch

-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

debian/patches/ullong_force.diff

-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, -, -);
  }