update patches

debian/README

-HDF5 for Debian
----------------
-
-Some general notes for developers: since 1.8 series HDF Group deprecates 
-enabling the thread-safe option for the C library and at the same time
-supporting C++ and Fortran bindings. Those options cannot cohexist for
-safety because non C libraries wrapper are not thread-aware. 
-Debian GNU/Linux still support a C thread-safe library and the alternative
-bindings, but it does not imply that the Debian distributed C++ and Fortran
-are thread-safe. 
-
-For short: DO NOT use C++ or Fortran bindings in multi-thread programs
-witihout providing yourself mutex infrastructure support for every wrapped 
-function. You can use safely only the C binding in a multi-thread environment.
-That was not different in 1.6 series, just the issue was ignored.
-
-Now, you are warned. 
-
- -- Francesco Paolo Lovergine <frankie@debian.org> Fri Jun 19 22:09:25 CEST 2009

debian/libhdf5-100.lintian-overrides

-libhdf5-100: package-name-doesnt-match-sonames libhdf5-serial100 libhdf5-serial-fortran100 libhdf5-serial-hl100 libhdf5-serialhl-fortran100

debian/patches/path_max.diff

-From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
-Date: Thu, 19 Sep 2019 19:39:22 +0200
-Subject: path_max
-
+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
 ===================================================================
----
- 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
+--- hdf5.orig/src/H5Fint.c
++++ hdf5/src/H5Fint.c
+@@ -2282,10 +2282,6 @@ H5F_build_actual_name(const H5F_t *f, co
      char **actual_name/*out*/)
  {
      hid_t       new_fapl_id = -1;       /* ID for duplicated FAPL */
@@ -22,7 +20,7 @@ index 253ec3c..f8193f6 100644
      herr_t      ret_value = SUCCEED;    /* Return value */
  
      FUNC_ENTER_NOAPI_NOINIT
-@@ -2319,10 +2315,6 @@ H5F_build_actual_name(const H5F_t *f, const H5P_genplist_t *fapl, const char *na
+@@ -2319,10 +2315,6 @@ H5F_build_actual_name(const H5F_t *f, co
              h5_stat_t fst;              /* Stat info from fstat() call */
              hbool_t want_posix_fd;      /* Flag for retrieving file descriptor from VFD */
  
@@ -33,7 +31,7 @@ index 253ec3c..f8193f6 100644
              /* 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, const H5P_genplist_t *fapl, const char *na
+@@ -2357,12 +2349,8 @@ H5F_build_actual_name(const H5F_t *f, co
                  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/ullong_force.diff

-From: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
-Date: Thu, 19 Sep 2019 19:39:22 +0200
-Subject: ullong_force
-
+Description: force the ullong conversion anywhere.
+Author: Sylvestre Ledru <sylvestre.ledru@scilab-enterprises.com>
+Index: hdf5/src/H5Tconv.c
 ===================================================================
----
- 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,
+--- hdf5.orig/src/H5Tconv.c
++++ hdf5/src/H5Tconv.c
+@@ -7548,7 +7548,6 @@ H5T__conv_ullong_double (hid_t src_id, h
   *
   *-------------------------------------------------------------------------
   */
@@ -19,7 +12,7 @@ index 803a6da..d4928ad 100644
  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, hid_t dst_id, H5T_cdata_t *cdata,
+@@ -7556,7 +7555,6 @@ H5T__conv_ullong_ldouble (hid_t src_id,
  {
      H5T_CONV_xF(ULLONG, LDOUBLE, unsigned long long, long double, -, -);
  }

debian/source.lintian-overrides

-# libhdf5-mpich2-* packages are dummy transitional packages
-hdf5 source: debhelper-but-no-misc-depends libhdf5-mpich2-dev