[hdf5] 06/17: Refresh patches
Gilles Filippini
pini at debian.org
Thu Dec 21 22:06:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
pini pushed a commit to branch master
in repository hdf5.
commit b270aaefbfa7b46e13b80b29a8db2ac5a6d911e6
Author: Gilles Filippini <pini at debian.org>
Date: Wed Oct 4 19:52:24 2017 +0200
Refresh patches
Drop CVE-2016-433*.patch (fixed upstream).
---
debian/changelog | 5 +
debian/patches/CVE-2016-4330.patch | 20 ---
debian/patches/CVE-2016-4331-1.patch | 229 ---------------------------
debian/patches/CVE-2016-4331-2.patch | 19 ---
debian/patches/CVE-2016-4332.patch | 37 -----
debian/patches/CVE-2016-4333.patch | 23 ---
debian/patches/flavor-configure-option.patch | 186 +++++++++++-----------
debian/patches/java-runtime-exception.patch | 2 +-
debian/patches/path_max.diff | 35 +++-
debian/patches/relax-version-check.patch | 18 +--
debian/patches/series | 5 -
debian/patches/ullong_force.diff | 4 +-
12 files changed, 140 insertions(+), 443 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index ba3032b..15e6ef2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,10 @@
hdf5 (1.10.1+docs-1) UNRELEASED; urgency=medium
+ * New upstream release
+
+ * Drop patches CVE-2016-433*.patch (fixed upstream)
+ * Refresh other patches
+
* Improve flavor-configure-option.patch to manage -dev packages'
symlinks and clean-up debian/rules a bit
* Enable dh_auto_test for serial flavor
diff --git a/debian/patches/CVE-2016-4330.patch b/debian/patches/CVE-2016-4330.patch
deleted file mode 100644
index cbc09b3..0000000
--- a/debian/patches/CVE-2016-4330.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-commit b1eb1b3ee8693e2a56b074315b521c66255acca1
-Author: Neil Fortner <nfortne2 at hdfgroup.org>
-Date: Thu Sep 1 17:24:24 2016 -0500
-
- Replace assertion in H5O_dtype_decode_helper for number of array dimensions with a check and error. The assertion was inappropriate because it is operating on data read from the file, which the library does not always have direct control of.
-
-diff --git a/src/H5Odtype.c b/src/H5Odtype.c
-index e51d319..eae542b 100644
---- a/src/H5Odtype.c
-+++ b/src/H5Odtype.c
-@@ -519,7 +519,8 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags/*in,out*/, const uint8_t **p
- dt->shared->u.array.ndims = *(*pp)++;
-
- /* Double-check the number of dimensions */
-- HDassert(dt->shared->u.array.ndims <= H5S_MAX_RANK);
-+ if(dt->shared->u.array.ndims > H5S_MAX_RANK)
-+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTLOAD, FAIL, "too many dimensions for array datatype")
-
- /* Skip reserved bytes, if version has them */
- if(version < H5O_DTYPE_VERSION_3)
diff --git a/debian/patches/CVE-2016-4331-1.patch b/debian/patches/CVE-2016-4331-1.patch
deleted file mode 100644
index 078c982..0000000
--- a/debian/patches/CVE-2016-4331-1.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-commit 2409f991667283f8fa1dacc66f245950693495aa
-Author: Neil Fortner <nfortne2 at hdfgroup.org>
-Date: Thu Sep 8 10:48:54 2016 -0500
-
- Fix issues in H5Znbit.c where the decompression algorithm would not check the compressed data for validity, potentially causing a buffer overflow.
-
-Index: hdf5/src/H5Znbit.c
-===================================================================
---- hdf5.orig/src/H5Znbit.c
-+++ hdf5/src/H5Znbit.c
-@@ -60,11 +60,11 @@ static void H5Z_nbit_decompress_one_noop
- unsigned char *buffer, size_t *j, int *buf_len, unsigned size);
- static void H5Z_nbit_decompress_one_atomic(unsigned char *data, size_t data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, parms_atomic p);
--static void H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
-+static herr_t H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[]);
--static void H5Z_nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
-+static herr_t H5Z__nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[]);
--static void H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
-+static herr_t H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
- const unsigned parms[]);
- static void H5Z_nbit_compress_one_nooptype(unsigned char *data, size_t data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, unsigned size);
-@@ -990,7 +990,8 @@ H5Z_filter_nbit(unsigned flags, size_t c
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for nbit decompression")
-
- /* decompress the buffer */
-- H5Z_nbit_decompress(outbuf, d_nelmts, (unsigned char *)*buf, cd_values);
-+ if(H5Z__nbit_decompress(outbuf, d_nelmts, (unsigned char *)*buf, cd_values) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, 0, "can't decompress buffer")
- } /* end if */
- /* output; compress */
- else {
-@@ -1139,12 +1140,15 @@ H5Z_nbit_decompress_one_atomic(unsigned
- }
- }
-
--static void
--H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
-+static herr_t
-+H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[])
- {
- unsigned i, total_size, base_class, base_size, n, begin_index;
- parms_atomic p;
-+ herr_t ret_value = SUCCEED; /* Return value */
-+
-+ FUNC_ENTER_STATIC
-
- total_size = parms[parms_index++];
- base_class = parms[parms_index++];
-@@ -1155,6 +1159,11 @@ H5Z_nbit_decompress_one_array(unsigned c
- p.order = parms[parms_index++];
- p.precision = parms[parms_index++];
- p.offset = parms[parms_index++];
-+
-+ /* Check values of precision and offset */
-+ if(p.precision > p.size * 8 || (p.precision + p.offset) > p.size * 8)
-+ HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset")
-+
- n = total_size/p.size;
- for(i = 0; i < n; i++)
- H5Z_nbit_decompress_one_atomic(data, data_offset + i*p.size,
-@@ -1165,8 +1174,9 @@ H5Z_nbit_decompress_one_array(unsigned c
- n = total_size/base_size; /* number of base_type elements inside the array datatype */
- begin_index = parms_index;
- for(i = 0; i < n; i++) {
-- H5Z_nbit_decompress_one_array(data, data_offset + i*base_size,
-- buffer, j, buf_len, parms);
-+ if(H5Z__nbit_decompress_one_array(data, data_offset + i * base_size,
-+ buffer, j, buf_len, parms) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array")
- parms_index = begin_index;
- }
- break;
-@@ -1175,8 +1185,9 @@ H5Z_nbit_decompress_one_array(unsigned c
- n = total_size/base_size; /* number of base_type elements inside the array datatype */
- begin_index = parms_index;
- for(i = 0; i < n; i++) {
-- H5Z_nbit_decompress_one_compound(data, data_offset + i*base_size,
-- buffer, j, buf_len, parms);
-+ if(H5Z__nbit_decompress_one_compound(data, data_offset + i * base_size,
-+ buffer, j, buf_len, parms) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound")
- parms_index = begin_index;
- }
- break;
-@@ -1187,40 +1198,62 @@ H5Z_nbit_decompress_one_array(unsigned c
- default:
- HDassert(0 && "This Should never be executed!");
- } /* end switch */
-+
-+done:
-+ FUNC_LEAVE_NOAPI(ret_value)
- }
-
--static void
--H5Z_nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
-+static herr_t
-+H5Z__nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[])
- {
-- unsigned i, nmembers, member_offset, member_class, size;
-+ unsigned i, nmembers, member_offset, member_class, member_size, used_size = 0, size;
- parms_atomic p;
-+ herr_t ret_value = SUCCEED; /* Return value */
-+
-+ FUNC_ENTER_STATIC
-
-- parms_index++; /* skip total size of compound datatype */
-+ size = parms[parms_index++];
- nmembers = parms[parms_index++];
-
- for(i = 0; i < nmembers; i++) {
- member_offset = parms[parms_index++];
- member_class = parms[parms_index++];
-+
-+ /* Check for overflow */
-+ member_size = parms[parms_index];
-+ used_size += member_size;
-+ if(used_size > size)
-+ HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "compound member offset overflowed compound size")
- switch(member_class) {
- case H5Z_NBIT_ATOMIC:
-- p.size = parms[parms_index++];
-+ p.size = member_size;
-+ /* Advance past member size */
-+ parms_index++;
- p.order = parms[parms_index++];
- p.precision = parms[parms_index++];
- p.offset = parms[parms_index++];
-+
-+ /* Check values of precision and offset */
-+ if(p.precision > p.size * 8 || (p.precision + p.offset) > p.size * 8)
-+ HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset")
-+
- H5Z_nbit_decompress_one_atomic(data, data_offset + member_offset,
- buffer, j, buf_len, p);
- break;
- case H5Z_NBIT_ARRAY:
-- H5Z_nbit_decompress_one_array(data, data_offset + member_offset,
-- buffer, j, buf_len, parms);
-+ if(H5Z__nbit_decompress_one_array(data, data_offset + member_offset,
-+ buffer, j, buf_len, parms) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array")
- break;
- case H5Z_NBIT_COMPOUND:
-- H5Z_nbit_decompress_one_compound(data, data_offset+member_offset,
-- buffer, j, buf_len, parms);
-+ if(H5Z__nbit_decompress_one_compound(data, data_offset+member_offset,
-+ buffer, j, buf_len, parms) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound")
- break;
- case H5Z_NBIT_NOOPTYPE:
-- size = parms[parms_index++];
-+ /* Advance past member size */
-+ parms_index++;
- H5Z_nbit_decompress_one_nooptype(data, data_offset+member_offset,
- buffer, j, buf_len, size);
- break;
-@@ -1228,10 +1261,13 @@ H5Z_nbit_decompress_one_compound(unsigne
- HDassert(0 && "This Should never be executed!");
- } /* end switch */
- }
-+
-+done:
-+ FUNC_LEAVE_NOAPI(ret_value)
- }
-
--static void
--H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
-+static herr_t
-+H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
- const unsigned parms[])
- {
- /* i: index of data, j: index of buffer,
-@@ -1239,6 +1275,9 @@ H5Z_nbit_decompress(unsigned char *data,
- size_t i, j, size;
- int buf_len;
- parms_atomic p;
-+ herr_t ret_value = SUCCEED; /* Return value */
-+
-+ FUNC_ENTER_STATIC
-
- /* may not have to initialize to zeros */
- for(i = 0; i < d_nelmts*parms[4]; i++) data[i] = 0;
-@@ -1254,6 +1293,11 @@ H5Z_nbit_decompress(unsigned char *data,
- p.order = parms[5];
- p.precision = parms[6];
- p.offset = parms[7];
-+
-+ /* Check values of precision and offset */
-+ if(p.precision > p.size * 8 || (p.precision + p.offset) > p.size * 8)
-+ HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset")
-+
- for(i = 0; i < d_nelmts; i++) {
- H5Z_nbit_decompress_one_atomic(data, i*p.size, buffer, &j, &buf_len, p);
- }
-@@ -1262,7 +1306,8 @@ H5Z_nbit_decompress(unsigned char *data,
- size = parms[4];
- parms_index = 4;
- for(i = 0; i < d_nelmts; i++) {
-- H5Z_nbit_decompress_one_array(data, i*size, buffer, &j, &buf_len, parms);
-+ if(H5Z__nbit_decompress_one_array(data, i * size, buffer, &j, &buf_len, parms) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array")
- parms_index = 4;
- }
- break;
-@@ -1270,13 +1315,17 @@ H5Z_nbit_decompress(unsigned char *data,
- size = parms[4];
- parms_index = 4;
- for(i = 0; i < d_nelmts; i++) {
-- H5Z_nbit_decompress_one_compound(data, i*size, buffer, &j, &buf_len, parms);
-+ if(H5Z__nbit_decompress_one_compound(data, i * size, buffer, &j, &buf_len, parms) < 0)
-+ HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound")
- parms_index = 4;
- }
- break;
- default:
- HDassert(0 && "This Should never be executed!");
- } /* end switch */
-+
-+done:
-+ FUNC_LEAVE_NOAPI(ret_value)
- }
-
- static void H5Z_nbit_compress_one_byte(unsigned char *data, size_t data_offset, int k, int begin_i,
diff --git a/debian/patches/CVE-2016-4331-2.patch b/debian/patches/CVE-2016-4331-2.patch
deleted file mode 100644
index 9381adf..0000000
--- a/debian/patches/CVE-2016-4331-2.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-commit 391a231b76c1200ecda5d74636213e9e479fa51a
-Author: Neil Fortner <nfortne2 at hdfgroup.org>
-Date: Fri Sep 9 12:08:30 2016 -0500
-
- Fix bug in "nooptype" decode in fix for TALOS-0177.
-
-Index: hdf5/src/H5Znbit.c
-===================================================================
---- hdf5.orig/src/H5Znbit.c
-+++ hdf5/src/H5Znbit.c
-@@ -1255,7 +1255,7 @@ H5Z__nbit_decompress_one_compound(unsign
- /* Advance past member size */
- parms_index++;
- H5Z_nbit_decompress_one_nooptype(data, data_offset+member_offset,
-- buffer, j, buf_len, size);
-+ buffer, j, buf_len, member_size);
- break;
- default:
- HDassert(0 && "This Should never be executed!");
diff --git a/debian/patches/CVE-2016-4332.patch b/debian/patches/CVE-2016-4332.patch
deleted file mode 100644
index 07b4192..0000000
--- a/debian/patches/CVE-2016-4332.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-commit bfae878d8f2f65bc5f22f0d4bb314f326278ba7b
-Author: Neil Fortner <nfortne2 at hdfgroup.org>
-Date: Fri Jul 1 10:31:44 2016 -0500
-
- [svn-r30131] Fix bug reported by Cisco Talos TALOS-CAN-0178. Added check for a message that
- should not be sharable being marked as sharable on disk, returns failure in
- this case. Needs testing.
-
- Tested: ummon
-
-Index: hdf5/src/H5Ocache.c
-===================================================================
---- hdf5.orig/src/H5Ocache.c
-+++ hdf5/src/H5Ocache.c
-@@ -1433,6 +1433,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_
- HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "bad flag combination for message")
- if((flags & H5O_MSG_FLAG_WAS_UNKNOWN) && !(flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN))
- HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "bad flag combination for message")
-+ if((flags & H5O_MSG_FLAG_SHAREABLE)
-+ && H5O_msg_class_g[id]
-+ && !(H5O_msg_class_g[id]->share_flags & H5O_SHARE_IS_SHARABLE))
-+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "message of unsharable class flagged as sharable")
-
- /* Reserved bytes/creation index */
- if(oh->version == H5O_VERSION_1)
-Index: hdf5/src/H5Opkg.h
-===================================================================
---- hdf5.orig/src/H5Opkg.h
-+++ hdf5/src/H5Opkg.h
-@@ -212,6 +212,7 @@
- \
- /* Set the message's "shared info", if it's shareable */ \
- if((MSG)->flags & H5O_MSG_FLAG_SHAREABLE) { \
-+ HDassert(msg_type->share_flags & H5O_SHARE_IS_SHARABLE); \
- H5O_UPDATE_SHARED((H5O_shared_t *)(MSG)->native, H5O_SHARE_TYPE_HERE, (F), msg_type->id, (MSG)->crt_idx, (OH)->chunk[0].addr) \
- } /* end if */ \
- \
diff --git a/debian/patches/CVE-2016-4333.patch b/debian/patches/CVE-2016-4333.patch
deleted file mode 100644
index 5b0ec5b..0000000
--- a/debian/patches/CVE-2016-4333.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-commit bc10fd219e60fc4b9df7d80567ecb1e39ae5b6e3
-Author: Neil Fortner <nfortne2 at hdfgroup.org>
-Date: Thu Sep 8 13:47:22 2016 -0500
-
- Change check for number of dimensions for old-style arrays in datatype decoding routine from an assertion to an if/HGOTO_ERROR check, since it is inappropriate to assert the contents of a file will be what we expect.
-
-diff --git a/src/H5Odtype.c b/src/H5Odtype.c
-index e51d319..3c3f284 100644
---- a/src/H5Odtype.c
-+++ b/src/H5Odtype.c
-@@ -311,7 +311,11 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags/*in,out*/, const uint8_t **p
- if(version == H5O_DTYPE_VERSION_1) {
- /* Decode the number of dimensions */
- ndims = *(*pp)++;
-- HDassert(ndims <= 4);
-+
-+ /* Check that ndims is valid */
-+ if(ndims > 4)
-+ HGOTO_ERROR(H5E_DATATYPE, H5E_BADTYPE, FAIL, "invalid number of dimensions for array")
-+
- *pp += 3; /*reserved bytes */
-
- /* Skip dimension permutation */
diff --git a/debian/patches/flavor-configure-option.patch b/debian/patches/flavor-configure-option.patch
index 55e0e26..ef92088 100644
--- a/debian/patches/flavor-configure-option.patch
+++ b/debian/patches/flavor-configure-option.patch
@@ -6,11 +6,11 @@ Description: Add option --with-flavor=<flavor-name> to configure
* serial is built with no flavor name
* $mpi parallel versions use --with-flavor=$mpi
Author: Gilles Filippini <pini at debian.org>
-Index: hdf5-1.10.0-patch1+docs/configure.ac
+Index: hdf5/configure.ac
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/configure.ac
-+++ hdf5-1.10.0-patch1+docs/configure.ac
-@@ -3507,6 +3507,26 @@ fi
+--- hdf5.orig/configure.ac
++++ hdf5/configure.ac
+@@ -3352,6 +3352,26 @@ fi
##
AM_CONDITIONAL([HAVE_SHARED_CONDITIONAL], [test "X$enable_shared" = "Xyes"])
@@ -37,10 +37,10 @@ Index: hdf5-1.10.0-patch1+docs/configure.ac
AC_CONFIG_FILES([src/libhdf5.settings
Makefile
src/Makefile
-Index: hdf5-1.10.0-patch1+docs/src/libhdf5.settings.in
+Index: hdf5/src/libhdf5.settings.in
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/src/libhdf5.settings.in
-+++ hdf5-1.10.0-patch1+docs/src/libhdf5.settings.in
+--- hdf5.orig/src/libhdf5.settings.in
++++ hdf5/src/libhdf5.settings.in
@@ -10,6 +10,7 @@ General Information:
Uname information: @UNAME_INFO@
Byte sex: @BYTESEX@
@@ -49,11 +49,11 @@ Index: hdf5-1.10.0-patch1+docs/src/libhdf5.settings.in
Compiling Options:
------------------
-Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
+Index: hdf5/src/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/src/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/src/Makefile.am
-@@ -29,10 +29,10 @@ include $(top_srcdir)/config/lt_vers.am
+--- hdf5.orig/src/Makefile.am
++++ hdf5/src/Makefile.am
+@@ -27,10 +27,10 @@ include $(top_srcdir)/config/lt_vers.am
noinst_PROGRAMS = H5detect H5make_libsettings
# Our main target, the HDF5 library
@@ -66,16 +66,16 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
# H5Tinit.c and H5lib_settings.c are generated files and should be cleaned.
MOSTLYCLEANFILES=H5Tinit.c H5lib_settings.c
-@@ -40,7 +40,7 @@ MOSTLYCLEANFILES=H5Tinit.c H5lib_setting
+@@ -38,7 +38,7 @@ MOSTLYCLEANFILES=H5Tinit.c H5lib_setting
DISTCLEANFILES=H5pubconf.h
# library sources
-libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
+libhdf5 at FLAVOR@_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
H5A.c H5Abtree2.c H5Adense.c H5Adeprec.c H5Aint.c H5Atest.c \
- H5AC.c H5AClog.c \
+ H5AC.c H5ACdbg.c H5AClog.c H5ACproxy_entry.c \
H5B.c H5Bcache.c H5Bdbg.c \
-@@ -115,12 +115,12 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5
+@@ -118,12 +118,12 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5
# Only compile parallel sources if necessary
if BUILD_PARALLEL_CONDITIONAL
@@ -90,7 +90,7 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
endif
# Public headers
-@@ -139,7 +139,11 @@ include_HEADERS = hdf5.h H5api_adpt.h H5
+@@ -142,7 +142,11 @@ include_HEADERS = hdf5.h H5api_adpt.h H5
# install libhdf5.settings in lib directory
settingsdir=$(libdir)
@@ -103,7 +103,7 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
# Number format detection
# The LD_LIBRARY_PATH setting is a kludge.
-@@ -181,6 +185,7 @@ $(top_srcdir)/src/H5version.h: $(top_src
+@@ -184,6 +188,7 @@ $(top_srcdir)/src/H5version.h: $(top_src
$(top_srcdir)/src/H5overflow.h: $(top_srcdir)/src/H5overflow.txt
perl $(top_srcdir)/bin/make_overflow $?
@@ -111,7 +111,7 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
# Add TRACE macros to library source files. This is done via the trace script
# in the hdf5/bin directory. If the file contains HDF5 API macros, a "clean"
# version of the source file is saved with a tilde (~) after its name and
-@@ -188,7 +193,7 @@ $(top_srcdir)/src/H5overflow.h: $(top_sr
+@@ -191,7 +196,7 @@ $(top_srcdir)/src/H5overflow.h: $(top_sr
# without HDF5 macros.
.PHONY: trace
@@ -120,7 +120,7 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
@for dep in $? dummy; do \
if test $$dep != "dummy" -a -n "$(PERL)"; then \
case "$$dep" in \
-@@ -199,4 +204,24 @@ trace: $(libhdf5_la_SOURCES)
+@@ -202,4 +207,24 @@ trace: $(libhdf5_la_SOURCES)
fi; \
done
@@ -145,11 +145,11 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am
+endif
+
include $(top_srcdir)/config/conclude.am
-Index: hdf5-1.10.0-patch1+docs/test/testlibinfo.sh.in
+Index: hdf5/test/testlibinfo.sh.in
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/test/testlibinfo.sh.in
-+++ hdf5-1.10.0-patch1+docs/test/testlibinfo.sh.in
-@@ -79,7 +79,7 @@ fi
+--- hdf5.orig/test/testlibinfo.sh.in
++++ hdf5/test/testlibinfo.sh.in
+@@ -77,7 +77,7 @@ fi
# built too.
if [ -n $Shared_Lib ]; then
h5libdir=../src/.libs
@@ -158,7 +158,7 @@ Index: hdf5-1.10.0-patch1+docs/test/testlibinfo.sh.in
else
h5libdir=../src
fi
-@@ -98,9 +98,9 @@ fi
+@@ -96,9 +96,9 @@ fi
# Though rare, libhdf5.a may not have been built.
if [ x-$Static_Lib = x-yes ]; then
@@ -170,11 +170,11 @@ Index: hdf5-1.10.0-patch1+docs/test/testlibinfo.sh.in
fi
# Check if executables has the lib information only if shared lib is not
-Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
+Index: hdf5/tools/src/misc/h5cc.in
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/tools/misc/h5cc.in
-+++ hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
-@@ -29,6 +29,7 @@
+--- hdf5.orig/tools/src/misc/h5cc.in
++++ hdf5/tools/src/misc/h5cc.in
+@@ -27,6 +27,7 @@
prefix="@prefix@"
exec_prefix="@exec_prefix@"
libdir="@libdir@"
@@ -182,7 +182,7 @@ Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
includedir="@includedir@"
HL="@HL@"
-@@ -172,7 +173,7 @@ usage() {
+@@ -170,7 +171,7 @@ usage() {
# libhdf5.settings file reside in the lib directory.
showconfigure()
{
@@ -191,7 +191,7 @@ Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
status=$?
}
-@@ -333,7 +334,7 @@ if test "x$do_link" = "xyes"; then
+@@ -331,7 +332,7 @@ if test "x$do_link" = "xyes"; then
else
libraries=" $libraries -lhdf5 "
fi
@@ -200,7 +200,7 @@ Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
case "$kind" in
gcc|linux*)
-@@ -352,7 +353,7 @@ if test "x$do_link" = "xyes"; then
+@@ -350,7 +351,7 @@ if test "x$do_link" = "xyes"; then
esac
if test -n "$flag"; then
@@ -209,7 +209,7 @@ Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
fi
if test "x$USE_SHARED_LIB" != "xyes"; then
-@@ -362,10 +363,10 @@ if test "x$do_link" = "xyes"; then
+@@ -360,10 +361,10 @@ if test "x$do_link" = "xyes"; then
for lib in $libraries; do
case "$lib" in
-lhdf5)
@@ -222,7 +222,7 @@ Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
;;
*)
new_libraries="$new_libraries $lib"
-@@ -394,7 +395,7 @@ if test "x$do_link" = "xyes"; then
+@@ -392,7 +393,7 @@ if test "x$do_link" = "xyes"; then
# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
# from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags.
@@ -231,11 +231,11 @@ Index: hdf5-1.10.0-patch1+docs/tools/misc/h5cc.in
status=$?
fi
-Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
+Index: hdf5/c++/src/h5c++.in
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/c++/src/h5c++.in
-+++ hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
-@@ -27,6 +27,7 @@
+--- hdf5.orig/c++/src/h5c++.in
++++ hdf5/c++/src/h5c++.in
+@@ -25,6 +25,7 @@
prefix="@prefix@"
exec_prefix="@exec_prefix@"
libdir="@libdir@"
@@ -243,7 +243,7 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
includedir="@includedir@"
HL="@HL@"
-@@ -161,7 +162,7 @@ usage() {
+@@ -159,7 +160,7 @@ usage() {
# libhdf5.settings file reside in the lib directory.
showconfigure()
{
@@ -252,7 +252,7 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
status=$?
}
-@@ -319,7 +320,7 @@ if test "x$do_link" = "xyes"; then
+@@ -317,7 +318,7 @@ if test "x$do_link" = "xyes"; then
else
libraries=" $libraries -lhdf5_cpp -lhdf5 "
fi
@@ -261,7 +261,7 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
case "$kind" in
gcc|linux*)
-@@ -338,7 +339,7 @@ if test "x$do_link" = "xyes"; then
+@@ -336,7 +337,7 @@ if test "x$do_link" = "xyes"; then
esac
if test -n "$flag"; then
@@ -270,7 +270,7 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
fi
if test "x$USE_SHARED_LIB" != "xyes"; then
-@@ -348,16 +349,16 @@ if test "x$do_link" = "xyes"; then
+@@ -346,16 +347,16 @@ if test "x$do_link" = "xyes"; then
for lib in $libraries; do
case "$lib" in
-lhdf5)
@@ -291,7 +291,7 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
;;
*)
new_libraries="$new_libraries $lib"
-@@ -387,7 +388,7 @@ if test "x$do_link" = "xyes"; then
+@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then
# from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags.
@@ -300,11 +300,11 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/h5c++.in
status=$?
fi
-Index: hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
+Index: hdf5/fortran/src/h5fc.in
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/fortran/src/h5fc.in
-+++ hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
-@@ -27,6 +27,7 @@
+--- hdf5.orig/fortran/src/h5fc.in
++++ hdf5/fortran/src/h5fc.in
+@@ -25,6 +25,7 @@
prefix="@prefix@"
exec_prefix="@exec_prefix@"
libdir="@libdir@"
@@ -312,7 +312,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
includedir="@includedir@"
HL="@HL@"
-@@ -156,7 +157,7 @@ usage() {
+@@ -154,7 +155,7 @@ usage() {
# libhdf5.settings file reside in the lib directory.
showconfigure()
{
@@ -321,7 +321,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
status=$?
}
-@@ -306,7 +307,7 @@ if test "x$do_link" = "xyes"; then
+@@ -304,7 +305,7 @@ if test "x$do_link" = "xyes"; then
else
libraries=" $libraries -lhdf5_fortran -lhdf5 "
fi
@@ -330,7 +330,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
case "$host_os" in
linux*) flag="-Wl,-rpath -Wl," ;;
-@@ -318,7 +319,7 @@ if test "x$do_link" = "xyes"; then
+@@ -316,7 +317,7 @@ if test "x$do_link" = "xyes"; then
esac
if test -n "$flag"; then
@@ -339,7 +339,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
fi
if test "x$USE_SHARED_LIB" != "xyes"; then
-@@ -328,16 +329,16 @@ if test "x$do_link" = "xyes"; then
+@@ -326,16 +327,16 @@ if test "x$do_link" = "xyes"; then
for lib in $libraries; do
case "$lib" in
-lhdf5)
@@ -360,11 +360,11 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/h5fc.in
;;
*)
new_libraries="$new_libraries $lib"
-Index: hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
+Index: hdf5/fortran/src/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/fortran/src/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
-@@ -29,10 +29,10 @@ AM_FCFLAGS+=-I$(top_srcdir)/src -I$(top_
+--- hdf5.orig/fortran/src/Makefile.am
++++ hdf5/fortran/src/Makefile.am
+@@ -27,10 +27,10 @@ AM_FCFLAGS+=-I$(top_srcdir)/src -I$(top_
AM_FCLIBS=$(LIBHDF5)
# This is our main target, the fortran library
@@ -377,7 +377,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
# Some Fortran compilers can't build shared libraries, so sometimes we
# want to build a shared C library and a static Fortran library. If so,
-@@ -43,7 +43,7 @@ else
+@@ -41,7 +41,7 @@ else
endif
# Source files for the library.
@@ -386,7 +386,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
H5fortran_types.F90 H5_ff.F90 H5Aff.F90 H5Dff.F90 H5Eff.F90 \
H5Fff.F90 H5Gff.F90 H5Iff.F90 H5Lff.F90 H5Off.F90 H5Pff.F90 H5Rff.F90 H5Sff.F90 \
H5Tff.F90 H5Zff.F90 H5_gen.F90 H5fortkit.F90 \
-@@ -51,7 +51,7 @@ libhdf5_fortran_la_SOURCES=H5f90global.F
+@@ -49,7 +49,7 @@ libhdf5_fortran_la_SOURCES=H5f90global.F
H5If.c H5Lf.c H5Of.c H5Pf.c H5Rf.c H5Sf.c H5Tf.c H5Zf.c HDF5.F90
# HDF5 Fortran library depends on HDF5 Library.
@@ -395,7 +395,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
# h5fc is generated during configure.
# Remove it only when distclean.
-@@ -95,7 +95,11 @@ install-exec-local:
+@@ -93,7 +93,11 @@ install-exec-local:
# Custom rule for installing h5fc, since it will be named h5pfc if hdf5
# is configured for parallel mode
if BUILD_PARALLEL_CONDITIONAL
@@ -407,7 +407,7 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
else
H5FC_NAME = h5fc
endif
-@@ -166,4 +170,16 @@ HDF5.lo: $(srcdir)/HDF5.F90
+@@ -164,4 +168,16 @@ HDF5.lo: $(srcdir)/HDF5.F90
H5Off.lo H5Pff.lo H5Rff.lo \
H5Sff.lo H5Tff.lo H5Zff.lo H5_gen.lo
@@ -424,11 +424,11 @@ Index: hdf5-1.10.0-patch1+docs/fortran/src/Makefile.am
+endif
+
include $(top_srcdir)/config/conclude_fc.am
-Index: hdf5-1.10.0-patch1+docs/hl/fortran/src/Makefile.am
+Index: hdf5/hl/fortran/src/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/hl/fortran/src/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/hl/fortran/src/Makefile.am
-@@ -27,10 +27,10 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top
+--- hdf5.orig/hl/fortran/src/Makefile.am
++++ hdf5/hl/fortran/src/Makefile.am
+@@ -25,10 +25,10 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top
AM_FCFLAGS+=-I$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src
# Our main target, the high-level fortran library
@@ -441,7 +441,7 @@ Index: hdf5-1.10.0-patch1+docs/hl/fortran/src/Makefile.am
# Some Fortran compilers can't build shared libraries, so sometimes we
# want to build a shared C library and a static Fortran library. If so,
-@@ -46,11 +46,11 @@ endif
+@@ -44,11 +44,11 @@ endif
#endif
# List sources to include in the HDF5 HL Fortran library.
@@ -455,7 +455,7 @@ Index: hdf5-1.10.0-patch1+docs/hl/fortran/src/Makefile.am
# Fortran module files can have different extensions and different names
# (e.g., different capitalizations) on different platforms. Write rules
-@@ -102,4 +102,17 @@ H5IMff.lo: $(srcdir)/H5IMff.F90
+@@ -98,4 +98,17 @@ H5IMff.lo: $(srcdir)/H5IMff.F90
H5TBff.lo: $(srcdir)/H5TBff.F90
H5LTff_gen.lo: H5LTff.lo H5LTff_gen.F90
H5TBff_gen.lo: H5TBff.lo H5LTff_gen.F90 H5TBff_gen.F90
@@ -473,11 +473,11 @@ Index: hdf5-1.10.0-patch1+docs/hl/fortran/src/Makefile.am
+endif
+
include $(top_srcdir)/config/conclude_fc.am
-Index: hdf5-1.10.0-patch1+docs/hl/src/Makefile.am
+Index: hdf5/hl/src/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/hl/src/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/hl/src/Makefile.am
-@@ -25,18 +25,30 @@ include $(top_srcdir)/config/lt_vers.am
+--- hdf5.orig/hl/src/Makefile.am
++++ hdf5/hl/src/Makefile.am
+@@ -23,18 +23,30 @@ include $(top_srcdir)/config/lt_vers.am
AM_CPPFLAGS+=-I$(top_srcdir)/src
# This library is our main target.
@@ -512,11 +512,11 @@ Index: hdf5-1.10.0-patch1+docs/hl/src/Makefile.am
+endif
+
include $(top_srcdir)/config/conclude.am
-Index: hdf5-1.10.0-patch1+docs/config/commence.am
+Index: hdf5/config/commence.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/config/commence.am
-+++ hdf5-1.10.0-patch1+docs/config/commence.am
-@@ -32,15 +32,15 @@ CP=cp
+--- hdf5.orig/config/commence.am
++++ hdf5/config/commence.am
+@@ -30,15 +30,15 @@ CP=cp
RUNEXEC=$(RUNSERIAL)
# Libraries to link to while building
@@ -536,16 +536,16 @@ Index: hdf5-1.10.0-patch1+docs/config/commence.am
LIBH5CPP_HL=$(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
# Install directories that automake doesn't know about
-@@ -104,3 +104,4 @@ CHECK_CLEANFILES=*.chkexe *.chklog *.clo
+@@ -102,3 +102,4 @@ CHECK_CLEANFILES=*.chkexe *.chklog *.clo
help:
@$(top_srcdir)/bin/makehelp
+abs2rel = $(shell perl -e 'use File::Spec; print File::Spec->abs2rel($(1), $(2)) . "\n";')
-Index: hdf5-1.10.0-patch1+docs/c++/src/Makefile.am
+Index: hdf5/c++/src/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/c++/src/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/c++/src/Makefile.am
-@@ -68,4 +68,16 @@ mostlyclean-local:
+--- hdf5.orig/c++/src/Makefile.am
++++ hdf5/c++/src/Makefile.am
+@@ -69,4 +69,16 @@ mostlyclean-local:
# Mark this directory as part of the C++ API
CXX_API=yes
@@ -562,11 +562,11 @@ Index: hdf5-1.10.0-patch1+docs/c++/src/Makefile.am
+endif
+
include $(top_srcdir)/config/conclude.am
-Index: hdf5-1.10.0-patch1+docs/hl/c++/src/Makefile.am
+Index: hdf5/hl/c++/src/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/hl/c++/src/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/hl/c++/src/Makefile.am
-@@ -40,4 +40,16 @@ libhdf5_hl_cpp_la_LIBADD=$(LIBH5_HL) $(L
+--- hdf5.orig/hl/c++/src/Makefile.am
++++ hdf5/hl/c++/src/Makefile.am
+@@ -38,4 +38,16 @@ libhdf5_hl_cpp_la_LIBADD=$(LIBH5_HL) $(L
# Public headers
include_HEADERS=H5PacketTable.h
@@ -583,11 +583,11 @@ Index: hdf5-1.10.0-patch1+docs/hl/c++/src/Makefile.am
+endif
+
include $(top_srcdir)/config/conclude.am
-Index: hdf5-1.10.0-patch1+docs/tools/misc/Makefile.am
+Index: hdf5/tools/src/misc/Makefile.am
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/tools/misc/Makefile.am
-+++ hdf5-1.10.0-patch1+docs/tools/misc/Makefile.am
-@@ -63,7 +63,11 @@ LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+--- hdf5.orig/tools/src/misc/Makefile.am
++++ hdf5/tools/src/misc/Makefile.am
+@@ -43,7 +43,11 @@ LDADD=$(LIBH5TOOLS) $(LIBHDF5)
# h5cc needs custom install and uninstall rules, since it may be
# named h5pcc if hdf5 is being built in parallel mode.
if BUILD_PARALLEL_CONDITIONAL
@@ -603,20 +603,20 @@ Index: hdf5/java/test/junit.sh.in
===================================================================
--- hdf5.orig/java/test/junit.sh.in
+++ hdf5/java/test/junit.sh.in
-@@ -59,7 +59,7 @@ $HDFLIB_HOME/hamcrest-core.jar
- $HDFLIB_HOME/junit.jar
- $HDFLIB_HOME/slf4j-api-1.7.5.jar
- $HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
+@@ -53,7 +53,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
+ # Comment '#' without space can be used.
+ # --------------------------------------------------------------------
+ LIST_LIBRARY_FILES="
-$top_builddir/src/.libs/libhdf5.*
+$top_builddir/src/.libs/libhdf5 at FLAVOR@.*
$top_builddir/java/src/jni/.libs/libhdf5_java.*
- $top_builddir/java/src/$JARFILE
"
+ LIST_JAR_FILES="
Index: hdf5/java/examples/datasets/runExample.sh.in
===================================================================
--- hdf5.orig/java/examples/datasets/runExample.sh.in
+++ hdf5/java/examples/datasets/runExample.sh.in
-@@ -56,7 +56,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
+@@ -54,7 +54,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
LIST_LIBRARY_FILES="
$HDFLIB_HOME/slf4j-api-1.7.5.jar
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
@@ -629,7 +629,7 @@ Index: hdf5/java/examples/datatypes/runExample.sh.in
===================================================================
--- hdf5.orig/java/examples/datatypes/runExample.sh.in
+++ hdf5/java/examples/datatypes/runExample.sh.in
-@@ -53,7 +53,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
+@@ -51,7 +51,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
LIST_LIBRARY_FILES="
$HDFLIB_HOME/slf4j-api-1.7.5.jar
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
@@ -642,7 +642,7 @@ Index: hdf5/java/examples/groups/runExample.sh.in
===================================================================
--- hdf5.orig/java/examples/groups/runExample.sh.in
+++ hdf5/java/examples/groups/runExample.sh.in
-@@ -55,7 +55,7 @@ test -d $BLDREFDIR || mkdir -p $BLDREFDI
+@@ -53,7 +53,7 @@ test -d $BLDREFDIR || mkdir -p $BLDREFDI
LIST_LIBRARY_FILES="
$HDFLIB_HOME/slf4j-api-1.7.5.jar
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
@@ -655,7 +655,7 @@ Index: hdf5/java/examples/intro/runExample.sh.in
===================================================================
--- hdf5.orig/java/examples/intro/runExample.sh.in
+++ hdf5/java/examples/intro/runExample.sh.in
-@@ -53,7 +53,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
+@@ -51,7 +51,7 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDI
LIST_LIBRARY_FILES="
$HDFLIB_HOME/slf4j-api-1.7.5.jar
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
diff --git a/debian/patches/java-runtime-exception.patch b/debian/patches/java-runtime-exception.patch
index e0c9972..62a7b11 100644
--- a/debian/patches/java-runtime-exception.patch
+++ b/debian/patches/java-runtime-exception.patch
@@ -2,7 +2,7 @@ Index: hdf5/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
===================================================================
--- hdf5.orig/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
+++ hdf5/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
-@@ -32,7 +32,7 @@ package hdf.hdf5lib.exceptions;
+@@ -30,7 +30,7 @@ package hdf.hdf5lib.exceptions;
* error code returned by the HDF5 library.
*
*/
diff --git a/debian/patches/path_max.diff b/debian/patches/path_max.diff
index a86c76f..3114fd8 100644
--- a/debian/patches/path_max.diff
+++ b/debian/patches/path_max.diff
@@ -9,15 +9,29 @@ Index: hdf5/src/H5Fint.c
===================================================================
--- hdf5.orig/src/H5Fint.c
+++ hdf5/src/H5Fint.c
-@@ -1756,7 +1756,6 @@ H5F_build_actual_name(const H5F_t *f, co
- int *fd; /* POSIX I/O file descriptor */
- h5_stat_t st; /* Stat info from stat() call */
+@@ -2002,10 +2002,6 @@ H5F_build_actual_name(const H5F_t *f, co
+ char **actual_name/*out*/)
+ {
+ hid_t new_fapl_id = -1; /* ID for duplicated FAPL */
+-#ifdef H5_HAVE_SYMLINK
+- /* This has to be declared here to avoid unfreed resources on errors */
+- char *realname = NULL; /* Fully resolved path name of file */
+-#endif /* H5_HAVE_SYMLINK */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT
+@@ -2039,10 +2035,6 @@ H5F_build_actual_name(const H5F_t *f, co
h5_stat_t fst; /* Stat info from fstat() call */
-- char realname[PATH_MAX]; /* Fully resolved path name of file */
hbool_t want_posix_fd; /* Flag for retrieving file descriptor from VFD */
+- /* Allocate realname buffer */
+- if(NULL == (realname = (char *)H5MM_calloc((size_t)PATH_MAX * sizeof(char))))
+- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+-
/* Perform a sanity check that the file or link wasn't switched
-@@ -1793,12 +1792,8 @@ H5F_build_actual_name(const H5F_t *f, co
+ * between when we opened it and when we called lstat(). This is
+ * according to the security best practices for lstat() documented
+@@ -2077,12 +2069,8 @@ 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 */
@@ -31,3 +45,14 @@ Index: hdf5/src/H5Fint.c
} /* end if */
} /* end if */
#endif /* H5_HAVE_SYMLINK */
+@@ -2099,10 +2087,6 @@ done:
+ if(new_fapl_id > 0)
+ if(H5I_dec_app_ref(new_fapl_id) < 0)
+ HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEOBJ, FAIL, "can't close duplicated FAPL")
+-#ifdef H5_HAVE_SYMLINK
+- if(realname)
+- realname = (char *)H5MM_xfree(realname);
+-#endif /* H5_HAVE_SYMLINK */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+ } /* H5F_build_actual_name() */
diff --git a/debian/patches/relax-version-check.patch b/debian/patches/relax-version-check.patch
index 12c1cdd..a1e2f3e 100644
--- a/debian/patches/relax-version-check.patch
+++ b/debian/patches/relax-version-check.patch
@@ -6,11 +6,11 @@ Description: remove check on patch version
access see e.g. H5F_ACC_RDONLY in src/H5Fpublic.h
Author: Julian Taylor <jtaylor at ubuntu.com>
Bug-Debian: http://bugs.debian.org/693610
-Index: hdf5-1.10.0-patch1+docs/src/H5.c
+Index: hdf5/src/H5.c
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/src/H5.c
-+++ hdf5-1.10.0-patch1+docs/src/H5.c
-@@ -778,8 +778,7 @@ H5check_version(unsigned majnum, unsigne
+--- hdf5.orig/src/H5.c
++++ hdf5/src/H5.c
+@@ -776,8 +776,7 @@ H5check_version(unsigned majnum, unsigne
disable_version_check = (unsigned int)HDstrtol (s, NULL, 0);
}
@@ -20,11 +20,11 @@ Index: hdf5-1.10.0-patch1+docs/src/H5.c
switch (disable_version_check) {
case 0:
HDfprintf(stderr, "%s%s", version_mismatch_warning,
-Index: hdf5-1.10.0-patch1+docs/test/testcheck_version.sh.in
+Index: hdf5/test/testcheck_version.sh.in
===================================================================
---- hdf5-1.10.0-patch1+docs.orig/test/testcheck_version.sh.in
-+++ hdf5-1.10.0-patch1+docs/test/testcheck_version.sh.in
-@@ -154,8 +154,12 @@ TESTING() {
+--- hdf5.orig/test/testcheck_version.sh.in
++++ hdf5/test/testcheck_version.sh.in
+@@ -152,8 +152,12 @@ TESTING() {
esac
case "$h5DisableVersion" in
1)
@@ -39,7 +39,7 @@ Index: hdf5-1.10.0-patch1+docs/test/testcheck_version.sh.in
expect_code=0
;;
[2-9]|[1-9][0-9]*)
-@@ -164,8 +168,13 @@ TESTING() {
+@@ -162,8 +166,13 @@ TESTING() {
expect_code=0
;;
*) # W/A: Warning, abort and exit non-0.
diff --git a/debian/patches/series b/debian/patches/series
index bd5dc24..27b1afc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,9 +2,4 @@ flavor-configure-option.patch
path_max.diff
ullong_force.diff
relax-version-check.patch
-CVE-2016-4330.patch
-CVE-2016-4331-1.patch
-CVE-2016-4331-2.patch
-CVE-2016-4332.patch
-CVE-2016-4333.patch
java-runtime-exception.patch
diff --git a/debian/patches/ullong_force.diff b/debian/patches/ullong_force.diff
index c72dc2b..41ac170 100644
--- a/debian/patches/ullong_force.diff
+++ b/debian/patches/ullong_force.diff
@@ -4,7 +4,7 @@ Index: hdf5/src/H5Tconv.c
===================================================================
--- hdf5.orig/src/H5Tconv.c
+++ hdf5/src/H5Tconv.c
-@@ -8017,7 +8017,6 @@ H5T__conv_ullong_double (hid_t src_id, h
+@@ -8015,7 +8015,6 @@ H5T__conv_ullong_double (hid_t src_id, h
*
*-------------------------------------------------------------------------
*/
@@ -12,7 +12,7 @@ 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,
-@@ -8026,7 +8025,6 @@ H5T__conv_ullong_ldouble (hid_t src_id,
+@@ -8024,7 +8023,6 @@ H5T__conv_ullong_ldouble (hid_t src_id,
{
H5T_CONV_xF(ULLONG, LDOUBLE, unsigned long long, long double, -, -);
}
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-grass/hdf5.git
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