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commit b270aaefbfa7b46e13b80b29a8db2ac5a6d911e6 Author: Gilles Filippini <[email protected]> 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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 $(top_srcdir)/config/lt_vers.am noinst_PROGRAMS = H5detect H5make_libsettings # Our main target, the HDF5 library @@ -66,16 +66,16 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am # H5Tinit.c and H5lib_settings.c are generated files and should be cleaned. MOSTLYCLEANFILES=H5Tinit.c H5lib_settings.c -@@ -40,7 +40,7 @@ MOSTLYCLEANFILES=H5Tinit.c H5lib_setting +@@ -38,7 +38,7 @@ MOSTLYCLEANFILES=H5Tinit.c H5lib_setting DISTCLEANFILES=H5pubconf.h # library sources -libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ +libhdf5@FLAVOR@_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5A.c H5Abtree2.c H5Adense.c H5Adeprec.c H5Aint.c H5Atest.c \ - H5AC.c H5AClog.c \ + H5AC.c H5ACdbg.c H5AClog.c H5ACproxy_entry.c \ H5B.c H5Bcache.c H5Bdbg.c \ -@@ -115,12 +115,12 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5 +@@ -118,12 +118,12 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5 # Only compile parallel sources if necessary if BUILD_PARALLEL_CONDITIONAL @@ -90,7 +90,7 @@ Index: hdf5-1.10.0-patch1+docs/src/Makefile.am endif # Public headers -@@ -139,7 +139,11 @@ include_HEADERS = hdf5.h H5api_adpt.h H5 +@@ -142,7 +142,11 @@ include_HEADERS = hdf5.h H5api_adpt.h H5 # install libhdf5.settings in lib directory settingsdir=$(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@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 <[email protected]> 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 _______________________________________________ Pkg-grass-devel mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-grass-devel
