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[AUTO-CHERRYPICK] Upgrade hdf5 to 1.14.4. to under several CVEs. - branch main (#9182) 

Co-authored-by: George Mileka <gmileka@users.noreply.github.com>
This commit is contained in:
CBL-Mariner-Bot 2024-05-22 10:02:40 -07:00 коммит произвёл GitHub
Родитель c5f4ef7e9b
Коммит 08a425ff5f
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Идентификатор ключа GPG: B5690EEEBB952194
11 изменённых файлов: 183 добавлений и 346 удалений
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9
SPECS-EXTENDED/gdal/gdal.spec
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@ -15,7 +15,7 @@ Summary: GIS file format library
#global pre rc1
Name: gdal
Version: 3.6.3
Release: 2%{?dist}
Release: 3%{?dist}
License: MIT
Vendor: Microsoft Corporation
Distribution: Mariner
@ -41,7 +41,7 @@ BuildRequires: geos-devel
BuildRequires: giflib-devel
BuildRequires: gtest-devel
BuildRequires: hdf-devel
BuildRequires: hdf5-devel
BuildRequires: hdf5-devel >= 1.14.4
BuildRequires: json-c-devel
BuildRequires: libdap-devel
BuildRequires: libgeotiff-devel
@ -97,6 +97,7 @@ BuildRequires: java-devel >= 1:1.6.0
BuildRequires: javapackages-local
BuildRequires: jpackage-utils
%endif
Requires: hdf5 >= 1.14.4
%description
Geospatial Data Abstraction Library (GDAL/OGR) is a cross platform
@ -315,6 +316,10 @@ ctest -E "autotest_osr|autotest_alg|autotest_gdrivers|autotest_gcore"
%changelog
- Bumping the release version so that this package is re-built with the newer
1.14.4 hdf5 libraries. This ensures that the matching 1.14.4 .so files Will
be used at run time.
* Thu Aug 17 2023 Archana Choudhary <archana1@microsoft.com> - 3.6.3-2
- Initial CBL-Mariner import from Fedora 38 (license: MIT).
- License verified.

10
SPECS-EXTENDED/netcdf/netcdf.spec
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@ -12,7 +12,7 @@
Summary: Libraries for the Unidata network Common Data Form
Name: netcdf
Version: 4.9.0
Release: 4%{?dist}
Release: 5%{?dist}
License: NetCDF
Vendor: Microsoft Corporation
Distribution: Mariner
@ -27,7 +27,7 @@ BuildRequires: curl-devel
BuildRequires: doxygen
BuildRequires: gawk
BuildRequires: hdf-static
BuildRequires: hdf5-devel
BuildRequires: hdf5-devel = %{_hdf5_version}
BuildRequires: libtool
BuildRequires: libxml2-devel
BuildRequires: libzstd-devel
@ -77,7 +77,7 @@ NetCDF data is:
Summary: Development files for netcdf
Requires: %{name}%{?_isa} = %{version}-%{release}
Requires: curl-devel%{?_isa}
Requires: hdf5-devel%{?_isa}
Requires: hdf5-devel%{?_isa} >= 1.14.4
Requires: pkgconfig%{?_isa}
%description devel
@ -398,6 +398,10 @@ done
%changelog
- Bumping the release version so that this package is re-built with the newer
1.14.4 hdf5 libraries. This ensures that the matching 1.14.4 .so files Will
be used at run time.
* Thu Aug 10 2023 Archana Choudhary <archana1@microsoft.com> - 4.9.0-4
- Initial CBL-Mariner import from Fedora 37 (license: MIT).
- License verified.

134
SPECS/hdf5/CVE-2021-37501.patch
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@ -1,134 +0,0 @@
From 22917cd03c688a2810adc8571fcf1285a4d23d68 Mon Sep 17 00:00:00 2001
From: Egbert Eich <eich@suse.com>
Date: Thu, 2 Mar 2023 18:17:49 +0100
Subject: [PATCH] Check for overflow when calculating on-disk attribute data
size (#2459)
* Remove duplicate code
Signed-off-by: Egbert Eich <eich@suse.com>
* Add test case for CVE-2021-37501
Bogus sizes in this test case causes the on-disk data size
calculation in H5O__attr_decode() to overflow so that the
calculated size becomes 0. This causes the read to overflow
and h5dump to segfault.
This test case was crafted, the test file was not directly
generated by HDF5.
Test case from:
https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md
---
release_docs/RELEASE.txt | 13 +++++++++++++
src/H5Oattr.c | 7 +++----
tools/test/h5dump/CMakeTests.cmake | 5 +++++
tools/test/h5dump/testh5dump.sh.in | 14 ++++++++++++++
tools/testfiles/tCVE-2021-37501_attr_decode.h5 | Bin 0 -> 48544 bytes
5 files changed, 35 insertions(+), 4 deletions(-)
create mode 100644 tools/testfiles/tCVE-2021-37501_attr_decode.h5
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 1a93f89307..3d9336dc4b 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -635,6 +635,19 @@ Bug Fixes since HDF5-1.12.0 release
Library
-------
+ - Fix CVE-2021-37501 / GHSA-rfgw-5vq3-wrjf
+
+ Check for overflow when calculating on-disk attribute data size.
+
+ A bogus hdf5 file may contain dataspace messages with sizes
+ which lead to the on-disk data sizes to exceed what is addressable.
+ When calculating the size, make sure, the multiplication does not
+ overflow.
+ The test case was crafted in a way that the overflow caused the
+ size to be 0.
+
+ (EFE - 2023/02/11 GH-2458)
+
- Fixed CVE-2018-14460
The tool h5repack produced a segfault when the rank in dataspace
diff --git a/src/H5Oattr.c b/src/H5Oattr.c
index ac643eafac0..cb06f25a725 100644
--- a/src/H5Oattr.c
+++ b/src/H5Oattr.c
@@ -221,10 +221,6 @@ H5O__attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, u
else
p += attr->shared->ds_size;
- /* Get the datatype's size */
- if (0 == (dt_size = H5T_get_size(attr->shared->dt)))
- HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, NULL, "unable to get datatype size")
-
/* Get the datatype & dataspace sizes */
if (0 == (dt_size = H5T_get_size(attr->shared->dt)))
HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, NULL, "unable to get datatype size")
@@ -234,6 +230,9 @@ H5O__attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, u
/* Compute the size of the data */
H5_CHECKED_ASSIGN(attr->shared->data_size, size_t, ds_size * (hsize_t)dt_size, hsize_t);
+ /* Check if multiplication has overflown */
+ if ((attr->shared->data_size / dt_size) != ds_size)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_OVERFLOW, NULL, "data size exceeds addressable range")
/* Go get the data */
if (attr->shared->data_size) {
diff --git a/tools/test/h5dump/CMakeTests.cmake b/tools/test/h5dump/CMakeTests.cmake
index 2505e847bc6..be1a414fce7 100644
--- a/tools/test/h5dump/CMakeTests.cmake
+++ b/tools/test/h5dump/CMakeTests.cmake
@@ -339,6 +339,7 @@
${HDF5_TOOLS_DIR}/testfiles/tCVE_2018_11206_fill_old.h5
${HDF5_TOOLS_DIR}/testfiles/tCVE_2018_11206_fill_new.h5
${HDF5_TOOLS_DIR}/testfiles/zerodim.h5
+ ${HDF5_TOOLS_DIR}/testfiles/tCVE-2021-37501_attr_decode.h5
#STD_REF_OBJ files
${HDF5_TOOLS_DIR}/testfiles/trefer_attr.h5
${HDF5_TOOLS_DIR}/testfiles/trefer_compat.h5
@@ -1187,6 +1188,10 @@
ADD_H5_TEST (tCVE_2018_11206_fill_old 1 tCVE_2018_11206_fill_old.h5)
ADD_H5_TEST (tCVE_2018_11206_fill_new 1 tCVE_2018_11206_fill_new.h5)
+ # test to verify fix for CVE-2021-37501: multiplication overflow in H5O__attr_decode()
+ # https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.assets/poc
+ ADD_H5_TEST (tCVE-2021-37501_attr_decode 1 tCVE-2021-37501_attr_decode.h5)
+
##############################################################################
### P L U G I N T E S T S
##############################################################################
diff --git a/tools/test/h5dump/testh5dump.sh.in b/tools/test/h5dump/testh5dump.sh.in
index 5d7ff8828a1..899bd33db75 100644
--- a/tools/test/h5dump/testh5dump.sh.in
+++ b/tools/test/h5dump/testh5dump.sh.in
@@ -183,6 +183,16 @@ $SRC_H5DUMP_TESTFILES/tvms.h5
$SRC_H5DUMP_TESTFILES/err_attr_dspace.h5
$SRC_H5DUMP_TESTFILES/tCVE_2018_11206_fill_old.h5
$SRC_H5DUMP_TESTFILES/tCVE_2018_11206_fill_new.h5
+<<<<<<< HEAD
+=======
+$SRC_H5DUMP_TESTFILES/tCVE-2021-37501_attr_decode.h5
+$SRC_H5DUMP_TESTFILES/tst_onion_objs.h5
+$SRC_H5DUMP_TESTFILES/tst_onion_objs.h5.onion
+$SRC_H5DUMP_TESTFILES/tst_onion_dset_ext.h5
+$SRC_H5DUMP_TESTFILES/tst_onion_dset_ext.h5.onion
+$SRC_H5DUMP_TESTFILES/tst_onion_dset_1d.h5
+$SRC_H5DUMP_TESTFILES/tst_onion_dset_1d.h5.onion
+>>>>>>> b16ec83... Check for overflow when calculating on-disk attribute data size (#2459)
"
LIST_OTHER_TEST_FILES="
@@ -1485,6 +1495,10 @@ TOOLTEST err_attr_dspace.ddl err_attr_dspace.h5
TOOLTEST_FAIL tCVE_2018_11206_fill_old.h5
TOOLTEST_FAIL tCVE_2018_11206_fill_new.h5
+# test to verify fix for CVE-2021-37501: multiplication overflow in H5O__attr_decode()
+# https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.assets/poc
+TOOLTEST_FAIL tCVE-2021-37501_attr_decode.h5
+
# Clean up temporary files/directories
CLEAN_TESTFILES_AND_TESTDIR

20
SPECS/hdf5/hdf5-LD_LIBRARY_PATH.patch
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@ -1,20 +0,0 @@
--- hdf5-1.12.0/src/Makefile.am~ 2020-02-29 00:29:58.000000000 +0100
+++ hdf5-1.12.0/src/Makefile.am 2021-02-26 16:10:03.612252484 +0100
@@ -156,8 +156,6 @@
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT)
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5detect$(EXEEXT) $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)
@@ -168,8 +166,6 @@
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)

183
SPECS/hdf5/hdf5-build.patch
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@ -1,8 +1,7 @@
diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in
index f29739a..fc9cddb 100644
--- a/java/examples/datasets/JavaDatasetExample.sh.in
+++ b/java/examples/datasets/JavaDatasetExample.sh.in
@@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
diff -ruN a/HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in b/HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in
--- a/HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in
+++ b/HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in
@@ -40,7 +40,7 @@
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/datasets"
@ -11,50 +10,22 @@ index f29739a..fc9cddb 100644
TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am
index 41a914b..195201a 100644
--- a/java/examples/datasets/Makefile.am
+++ b/java/examples/datasets/Makefile.am
@@ -26,7 +26,7 @@ classes:
diff -ruN a/HDF5Examples/JAVA/H5D/Makefile.am b/HDF5Examples/JAVA/H5D/Makefile.am
--- a/HDF5Examples/JAVA/H5D/Makefile.am
+++ b/HDF5Examples/JAVA/H5D/Makefile.am
@@ -26,7 +26,7 @@
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/datasets
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)datasets.jar
diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in
index e26d8c0..f6a9d87 100644
--- a/java/examples/datatypes/JavaDatatypeExample.sh.in
+++ b/java/examples/datatypes/JavaDatatypeExample.sh.in
@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/datatypes"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am
index 90790f7..450edef 100644
--- a/java/examples/datatypes/Makefile.am
+++ b/java/examples/datatypes/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/datatypes
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)datatypes.jar
diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index 3b0e9d1..416c69f 100644
--- a/java/examples/groups/JavaGroupExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -37,7 +37,7 @@ BLDDIR="."
diff -ruN a/HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in b/HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in
--- a/HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in
+++ b/HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in
@@ -38,7 +38,7 @@
BLDLIBDIR="$BLDDIR/testlibs"
BLDITERDIR="./groups"
HDFTEST_HOME="$top_srcdir/java/examples/groups"
@ -63,83 +34,123 @@ index 3b0e9d1..416c69f 100644
TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
test -d $BLDITERDIR || mkdir -p $BLDITERDIR
diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am
index bfde9ae..f48a5b9 100644
--- a/java/examples/groups/Makefile.am
+++ b/java/examples/groups/Makefile.am
@@ -26,7 +26,7 @@ classes:
diff -ruN a/HDF5Examples/JAVA/H5G/Makefile.am b/HDF5Examples/JAVA/H5G/Makefile.am
--- a/HDF5Examples/JAVA/H5G/Makefile.am
+++ b/HDF5Examples/JAVA/H5G/Makefile.am
@@ -26,7 +26,7 @@
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/groups
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)groups.jar
diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
index db741e5..d0ba65d 100644
--- a/java/examples/intro/JavaIntroExample.sh.in
+++ b/java/examples/intro/JavaIntroExample.sh.in
@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
diff -ruN a/HDF5Examples/JAVA/H5J/Makefile.am b/HDF5Examples/JAVA/H5J/Makefile.am
--- a/HDF5Examples/JAVA/H5J/Makefile.am
+++ b/HDF5Examples/JAVA/H5J/Makefile.am
@@ -20,7 +20,7 @@
$(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/intro
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)intro.jar
diff -ruN a/HDF5Examples/JAVA/H5J/runExample.sh.in b/HDF5Examples/JAVA/H5J/runExample.sh.in
--- a/HDF5Examples/JAVA/H5J/runExample.sh.in
+++ b/HDF5Examples/JAVA/H5J/runExample.sh.in
@@ -35,7 +35,7 @@
BLDLIBDIR="./lib"
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/intro"
HDFTEST_HOME="$top_srcdir/JAVA/intro"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am
index 7d1aeab..01a10c9 100644
--- a/java/examples/intro/Makefile.am
+++ b/java/examples/intro/Makefile.am
@@ -26,7 +26,7 @@ classes:
diff -ruN a/HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in b/HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in
--- a/HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in
+++ b/HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in
@@ -37,7 +37,7 @@
BLDDIR="."
BLDLIBDIR="$BLDDIR/testlibs"
HDFTEST_HOME="$top_srcdir/java/examples/datatypes"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff -ruN a/HDF5Examples/JAVA/H5T/Makefile.am b/HDF5Examples/JAVA/H5T/Makefile.am
--- a/HDF5Examples/JAVA/H5T/Makefile.am
+++ b/HDF5Examples/JAVA/H5T/Makefile.am
@@ -26,7 +26,7 @@
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = examples/intro
pkgpath = examples/datatypes
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)intro.jar
diff --git a/java/src/Makefile.am b/java/src/Makefile.am
index 98630e6..fd8d057 100644
jarfile = jar$(PACKAGE_TARNAME)datatypes.jar
diff -ruN a/java/src/Makefile.am b/java/src/Makefile.am
--- a/java/src/Makefile.am
+++ b/java/src/Makefile.am
@@ -32,8 +32,8 @@ JAVAROOT = .classes
@@ -32,7 +32,7 @@
classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
-jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
-hdf5_javadir = $(libdir)
+jarfile = $(PACKAGE_TARNAME).jar
+hdf5_javadir = $(prefix)/lib/java
hdf5_javadir = $(libdir)
pkgpath = hdf/hdf5lib
CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH
diff --git a/java/test/Makefile.am b/java/test/Makefile.am
index 08e79e3..b336c2f 100644
--- a/java/test/Makefile.am
+++ b/java/test/Makefile.am
@@ -26,7 +26,7 @@ classes:
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = test
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)test.jar
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 39db296..83d6c7c 100644
diff -ruN a/java/src/Makefile.in b/java/src/Makefile.in
--- a/java/src/Makefile.in
+++ b/java/src/Makefile.in
@@ -647,7 +647,7 @@
JAVA_API = yes
SUBDIRS = jni
JAVAROOT = .classes
-jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+jarfile = $(PACKAGE_TARNAME).jar
hdf5_javadir = $(libdir)
pkgpath = hdf/hdf5lib
CLASSPATH_ENV = CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$$CLASSPATH
diff -ruN a/java/test/junit.sh.in b/java/test/junit.sh.in
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -47,7 +47,7 @@ BLDLIBDIR="$BLDDIR/testlibs"
@@ -48,7 +48,7 @@
HDFTEST_HOME="$top_srcdir/java/test"
TOOLS_TESTFILES="$top_srcdir/tools/testfiles"
DUMP_TESTFILES="$top_srcdir/tools/test/h5dump/testfiles"
-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
+JARFILE=@PACKAGE_TARNAME@.jar
TESTJARFILE=jar@PACKAGE_TARNAME@test.jar
test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
diff -ruN a/java/test/Makefile.am b/java/test/Makefile.am
--- a/java/test/Makefile.am
+++ b/java/test/Makefile.am
@@ -26,7 +26,7 @@
test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
pkgpath = test
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)test.jar
diff -ruN a/java/test/Makefile.in b/java/test/Makefile.in
--- a/java/test/Makefile.in
+++ b/java/test/Makefile.in
@@ -769,7 +769,7 @@
JAVA_API = yes
JAVAROOT = .classes
pkgpath = test
-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+hdfjarfile = $(PACKAGE_TARNAME).jar
CLASSPATH_ENV = CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH
jarfile = jar$(PACKAGE_TARNAME)test.jar
TESTPACKAGE =

37
SPECS/hdf5/hdf5-gfortran12.patch
Просмотреть файл

@ -1,37 +0,0 @@
commit 3ea6f8c17228d2629e419563138a6180bc4a5a6a
Author: Orion Poplawski <orion@nwra.com>
Date: Sun Jan 30 15:21:08 2022 -0700
Mark minusone as a PARAMETER in tH5A_1_8.F90.
diff --git a/fortran/test/tH5A_1_8.F90 b/fortran/test/tH5A_1_8.F90
index 4e02c58a39..c2f8e9984a 100644
--- a/fortran/test/tH5A_1_8.F90
+++ b/fortran/test/tH5A_1_8.F90
@@ -776,7 +776,7 @@ SUBROUTINE test_attr_info_by_idx(new_format, fcpl, fapl, total_error)
INTEGER :: Input1
INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T
- INTEGER :: minusone = -1
+ INTEGER, PARAMETER :: minusone = -1
INTEGER(HSIZE_T) :: htmp
data_dims = 0
@@ -1427,7 +1427,7 @@ SUBROUTINE test_attr_delete_by_idx(new_format, fcpl, fapl, total_error)
INTEGER :: u ! Local index variable
INTEGER :: Input1
INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T
- INTEGER :: minusone = -1
+ INTEGER, PARAMETER :: minusone = -1
data_dims = 0
@@ -2268,7 +2268,7 @@ SUBROUTINE test_attr_corder_create_basic( fcpl, fapl, total_error )
INTEGER :: error
INTEGER :: crt_order_flags
- INTEGER :: minusone = -1
+ INTEGER, PARAMETER :: minusone = -1
! Output message about test being performed
! WRITE(*,*) " - Testing Basic Code for Attributes with Creation Order Info"

52
SPECS/hdf5/hdf5-wrappers.patch
Просмотреть файл

@ -1,7 +1,7 @@
diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
--- hdf5-1.10.7/bin/h5cc.in.wrappers 2020-10-07 20:24:29.127283333 -0600
+++ hdf5-1.10.7/bin/h5cc.in 2020-10-07 20:27:05.289536904 -0600
@@ -89,10 +89,10 @@ CLINKERBASE="@CC@"
diff -ruN a/bin/h5cc.in b/bin/h5cc.in
--- a/bin/h5cc.in
+++ b/bin/h5cc.in
@@ -87,10 +87,10 @@
# 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.
@ -15,7 +15,7 @@ diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
CC="${HDF5_CC:-$CCBASE}"
CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
@@ -105,7 +105,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
@@ -103,7 +103,8 @@
# available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result
# in link errors.
@ -25,7 +25,7 @@ diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else
@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then
@@ -380,7 +381,7 @@
# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
# from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags.
@ -34,10 +34,10 @@ diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
status=$?
fi
diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
--- hdf5-1.10.7/c++/src/h5c++.in.wrappers 2020-08-27 21:38:23.000000000 -0600
+++ hdf5-1.10.7/c++/src/h5c++.in 2020-10-07 20:24:29.126283325 -0600
@@ -87,10 +87,10 @@ CXXLINKERBASE="@CXX@"
diff -ruN a/c++/src/h5c++.in b/c++/src/h5c++.in
--- a/c++/src/h5c++.in
+++ b/c++/src/h5c++.in
@@ -85,10 +85,10 @@
# 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.
@ -50,8 +50,8 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
+H5BLD_LIBS=
CXX="${HDF5_CXX:-$CXXBASE}"
CXXLINKER="${HDF5_CLINKER:-$CXXLINKERBASE}"
@@ -103,7 +103,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
CXXLINKER="${HDF5_CXXLINKER:-$CXXLINKERBASE}"
@@ -101,7 +101,8 @@
# available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result
# in link errors.
@ -61,7 +61,7 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else
@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then
@@ -372,7 +373,7 @@
# from the hdf5 build. The order of the flags is intended to give precedence
# to the user's flags.
@ -70,16 +70,15 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
status=$?
fi
diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.in
--- hdf5-1.10.7/fortran/src/h5fc.in.wrappers 2020-08-27 21:38:23.000000000 -0600
+++ hdf5-1.10.7/fortran/src/h5fc.in 2020-10-07 20:25:53.793962985 -0600
@@ -83,11 +83,11 @@ FLINKERBASE="@FC@"
# libraries in $link_args, followed by any external library paths and libraries
diff -ruN a/fortran/src/h5fc.in b/fortran/src/h5fc.in
--- a/fortran/src/h5fc.in
+++ b/fortran/src/h5fc.in
@@ -83,10 +83,10 @@
# from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
# The order of the flags is intended to give precedence to the user's flags.
-H5BLD_FCFLAGS="@AM_FCFLAGS@ @FCFLAGS@"
+H5BLD_FCFLAGS=
F9XMODFLAG="@F9XMODFLAG@"
H5BLD_FCFLAGS="@AM_FCFLAGS@ @FCFLAGS@"
-F9XMODFLAG="@F9XMODFLAG@"
+F9XMODFLAG=
F9XSUFFIXFLAG="@F9XSUFFIXFLAG@"
-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
-H5BLD_LIBS="@LIBS@"
@ -88,7 +87,7 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i
FC="${HDF5_FC:-$FCBASE}"
FLINKER="${HDF5_FLINKER:-$FLINKERBASE}"
@@ -99,7 +99,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
@@ -98,7 +98,8 @@
# available library is shared, it will be used by default. The user can
# override either default, although choosing an unavailable library will result
# in link errors.
@ -98,12 +97,3 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i
if test "${STATIC_AVAILABLE}" = "yes"; then
USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
else
@@ -363,7 +364,7 @@ if test "x$do_link" = "xyes"; then
# libraries in $link_args, followed by any external library 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.
- $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args $shared_link
+ $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args
status=$?
fi

8
SPECS/hdf5/hdf5.signatures.json
Просмотреть файл

@ -1,6 +1,6 @@
{
"Signatures": {
"h5comp": "d0d40ba5b894f9fa1e230cbf123120243cb3aa58c85fa563eb88742d97744c2b",
"hdf5-1.12.1.tar.bz2": "aaf9f532b3eda83d3d3adc9f8b40a9b763152218fa45349c3bc77502ca1f8f1c"
}
"Signatures": {
"h5comp": "d0d40ba5b894f9fa1e230cbf123120243cb3aa58c85fa563eb88742d97744c2b",
"hdf5-1.14.4-2.tar.gz": "618934b9d45e34f328393e1fde73a8a67e973f8e5a6bae8b609d098a84cb0efe"
}
}

61
SPECS/hdf5/hdf5.spec
Просмотреть файл

@ -1,6 +1,7 @@
%global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d)
%define version_main %(echo %{version} | cut -d. -f-2)
%global so_version 200
%global so_version_1 310
%global so_version_2 311
%global with_mpich 0
%global with_openmpi 0
%if %{with_mpich}
@ -11,24 +12,17 @@
%endif
Summary: A general purpose library and file format for storing scientific data
Name: hdf5
Version: 1.12.1
Release: 13%{?dist}
Version: 1.14.4
Release: 1%{?dist}
License: BSD
Vendor: Microsoft Corporation
Distribution: Mariner
URL: https://portal.hdfgroup.org/display/HDF5/HDF5
Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%{version_main}/hdf5-%{version}/src/hdf5-%{version}.tar.bz2
Source0: https://github.com/hdfgroup/hdf5/releases/download/%{name}_%{version}.2/%{name}-%{version}-2.tar.gz
Source1: h5comp
Patch0: hdf5-LD_LIBRARY_PATH.patch
# Fix fortran build with gcc 12
# https://github.com/HDFGroup/hdf5/pull/1412
Patch1: hdf5-gfortran12.patch
Patch3: hdf5-build.patch
# Remove Fedora build flags from h5cc/h5c++/h5fc
# https://bugzilla.redhat.com/show_bug.cgi?id=1794625
Patch5: hdf5-wrappers.patch
Patch6: CVE-2021-37501.patch
# For patches/rpath
Patch0: hdf5-build.patch
Patch1: hdf5-wrappers.patch
# For patches/rpath
BuildRequires: automake
# Needed for mpi tests
@ -133,7 +127,7 @@ HDF5 parallel openmpi static libraries
%prep
%autosetup -p1
%autosetup -p1 -n %{name}-%{version}-2
# Force shared by default for compiler wrappers (bug #1266645)
sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in
@ -150,11 +144,22 @@ sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags
--enable-hl \\\
--enable-shared \\\
--with-szlib \\\
--enable-mirror-vfd \\\
%{nil}
# --enable-cxx and --enable-parallel flags are incompatible
# --with-mpe=DIR Use MPE instrumentation [default=no]
# --enable-cxx/fortran/parallel and --enable-threadsafe flags are incompatible
# temporarily disable _FLOAT16 for ARM64 until a fix is checked-in.
# See:
# - https://github.com/HDFGroup/hdf5/pull/4495
# - https://github.com/HDFGroup/hdf5/pull/4507
%ifarch aarch64
%global disable_float16 \\\
--disable-nonstandard-feature-float16 \\\
%{nil}
%endif
#Serial build
export CC=gcc
export CXX=g++
@ -166,6 +171,8 @@ ln -s ../configure .
%configure \
%{configure_opts} \
--enable-cxx \
--enable-hlgiftools \
%{disable_float16} \
--with-default-plugindir=%{_libdir}/hdf5/plugin
sed -i -e 's| -shared | -Wl,--as-needed\0|g' libtool
sed -r -i 's|^prefix=/usr|prefix=%{buildroot}/usr|' java/test/junit.sh
@ -273,16 +280,18 @@ done
%files
%license COPYING
%doc MANIFEST README.txt release_docs/RELEASE.txt
%doc README.md release_docs/RELEASE.txt
%doc release_docs/HISTORY*.txt
%{_bindir}/gif2h5
%{_bindir}/h52gif
%{_bindir}/h5clear
%{_bindir}/h5copy
%{_bindir}/h5debug
%{_bindir}/h5delete
%{_bindir}/h5diff
%{_bindir}/h5dump
%{_bindir}/h5format_convert
%{_bindir}/h5fuse
%{_bindir}/h5import
%{_bindir}/h5jam
%{_bindir}/h5ls
@ -296,12 +305,12 @@ done
%{_bindir}/mirror_server
%{_bindir}/mirror_server_stop
%{_libdir}/hdf5/
%{_libdir}/libhdf5.so.%{so_version}*
%{_libdir}/libhdf5_cpp.so.%{so_version}*
%{_libdir}/libhdf5_fortran.so.%{so_version}*
%{_libdir}/libhdf5hl_fortran.so.%{so_version}*
%{_libdir}/libhdf5_hl.so.%{so_version}*
%{_libdir}/libhdf5_hl_cpp.so.%{so_version}*
%{_libdir}/libhdf5.so.%{so_version_2}*
%{_libdir}/libhdf5_cpp.so.%{so_version_1}*
%{_libdir}/libhdf5_fortran.so.%{so_version_2}*
%{_libdir}/libhdf5hl_fortran.so.%{so_version_1}*
%{_libdir}/libhdf5_hl.so.%{so_version_1}*
%{_libdir}/libhdf5_hl_cpp.so.%{so_version_1}*
%files devel
%{macrosdir}/macros.hdf5
@ -310,6 +319,7 @@ done
%{_bindir}/h5fc*
%{_bindir}/h5redeploy
%{_includedir}/*.h
%{_includedir}/*.inc
%{_libdir}/*.so
%{_libdir}/*.settings
%{_fmoddir}/*.mod
@ -347,7 +357,7 @@ done
%{_libdir}/mpich/bin/mirror_server_stop
%{_libdir}/mpich/bin/ph5diff
%{_libdir}/mpich/hdf5/
%{_libdir}/mpich/lib/*.so.%{so_version}*
%{_libdir}/mpich/lib/*.so.%{so_version_1}*
%files mpich-devel
%{_includedir}/mpich-%{_arch}
@ -391,7 +401,7 @@ done
%{_libdir}/openmpi/bin/mirror_server_stop
%{_libdir}/openmpi/bin/ph5diff
%{_libdir}/openmpi/hdf5/
%{_libdir}/openmpi/lib/*.so.%{so_version}*
%{_libdir}/openmpi/lib/*.so.%{so_version_1}*
%files openmpi-devel
%{_includedir}/openmpi-%{_arch}
@ -410,6 +420,9 @@ done
%changelog
* Mon May 20 2024 George Mileka <gmileka@microsoft.com> - 1.14.4-1
- Upgrade to 1.14.4 - Fix critical CVEs
* Thu Oct 19 2023 Jon Slobodzian <joslobo@microsoft.com> - 1.12.1-13
- Patch hdf5 for CVE-2021-37501.

11
SPECS/python-h5py/python-h5py.spec
Просмотреть файл

@ -13,7 +13,7 @@ simplifies the process of reading and writing data from Python.
Summary: A Python interface to the HDF5 library
Name: h5py
Version: 3.7.0
Release: 4%{?dist}
Release: 5%{?dist}
License: BSD
Vendor: Microsoft Corporation
Distribution: Mariner
@ -24,7 +24,7 @@ Source0: https://files.pythonhosted.org/packages/source/h/h5py/h5py-%{ver
# in F-36
Patch0: h5py-3.7.0-ppc-float128.patch
BuildRequires: gcc
BuildRequires: hdf5-devel
BuildRequires: hdf5-devel >= 1.14.4
BuildRequires: liblzf-devel
BuildRequires: python%{python3_pkgversion}-Cython >= 0.23
BuildRequires: python%{python3_pkgversion}-cached_property
@ -41,7 +41,7 @@ BuildRequires: python%{python3_pkgversion}-sphinx
%package -n python%{python3_pkgversion}-h5py
%{?python_provide:%python_provide python%{python3_pkgversion}-h5py}
Summary: %{summary}
Requires: hdf5
Requires: hdf5 >= 1.14.4
Requires: python%{python3_pkgversion}-cached_property
Requires: python%{python3_pkgversion}-numpy >= 1.7
Requires: python%{python3_pkgversion}-six
@ -92,6 +92,11 @@ cd -
%{python3_sitearch}/%{name}-%{version}-*.egg-info
%changelog
* Mon May 20 2024 George Mileka <gmileka@microsoft.com> - 3.7.0-5
- Bumping the release version so that this package is re-built with the newer
1.14.4 hdf5 libraries. This ensures that the matching 1.14.4 .so files Will
be used at run time.
* Tue Nov 01 2022 Riken Maharjan <rmaharjan@microsoft.com> - 3.7.0-4
- License verified
- Initial CBL-Mariner import from Fedora 37 (license: MIT).

4
cgmanifest.json
Просмотреть файл

@ -5210,8 +5210,8 @@
"type": "other",
"other": {
"name": "hdf5",
"version": "1.12.1",
"downloadUrl": "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.bz2"
"version": "1.14.4",
"downloadUrl": "https://github.com/hdfgroup/hdf5/releases/download/hdf5_1.14.4.2/hdf5-1.14.4-2.tar.gz"
}
}
},