[med-svn] [Git][med-team/libsis-base-java][master] 2 commits: Applying a patch to avoid unaligned memory access
Pierre Gruet
gitlab at salsa.debian.org
Mon Dec 14 09:19:45 GMT 2020
Pierre Gruet pushed to branch master at Debian Med / libsis-base-java
Commits:
9379ae50 by Pierre Gruet at 2020-12-14T09:58:14+01:00
Applying a patch to avoid unaligned memory access
- - - - -
f345fc80 by Pierre Gruet at 2020-12-14T10:19:19+01:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/force_use_nio.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-3) unstable; urgency=medium
+
+ * Team upload
+ * Applying a patch to avoid unaligned memory access
+
+ -- Pierre Gruet <pgtdebian at free.fr> Mon, 14 Dec 2020 09:15:58 +0100
+
libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-2) unstable; urgency=medium
* Team upload
=====================================
debian/patches/force_use_nio.patch
=====================================
@@ -0,0 +1,175 @@
+--- a/source/java/ch/systemsx/cisd/base/convert/NativeData.java
++++ b/source/java/ch/systemsx/cisd/base/convert/NativeData.java
+@@ -15,8 +15,6 @@
+
+ import java.nio.ByteBuffer;
+
+-import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities;
+-
+ /**
+ * This class encapsulates native methods to deal with arrays of numbers, converting from numbers to
+ * bytes and bytes to numbers.
+@@ -28,27 +26,10 @@
+ * primitive numbers (int, short, ...)
+ * <p>
+ * Variant interfaces convert only a sub-array.
+- * <p>
+- * The class has optimized methods using jni-libraries for some common platforms and a pure-java
+- * implementation (called <i>javamode</i> if the jni-libraries are not available). If you want to
+- * enforce <i>javamode</i>, you need to pass the property <code>nativedata.javamode=true</code> to
+- * the JRE.
+ */
+ public class NativeData
+ {
+- private static final boolean useNativeLib;
+-
+- static
+- {
+- if (Boolean.getBoolean("nativedata.javamode"))
+- {
+- useNativeLib = false;
+- } else
+- {
+- System.loadLibrary("cisd_nativedata");
+- useNativeLib = true;
+- }
+- }
++ private static final boolean useNativeLib = false;
+
+ /** Size of a <code>short</code> value in <code>byte</code>s. */
+ public final static int SHORT_SIZE = 2;
+--- a/sourceTest/java/ch/systemsx/cisd/base/convert/NativeDataTests.java
++++ b/sourceTest/java/ch/systemsx/cisd/base/convert/NativeDataTests.java
+@@ -162,7 +162,6 @@
+ @Test(dataProvider = "getOfs")
+ public void testLongToByteToLong(int sourceOfs, int targetOfs)
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int sizeOfTarget = 8;
+ final long[] orignalArr = new long[]
+ { -1, 17, 100000, -1000000 };
+@@ -180,7 +179,6 @@
+ @Test(dataProvider = "getOfs")
+ public void testShortToByteToShort(int sourceOfs, int targetOfs)
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int sizeOfTarget = 2;
+ final short[] orignalArr = new short[]
+ { -1, 17, 20000, (short) -50000 };
+@@ -198,7 +196,6 @@
+ @Test(dataProvider = "getOfs")
+ public void testCharToByteToChar(int sourceOfs, int targetOfs)
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int sizeOfTarget = 2;
+ final char[] orignalArr = new char[]
+ { 'c', ';', '\u0222', '\u1000' };
+@@ -216,7 +213,6 @@
+ @Test(dataProvider = "getOfs")
+ public void testFloatToByteToFloat(int sourceOfs, int targetOfs)
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int sizeOfTarget = 4;
+ final float[] orignalArr = new float[]
+ { -1, 17, 3.14159f, -1e6f };
+@@ -234,7 +230,6 @@
+ @Test(dataProvider = "getOfs")
+ public void testDoubleToByteToDouble(int sourceOfs, int targetOfs)
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int sizeOfTarget = 8;
+ final double[] orignalArr = new double[]
+ { -1, 17, 3.14159, -1e42 };
+@@ -252,7 +247,6 @@
+ @Test
+ public void testShortEndianConversion()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final short[] values = new short[]
+ { 1, 2, 4, 8, 16, 256, 512 };
+ final short[] convertedValuesExpected = new short[]
+@@ -266,7 +260,6 @@
+ @Test
+ public void testIntEndianConversion()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int[] values = new int[]
+ { 1, 2, 4, 8, 16, 256, 1 << 16 };
+ final int[] convertedValuesExpected = new int[]
+@@ -280,7 +273,6 @@
+ @Test
+ public void testLongEndianConversion()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final long[] values = new long[]
+ { 1, 2, 4, 8, 16, 256, 1L << 16, 1L << 24 };
+ final long[] convertedValuesExpected = new long[]
+@@ -294,7 +286,6 @@
+ @Test
+ public void testFloatLittleEndianRoundtrip()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final float[] values = new float[]
+ { 1.1f, 2.2f, 3.3f, 1e-25f, 1e25f };
+ final float[] convertedValuesFound =
+@@ -306,7 +297,6 @@
+ @Test
+ public void testFloatBigEndianRoundtrip()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final float[] values = new float[]
+ { 1.1f, 2.2f, 3.3f, 1e-25f, 1e25f };
+ final float[] convertedValuesFound =
+@@ -318,7 +308,6 @@
+ @Test
+ public void testDoubleLittleEndianRoundtrip()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final double[] values = new double[]
+ { 1.1f, 2.2f, 3.3f, 1e-25f, 1e25f };
+ final double[] convertedValuesFound =
+@@ -330,7 +319,6 @@
+ @Test
+ public void testDoubleBigEndianRoundtrip()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final double[] values = new double[]
+ { 1.1, 2.2, 3.3, 1e-25, 1e25 };
+ final double[] convertedValuesFound =
+@@ -342,28 +330,24 @@
+ @Test(expectedExceptions = NullPointerException.class)
+ public void testNPE()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ NativeData.copyByteToLong(null, 0, null, 0, 0, ByteOrder.NATIVE);
+ }
+
+ @Test(expectedExceptions = IndexOutOfBoundsException.class)
+ public void testIOOB()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ NativeData.copyByteToLong(new byte[] {}, -1, new long[] {}, 0, 0, ByteOrder.NATIVE);
+ }
+
+ @Test(expectedExceptions = IndexOutOfBoundsException.class)
+ public void testIOOB2()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ NativeData.copyByteToLong(new byte[] {}, 0, new long[] {}, 10, 0, ByteOrder.NATIVE);
+ }
+
+ @Test
+ public void testPlatformEndiness()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final double[] values = new double[]
+ { 1.1, 2.2, 3.3, 1e-200, 1e200 };
+ final double[] valuesLE =
+@@ -387,7 +371,6 @@
+ @Test
+ public void testFloatToByteNonNativeByteOrderPartialOutputArray()
+ {
+- assertTrue(NativeData.isUseNativeLib());
+ final int sizeOfTarget = 4;
+ final ByteOrder nonNativeByteOrder =
+ (NativeData.getNativeByteOrder() == ByteOrder.LITTLE_ENDIAN) ? ByteOrder.BIG_ENDIAN
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ load_native_debian.patch
skip_testGetLinkInfoDirectory.patch
skip_testGetLinkInfoSymLinkDanglingLink.patch
deactivate_tests_causing_fail_dut_to_commons-io.patch
+force_use_nio.patch
View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/compare/73b8cbe8e70624d7ecacda4d5d3e1329e5f251af...f345fc80c9975037b856122ae9372cd06406e130
--
View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/compare/73b8cbe8e70624d7ecacda4d5d3e1329e5f251af...f345fc80c9975037b856122ae9372cd06406e130
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