[med-svn] [libbiod] 01/01: Fix some deprecated imports
Andreas Tille
tille at debian.org
Sun Feb 26 06:51:24 UTC 2017
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tille pushed a commit to branch master
in repository libbiod.
commit f1fce2d9ecc631246f73cc4b2c01a19cc13e8ed7
Author: Andreas Tille <tille at debian.org>
Date: Sun Feb 26 07:51:11 2017 +0100
Fix some deprecated imports
---
debian/patches/fix_deprecated_imports.patch | 81 +++++++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 82 insertions(+)
diff --git a/debian/patches/fix_deprecated_imports.patch b/debian/patches/fix_deprecated_imports.patch
new file mode 100644
index 0000000..d0d6b8f
--- /dev/null
+++ b/debian/patches/fix_deprecated_imports.patch
@@ -0,0 +1,81 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 25 Feb 2017 20:34:50 +0100
+Description: Fix deprecated imports
+
+--- a/bio/bam/bai/indexing.d
++++ b/bio/bam/bai/indexing.d
+@@ -35,7 +35,7 @@ import std.array;
+ import std.algorithm;
+ import std.system;
+ import std.exception;
+-import std.c.string;
++import core.std.c.string;
+
+ // Suppose we have an alignment which covers bases on a reference,
+ // starting from one position and ending at another position.
+--- a/bio/bam/thirdparty/msgpack.d
++++ b/bio/bam/thirdparty/msgpack.d
+@@ -82,7 +82,7 @@ static if (real.sizeof == double.sizeof)
+ import std.numeric;
+ }
+
+-version(unittest) import std.file, std.c.string;
++version(unittest) import std.file, core.std.c.string;
+
+
+ @trusted:
+--- a/bio/bam/utils/array.d
++++ b/bio/bam/utils/array.d
+@@ -23,7 +23,7 @@
+ */
+ module bio.bam.utils.array;
+
+-import std.c.string;
++import core.std.c.string;
+ import std.traits;
+
+ /// Modifies array in-place so that $(D slice) is replaced by
+--- a/bio/core/utils/bylinefast.d
++++ b/bio/core/utils/bylinefast.d
+@@ -6,7 +6,7 @@ module bio.core.utils.bylinefast;
+
+ import std.stdio;
+ import std.string: indexOf;
+-import std.c.string: memmove;
++import core.std.c.string: memmove;
+
+ /**
+ Reads by line in an efficient way (10 times faster than File.byLine from std.stdio).
+--- a/bio/core/utils/format.d
++++ b/bio/core/utils/format.d
+@@ -34,8 +34,8 @@
+ */
+ module bio.core.utils.format;
+
+-import std.c.stdio;
+-import std.c.stdlib;
++import core.stdc.stdio;
++import core.stdc.stdlib;
+ import std.string;
+ import std.traits;
+ import std.array;
+@@ -161,7 +161,7 @@ private {
+ if (isSomeString!T)
+ {
+ auto str = cast(const(char)[])s;
+- std.c.string.memcpy(sink, str.ptr, str.length);
++ core.std.c.string.memcpy(sink, str.ptr, str.length);
+ sink += str.length;
+ }
+
+--- a/bio/sam/reader.d
++++ b/bio/sam/reader.d
+@@ -49,7 +49,7 @@ import std.typecons;
+ import std.parallelism;
+ import std.process;
+ import std.exception;
+-import std.c.string;
++import core.std.c.string;
+
+ BamRead _parseSamRecord(Tuple!(char[], SamReader, OutBuffer) t) {
+ auto r = parseAlignmentLine(cast(string)t[0], t[1]._header, t[2]);
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..65d85ea
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_deprecated_imports.patch
--
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