[med-svn] [libbiod] 01/01: Fix some deprecated imports

[Andreas Tille]

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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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