Fix build

.travis.yml

@@ -1,3 +1,9 @@
 language: d
-script:
-- rdmd -unittest -d test/unittests.d
+
+os:
+  - linux
+  - osx
+
+d:
+  - dmd
+  - ldc

bio/bam/bai/indexing.d

@@ -30,12 +30,12 @@ import bio.bam.constants;
 import bio.bam.bai.bin;
 import bio.core.bgzf.chunk;
 
-import std.stream;
+import undead.stream;
 import std.array;
 import std.algorithm;
 import std.system;
 import std.exception;
-import std.c.string;
+import core.stdc.string;
 
 // Suppose we have an alignment which covers bases on a reference,
 // starting from one position and ending at another position.

bio/bam/baifile.d

@@ -28,7 +28,7 @@ public import bio.bam.bai.bin;
 import bio.core.bgzf.virtualoffset;
 import bio.bam.constants;
 
-import std.stream;
+import undead.stream;
 import std.system;
 import std.exception;
 import std.algorithm;

bio/bam/randomaccessmanager.d

@@ -50,6 +50,7 @@ import std.traits;
 import std.exception;
 import std.container;
 import std.parallelism;
+static import std.file;
 
 debug {
     import std.stdio;

bio/bam/read.d

@@ -72,7 +72,7 @@ import std.system;
 import std.traits;
 import std.array;
 import std.bitmanip;
-import std.c.stdlib;
+import core.stdc.stdlib;
 
 /**
   Represents single CIGAR operation
@@ -1579,6 +1579,7 @@ unittest {
 
     {
     import std.typecons;
+    static import bio.bam.thirdparty.msgpack;
     auto packer = bio.bam.thirdparty.msgpack.packer(Appender!(ubyte[])());
     read.toMsgpack(packer);
     auto data = packer.stream.data;

bio/bam/reader.d

@@ -94,8 +94,8 @@ class BamReader : IBamSamReader {
       }
       -------------------------------------------
      */
-    this(std.stream.Stream stream, 
-         std.parallelism.TaskPool task_pool = std.parallelism.taskPool) {
+    this(undead.stream.Stream stream,
+         TaskPool task_pool = taskPool) {
         _source_stream = new EndianStream(stream, Endian.littleEndian);
         _task_pool = task_pool;
 

bio/bam/readrange.d

@@ -29,7 +29,7 @@ import bio.bam.reader;
 import bio.core.bgzf.inputstream;
 import bio.core.bgzf.virtualoffset;
 
-import std.stream;
+import undead.stream;
 import std.algorithm;
 import std.system;
 import std.bitmanip;

bio/bam/reference.d

@@ -47,7 +47,7 @@ import bio.bam.region;
 import bio.bam.randomaccessmanager;
 import bio.core.bgzf.virtualoffset;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.array;
 

bio/bam/referenceinfo.d

@@ -23,7 +23,7 @@
 */
 module bio.bam.referenceinfo;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.array;
 

bio/bam/snpcallers/maq.d

@@ -5,7 +5,7 @@ module bio.bam.snpcallers.maq;
  */
 
 import core.stdc.math;
-import std.math : LN2, LN10, isnan;
+import std.math : LN2, LN10, isNaN;
 import std.traits;
 import std.range;
 import std.algorithm;

bio/bam/tagvalue.d

@@ -296,7 +296,7 @@ string injectOpCast() {
     }
 
     cs ~= `(is(T == string)) {` ~
-          `  if (is_string) {`
+          `  if (is_string) {` ~
           `    return bam_typeid == 'Z' ? u.Z : u.H;`~
           `  } else if (is_integer || is_float || is_character) {`~
           `    `~injectSwitchPrimitive("string")~

bio/bam/thirdparty/msgpack.d

@@ -59,7 +59,7 @@ else
 // for Converting Endian using ntohs and ntohl;
 version(Windows)
 {
-    import std.c.windows.winsock;
+    import core.stdc.windows.winsock;
 }
 else
 {
@@ -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.stdc.string;
 
 
 @trusted:
@@ -344,7 +344,7 @@ struct PackerImpl(Stream) if (isOutputRange!(Stream, ubyte) && isOutputRange!(St
      * Params:
      *  withFieldName = serialize class / struct with field name
      */
-    this(bool withFieldName = false)
+    this(bool withFieldName)
     {
         withFieldName_ = withFieldName;
     }
@@ -3145,7 +3145,7 @@ struct Value
      *  type  = the type of value.
      */
     @safe
-    this(Type type = Type.nil)
+    this(Type type)
     {
         this.type = type;
     }
@@ -3617,7 +3617,7 @@ struct Value
                         ret ^= value.toHash();
                     }
                     return ret;
-                } catch assert(0);
+                } catch (Exception) assert(0);
         }
     }
 }
@@ -4656,7 +4656,7 @@ mixin template MessagePackable(Members...)
             if (withFieldName) {
                 packer.beginMap(this.tupleof.length);
                 foreach (i, member; this.tupleof) {
-                    pack(getFieldName!(typeof(this), i));
+                    packer.pack(getFieldName!(typeof(this), i));
                     packer.pack(member);
                 }
             } else {

bio/bam/utils/array.d

@@ -23,7 +23,7 @@
 */
 module bio.bam.utils.array;
 
-import std.c.string;
+import core.stdc.string;
 import std.traits;
 
 /// Modifies array in-place so that $(D slice) is replaced by

bio/bam/writer.d

@@ -35,7 +35,7 @@ import bio.core.utils.stream;
 
 import std.parallelism;
 import std.exception;
-import std.stream;
+import undead.stream;
 import std.traits;
 import std.system;
 import std.algorithm;
@@ -73,7 +73,7 @@ final class BamWriter {
     ///     compression_level  = compression level, must be in range -1..9
     ///     task_pool          = task pool to use for parallel compression
     ///     buffer_size        = size of BgzfOutputStream buffer
-    this(std.stream.Stream stream,
+    this(undead.stream.Stream stream,
          int compression_level=-1,
          std.parallelism.TaskPool task_pool=std.parallelism.taskPool,
          size_t buffer_size=0)

bio/core/bgzf/inputstream.d

@@ -30,7 +30,7 @@ import bio.core.bgzf.chunk;
 import bio.bam.constants;
 import bio.core.utils.roundbuf;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.conv;
 import std.parallelism;

bio/core/bgzf/outputstream.d

@@ -28,13 +28,13 @@ import bio.core.bgzf.compress;
 
 import bio.core.utils.roundbuf;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.parallelism;
 import std.array;
 import std.algorithm : max;
 import std.typecons;
-import std.c.stdlib;
+import core.stdc.stdlib;
 
 alias void delegate(ubyte[], ubyte[]) BlockWriteHandler;
 
@@ -88,7 +88,7 @@ class BgzfOutputStream : Stream {
 
         // 1 extra block to which we can write while n_tasks are executed
         auto comp_buf_size = (2 * n_tasks + 2) * max_block_size;
-        auto p = cast(ubyte*)std.c.stdlib.malloc(comp_buf_size);
+        auto p = cast(ubyte*)core.stdc.stdlib.malloc(comp_buf_size);
         _compression_buffer = p[0 .. comp_buf_size];
         _buffer = _compression_buffer[0 .. block_size];
         _tmp = _compression_buffer[max_block_size .. max_block_size * 2];
@@ -210,7 +210,7 @@ class BgzfOutputStream : Stream {
         _stream.close();
 
         writeable = false;
-        std.c.stdlib.free(_compression_buffer.ptr);
+        core.stdc.stdlib.free(_compression_buffer.ptr);
     }
 
     /// Adds EOF block. This function is called in close() method.

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.stdc.string: memmove;
 
 /**
    Reads by line in an efficient way (10 times faster than File.byLine from std.stdio).

bio/core/utils/format.d

@@ -34,8 +34,9 @@
  */
 module bio.core.utils.format;
 
-import std.c.stdio;
-import std.c.stdlib;
+import core.stdc.stdio;
+import core.stdc.stdlib;
+static import core.stdc.string;
 import std.string;
 import std.traits;
 import std.array;
@@ -161,7 +162,7 @@ private {
         if (isSomeString!T)
     {
         auto str = cast(const(char)[])s;
-        std.c.string.memcpy(sink, str.ptr, str.length);
+        core.stdc.string.memcpy(sink, str.ptr, str.length);
         sink += str.length;
     }
 

bio/core/utils/outbuffer.d

@@ -93,7 +93,7 @@ class OutBuffer {
     /// Responsibility that there's enough capacity is on the user
     void putUnsafe(T)(T bytes) if (is(T == ubyte[])) {
         _heap_ptr[_heap_used .. _heap_used + bytes.length] = bytes[];
-        _heap_used += bytes.length;;
+        _heap_used += bytes.length;
     }
 
     /// ditto

bio/core/utils/stream.d

@@ -1,6 +1,6 @@
 module bio.core.utils.stream;
 
-public import std.stream;
+public import undead.stream;
 import core.stdc.stdio;
 import core.stdc.errno;
 import core.stdc.string;
@@ -15,7 +15,7 @@ version(Posix){
 version(Windows) {
     private import std.file;
     private import std.utf;
-    private import std.c.windows.windows;
+    private import core.stdc.windows.windows;
     extern (Windows) {
         DWORD GetFileType(HANDLE hFile);
     }
@@ -48,7 +48,7 @@ FileMode toFileMode(string mode) {
     return result;
 }
 
-final class File: std.stream.File {
+final class File: undead.stream.File {
     this(string filename, string mode="rb") {
         version (Posix) {
             // Issue 8528 workaround
@@ -135,7 +135,6 @@ final class File: std.stream.File {
                         if (ret <= 0) {
                             size = 0;
                             throw new ReadException("read timeout");
-                            break;
                         }
                     } else {
                         throw new ReadException(to!string(strerror(errno)));

bio/core/utils/switchendianness.d

@@ -1,5 +1,5 @@
 /**
-  (Almost) a copy-paste from std/stream.d
+  (Almost) a copy-paste from undead.stream.d
 */
 module bio.core.utils.switchendianness;