Verified Commit 2cf5a653 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

apply "size_t is uint on 32-bits platform" patch

parent 1116d37d

debian/changelog

+5 −0
Original line number Diff line number Diff line 
libbiod (0.2.1-2) UNRELEASED; urgency=medium



  [ Andreas Tille ]

  * debhelper 12

  * Standards-Version: 4.3.0



  [ Michael R. Crusoe ]

  * Apply patch from upstream: "size_t is uint on 32-bits platform"

    Closes: #912077



 -- Andreas Tille <tille@debian.org>  Fri, 18 Jan 2019 09:31:55 +0100



libbiod (0.2.1-1) unstable; urgency=medium

debian/patches/003_modernize_meson.patch

+5 −7
Original line number Diff line number Diff line
@@ -8,10 +8,8 @@ Origin: https://github.com/biod/BioD/pull/38/commits/c059165f359327c5a67aadabe18 
 meson.build | 131 +++++++++++++++++++++++++++-------------------------

 1 file changed, 67 insertions(+), 64 deletions(-)



diff --git a/meson.build b/meson.build

index 88f3bcc7..9d308efd 100644

--- a/meson.build

+++ b/meson.build

--- libbiod.orig/meson.build

+++ libbiod/meson.build

@@ -1,6 +1,9 @@

-project('BioD', 'd')

+project('BioD', 'd',
@@ -24,7 +22,7 @@ index 88f3bcc7..9d308efd 100644 
 project_soversion = '0'

 

 src_dir = include_directories('.')

@@ -16,79 +19,83 @@ zlib_dep = dependency('zlib')

@@ -16,79 +19,83 @@

 # Sources

 #

 biod_src = [
@@ -163,7 +161,7 @@ index 88f3bcc7..9d308efd 100644 
 

 bio2_src = [

     'bio2/bam/header.d',

@@ -114,18 +121,16 @@ install_subdir('bio2/', install_dir: 'include/d/bio/')

@@ -114,18 +121,16 @@

 # Library and pkg-config

 #

 biod_lib = library('biod',
@@ -184,7 +182,7 @@ index 88f3bcc7..9d308efd 100644 
               description: 'Bioinformatics library in D (utils for working with SAM, BAM, SFF formats).'

 )

 

@@ -134,11 +139,9 @@ pkgc.generate(name: 'biod',

@@ -134,11 +139,9 @@

 #

 biod_test_exe = executable('biod_test',

     ['test/unittests.d',

debian/patches/25068c1c439515a48f392bd85754a3465597c419.patch

0 → 100644
+32 −0
Original line number Diff line number Diff line 
From 25068c1c439515a48f392bd85754a3465597c419 Mon Sep 17 00:00:00 2001

From: Pjotr Prins <pjotr.guix@thebird.nl>

Date: Mon, 29 Oct 2018 11:23:07 -0500

Subject: [PATCH] size_t is uint on 32-bits platform. Fixes #43. Thanks

 @tillea.



---

 bio2/bgzf.d | 2 +-

 1 file changed, 1 insertion(+), 1 deletion(-)



--- libbiod.orig/bio2/bgzf.d

+++ libbiod/bio2/bgzf.d

@@ -211,7 +211,7 @@

         f.rawRead(buf);

         f.seek(lastpos);

         if (buf == BGZF_EOF)

-          return tuple(FilePos(),compressed_buf,cast(ulong)0,crc32); // sets fpos to null

+          return tuple(FilePos(),compressed_buf,cast(size_t)0,crc32); // sets fpos to null

       }

       return tuple(FilePos(f.tell()),compressed_buf,cast(size_t)uncompressed_size,crc32);

     } catch (Exception e) { throwBgzfException(e.msg,e.file,e.line); }

--- libbiod.orig/bio2/pileup.d

+++ libbiod/bio2/pileup.d

@@ -89,7 +89,7 @@

   T[] _items;

   RingBufferIndex _head;

   RingBufferIndex _tail;

-  size_t max_size = 0;

+  ulong max_size = 0;

 

   /** initializes round buffer of size $(D n) */

   this(size_t n) {

debian/patches/series

+1 −0
Original line number Diff line number Diff line 
001_fix_unit_tests.patch

002_include_bio2.patch

003_modernize_meson.patch

25068c1c439515a48f392bd85754a3465597c419.patch