[med-svn] [Git][med-team/libbiod][master] apply "size_t is uint on 32-bits platform" patch

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / libbiod


Commits:
2cf5a653 by Michael R. Crusoe at 2019-01-18T19:29:50Z
apply "size_t is uint on 32-bits platform" patch

- - - - -


4 changed files:

- debian/changelog
- debian/patches/003_modernize_meson.patch
- + debian/patches/25068c1c439515a48f392bd85754a3465597c419.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,13 @@
 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 at debian.org>  Fri, 18 Jan 2019 09:31:55 +0100
 
 libbiod (0.2.1-1) unstable; urgency=medium


=====================================
debian/patches/003_modernize_meson.patch
=====================================
@@ -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
=====================================
@@ -0,0 +1,32 @@
+From 25068c1c439515a48f392bd85754a3465597c419 Mon Sep 17 00:00:00 2001
+From: Pjotr Prins <pjotr.guix at 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
=====================================
@@ -1,3 +1,4 @@
 001_fix_unit_tests.patch
 002_include_bio2.patch
 003_modernize_meson.patch
+25068c1c439515a48f392bd85754a3465597c419.patch



View it on GitLab: https://salsa.debian.org/med-team/libbiod/commit/2cf5a6534a0f72640ae8d0d68a91865e0ecde1c4

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View it on GitLab: https://salsa.debian.org/med-team/libbiod/commit/2cf5a6534a0f72640ae8d0d68a91865e0ecde1c4
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