[med-svn] [Git][med-team/libslow5lib][master] 5 commits: use_debian_packaged_streamvbyte.patch: fix a type error.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Wed Jul 24 23:54:14 BST 2024



Étienne Mollier pushed to branch master at Debian Med / libslow5lib


Commits:
4846c5cd by Étienne Mollier at 2024-07-24T22:31:38+02:00
use_debian_packaged_streamvbyte.patch: fix a type error.

Closes: #1075205

- - - - -
5348f304 by Étienne Mollier at 2024-07-24T22:33:48+02:00
d/control: add myself to uploaders.

- - - - -
6567834c by Étienne Mollier at 2024-07-24T22:34:12+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
95aede79 by Étienne Mollier at 2024-07-24T22:36:43+02:00
d/s/lintian-overrides: flag error caused by t64 transition.

- - - - -
2f58d9e3 by Étienne Mollier at 2024-07-24T22:40:00+02:00
ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/use_debian_packaged_streamvbyte.patch
- + debian/source/lintian-overrides


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libslow5lib (0.7.0+dfsg-3) unstable; urgency=medium
+
+  * use_debian_packaged_streamvbyte.patch: fix a type error. (Closes: #1075205)
+  * d/control: add myself to uploaders.
+  * d/control: declare compliance to standards version 4.7.0.
+  * d/s/lintian-overrides: flag error caused by t64 transition.
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 24 Jul 2024 22:36:50 +0200
+
 libslow5lib (0.7.0+dfsg-2.1) unstable; urgency=medium
 
   * Non-maintainer upload.


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: libslow5lib
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
@@ -15,7 +16,7 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
                python3-setuptools,
                python3-numpy,
                python3-wheel
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/libslow5lib
 Vcs-Git: https://salsa.debian.org/med-team/libslow5lib.git
 Homepage: https://github.com/hasindu2008/slow5lib


=====================================
debian/patches/use_debian_packaged_streamvbyte.patch
=====================================
@@ -1,10 +1,12 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 29 Jun 2022 20:34:40 +0200
 Description: Use Debian packaged streamvbyte library
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Last-Update: 2024-07-24
+Forwarded: not-needed
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -26,7 +26,6 @@ unset(SLOW5_USE_ZSTD CACHE)
+--- libslow5lib.orig/CMakeLists.txt
++++ libslow5lib/CMakeLists.txt
+@@ -26,7 +26,6 @@
  # include_directories(${PROJECT_SOURCE_DIR}/src)
  # include_directories(${PROJECT_SOURCE_DIR}/test)
  include_directories(${PROJECT_SOURCE_DIR}/include)
@@ -12,7 +14,7 @@ Description: Use Debian packaged streamvbyte library
  
  set(slow5_ src/slow5.c)
  set(slow5_idx src/slow5_idx.c)
-@@ -42,7 +41,6 @@ set(slow5_press src/slow5_press.c)
+@@ -42,7 +41,6 @@
  # set(openmp_get_reads examples/random_read_openmp.c)
  # add_executable(slow5exmp ${openmp_get_reads})
  
@@ -20,7 +22,7 @@ Description: Use Debian packaged streamvbyte library
  
  option(SLOW5_LINK_STATIC "libslow5 will create a static lib" OFF) #OFF by default
  if(SLOW5_LINK_STATIC)
-@@ -54,7 +52,7 @@ else()
+@@ -54,7 +52,7 @@
  endif(SLOW5_LINK_STATIC)
  unset(SLOW5_LINK_STATIC CACHE)
  
@@ -29,9 +31,9 @@ Description: Use Debian packaged streamvbyte library
  
  # Build a static lib
  #add_library(slow5 STATIC ${slow5_} ${slow5_idx} ${slow5_misc} ${slow5_press})
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -4,7 +4,7 @@ LIB			= ../lib
+--- libslow5lib.orig/test/Makefile
++++ libslow5lib/test/Makefile
+@@ -4,7 +4,7 @@
  CPPFLAGS	+= -I ../include/ -I $(SRC)/
  #CFLAGS		+= -g -Wall -Werror -Wpedantic -std=c99
  CFLAGS		+= -g -Wall -Werror -std=gnu99
@@ -40,9 +42,9 @@ Description: Use Debian packaged streamvbyte library
  ifeq ($(zstd),1)
  CFLAGS		+= -DSLOW5_USE_ZSTD
  LDFLAGS		+= -lzstd
---- a/src/slow5_press.c
-+++ b/src/slow5_press.c
-@@ -1034,7 +1034,7 @@ static ssize_t fwrite_compress_zlib(stru
+--- libslow5lib.orig/src/slow5_press.c
++++ libslow5lib/src/slow5_press.c
+@@ -1034,7 +1034,7 @@
  static uint8_t *ptr_compress_svb(const uint32_t *ptr, size_t count, size_t *n) {
      uint32_t length = count / sizeof *ptr;
  
@@ -51,7 +53,7 @@ Description: Use Debian packaged streamvbyte library
      uint8_t *out = (uint8_t *) malloc(max_n + sizeof length);
      if (!out) {
          SLOW5_MALLOC_ERROR();
-@@ -1042,7 +1042,7 @@ static uint8_t *ptr_compress_svb(const u
+@@ -1042,7 +1042,7 @@
          return NULL;
      }
  
@@ -60,7 +62,7 @@ Description: Use Debian packaged streamvbyte library
      memcpy(out, &length, sizeof length); /* copy original length of ptr (needed for depress) */
      *n = *n + sizeof length;
      SLOW5_LOG_DEBUG("max svb bytes=%zu\nsvb bytes=%zu\n",
-@@ -1070,7 +1070,7 @@ static uint8_t *ptr_compress_svb_zd(cons
+@@ -1070,7 +1070,7 @@
          slow5_errno = SLOW5_ERR_MEM;
          return NULL;
      }
@@ -69,7 +71,7 @@ Description: Use Debian packaged streamvbyte library
  
  
      SLOW5_LOG_DEBUG("orig bytes=%zu\n", count); /* TESTING */
-@@ -1094,7 +1094,7 @@ static uint32_t *ptr_depress_svb(const u
+@@ -1094,7 +1094,7 @@
      }
  
      size_t bytes_read;
@@ -78,18 +80,18 @@ Description: Use Debian packaged streamvbyte library
          SLOW5_ERROR("Expected streamvbyte_decode to read '%zu' bytes, instead read '%zu' bytes.",
                  count - sizeof length, bytes_read);
          slow5_errno = SLOW5_ERR_PRESS;
-@@ -1122,7 +1122,7 @@ static int16_t *ptr_depress_svb_zd(const
+@@ -1122,7 +1122,7 @@
          slow5_errno = SLOW5_ERR_MEM;
          return NULL;
      }
 -    __slow5_zigzag_delta_decode(diff, orig, length, 0);
-+    zigzag_delta_decode(diff, orig, length, 0);
++    zigzag_delta_decode(diff, (int32_t *)orig, length, 0);
  
      // int16_t *orig = (int16_t *) malloc(length * sizeof *orig);
      // for (int64_t i = 0; i < length; ++ i) {
---- a/setup.py
-+++ b/setup.py
-@@ -18,9 +18,9 @@ include_dirs = []
+--- libslow5lib.orig/setup.py
++++ libslow5lib/setup.py
+@@ -18,9 +18,9 @@
  # for the install.
  try:
      import numpy as np
@@ -101,7 +103,7 @@ Description: Use Debian packaged streamvbyte library
      def np(*args, ** kwargs ):
          import numpy as np
          return np(*args, ** kwargs)
-@@ -38,13 +38,13 @@ except ImportError:
+@@ -38,13 +38,13 @@
  
  sources=['python/pyslow5.pyx', 'src/slow5.c', 'src/slow5_press.c', 'src/slow5_misc.c', 'src/slow5_idx.c',
              'python/slow5threads.c',
@@ -117,7 +119,7 @@ Description: Use Debian packaged streamvbyte library
  extra_compile_args = ['-g', '-Wall', '-O2', '-std=c99']
  # extra_compile_args = []
  # os.environ["CFLAGS"] = '-g -Wall -O2 -std=c99'
-@@ -58,8 +58,8 @@ elif arch in ["x86_64"]:
+@@ -58,8 +58,8 @@
      extra_compile_args.extend(['-DSTREAMVBYTE_SSSE3=1', '-mssse3'])   # WARNING: ancient x86_64 CPUs don't have SSSE3
  
  


=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# This is a false positive introduced by the time_t 64-bit transition.
+version-substvar-for-external-package Conflicts ${source:Version} libslow5-0t64 -> libslow5-0 [debian/control:*]



View it on GitLab: https://salsa.debian.org/med-team/libslow5lib/-/compare/401932583b3315a03433b2a24e4f6c1d93af5c9d...2f58d9e3c4047d5761daad9f14fd38ede0341aca

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