[med-svn] [Git][med-team/sra-sdk][master] 4 commits: Formally start work on sra-sdk 3.2.1+dfsg-4.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Wed Apr 16 20:46:31 BST 2025
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
9d1a8a0a by Aaron M. Ucko at 2025-04-16T15:40:07-04:00
Formally start work on sra-sdk 3.2.1+dfsg-4.
- - - - -
bad71b9d by Aaron M. Ucko at 2025-04-16T15:40:29-04:00
debian/patches: Add two patches for GCC 15 support (#1097930).
* fix_bm_for_gcc15.patch: BitMagic cherry-pick, location adjusted.
* include_cstdint_for_gcc15.patch: Compensate for libstdc++ changes.
- - - - -
5d2013a5 by Aaron M. Ucko at 2025-04-16T15:43:01-04:00
d/rules: Explicitly direct pybuild to use distutils (#1103330).
It can otherwise misfire when bypassing the test suite, which includes
a setup.py run.
- - - - -
80342ec2 by Aaron M. Ucko at 2025-04-16T15:44:48-04:00
Finalize sra-sdk 3.2.1+dfsg-4.
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/fix_bm_for_gcc15.patch
- + debian/patches/include_cstdint_for_gcc15.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+sra-sdk (3.2.1+dfsg-4) unstable; urgency=medium
+
+ * debian/patches: Add two patches for GCC 15 support. (Closes: #1097930.)
+ - fix_bm_for_gcc15.patch: BitMagic cherry-pick, location adjusted.
+ - include_cstdint_for_gcc15.patch: Compensate for libstdc++ changes.
+ * debian/rules: Explicitly direct pybuild to use distutils. It can
+ otherwise misfire when bypassing the test suite, which includes a
+ setup.py run. (Closes: #1103330.)
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 16 Apr 2025 15:44:48 -0400
+
sra-sdk (3.2.1+dfsg-3) unstable; urgency=medium
* Upload to unstable.
=====================================
debian/patches/fix_bm_for_gcc15.patch
=====================================
@@ -0,0 +1,31 @@
+From fab01f43eca266bf56efb1aca659773c911a83fb Mon Sep 17 00:00:00 2001
+From: Anatoliy Kuznetsov <anatoliy.kuznetsov at gmail.com>
+Date: Tue, 3 Sep 2024 15:29:08 -0400
+Subject: [PATCH] fixed clang compilation issues
+
+---
+ libs/inc/bm/bm.h | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/libs/inc/bm/bm.h b/libs/inc/bm/bm.h
+index 70996e53..05bb139c 100644
+--- a/libs/inc/bm/bm.h
++++ b/libs/inc/bm/bm.h
+@@ -523,7 +523,7 @@ class bvector
+ {
+ bvect_ = ii.bvect_;
+ if (!buf_)
+- buf_ = bvect_->allocate_tempblock();
++ buf_ = (value_type*) bvect_->blockman_.get_allocator().alloc_bit_block();
+ buf_size_ = ii.buf_size_;
+ ::memcpy(buf_, ii.buf_, buf_size_ * sizeof(*buf_));
+ sorted_ = ii.sorted_;
+@@ -534,7 +534,7 @@ class bvector
+ {
+ bvect_ = ii.bvect_;
+ if (buf_)
+- bvect_->free_tempblock(buf_);
++ bvect_->blockman_.get_allocator().free_bit_block((bm::word_t*)buf_);
+ buf_ = ii.buf_; ii.buf_ = 0;
+ buf_size_ = ii.buf_size_;
+ sorted_ = ii.sorted_;
=====================================
debian/patches/include_cstdint_for_gcc15.patch
=====================================
@@ -0,0 +1,61 @@
+Index: b/tools/external/driver-tool/tool-args.hpp
+===================================================================
+--- a/tools/external/driver-tool/tool-args.hpp
++++ b/tools/external/driver-tool/tool-args.hpp
+@@ -36,6 +36,7 @@
+ #include <string>
+ #include <iosfwd>
+ #include <cstring>
++#include <cstdint>
+
+ #include "util.hpp"
+ #define USE_TOOL_HELP 0
+Index: b/tools/external/driver-tool/json-parse.hpp
+===================================================================
+--- a/tools/external/driver-tool/json-parse.hpp
++++ b/tools/external/driver-tool/json-parse.hpp
+@@ -36,6 +36,8 @@
+ #include "debug.hpp"
+ #include "opt_string.hpp"
+
++#include <cstdint>
++
+ #if MS_Visual_C
+ #pragma warning(disable: 4061)
+ #endif
+Index: b/tools/test-tools/sam-analyze/alig.hpp
+===================================================================
+--- a/tools/test-tools/sam-analyze/alig.hpp
++++ b/tools/test-tools/sam-analyze/alig.hpp
+@@ -3,6 +3,7 @@
+
+ #include <string>
+ #include <algorithm>
++#include <cstdint>
+ #include "database.hpp"
+
+ struct sam_alig_t {
+Index: b/tools/test-tools/sam-factory/sam-factory.cpp
+===================================================================
+--- a/tools/test-tools/sam-factory/sam-factory.cpp
++++ b/tools/test-tools/sam-factory/sam-factory.cpp
+@@ -7,6 +7,7 @@
+ #include <sstream>
+ #include <memory>
+ #include <cstring>
++#include <cstdint>
+
+ const std::string empty_string( "" );
+ const std::string star_string( "*" );
+Index: b/tools/test-tools/qa-stats/input.hpp
+===================================================================
+--- a/tools/test-tools/qa-stats/input.hpp
++++ b/tools/test-tools/qa-stats/input.hpp
+@@ -34,6 +34,7 @@
+ #include <vector>
+ #include <memory>
+ #include <variant>
++#include <cstdint>
+
+ struct CIGAR {
+ struct OP {
=====================================
debian/patches/series
=====================================
@@ -42,3 +42,5 @@ fix_arm64_build.patch
support_libre2-11.patch
pyhon3.12-syntax.patch
setuptools.patch
+fix_bm_for_gcc15.patch
+include_cstdint_for_gcc15.patch
=====================================
debian/rules
=====================================
@@ -132,7 +132,7 @@ override_dh_install:
dh_install
# remove susipcious file which is not executable and conflicts with package magic
rm -f debian/*/usr/bin/magic
- pybuild --install --name ngs -d ngs/ngs-python
+ pybuild --install --name ngs -d ngs/ngs-python -s distutils
override_dh_installexamples:
dh_installexamples
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/0adc07ce7266d267cda482bc61e3ebdbbccff24d...80342ec2b0ee3c67ba29c3941addd00a865d542f
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/0adc07ce7266d267cda482bc61e3ebdbbccff24d...80342ec2b0ee3c67ba29c3941addd00a865d542f
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