+ debian/patches/fix_bm_for_gcc15 (#1097434).

Cherry-pick a BitMagic fix needed for modern compilers, adjusting the
path appropriately.

diff --git a/debian/changelog b/debian/changelog
index 18fc12a864a950e233b73235dddb783b591940d7..cf89c7deb3469bebb17fd7c98e73e2e0d0993390 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+ncbi-blast+ (2.16.0+ds-7) UNRELEASED; urgency=medium
+
+  * NOT RELEASED YET.
+  * debian/patches/fix_bm_for_gcc15 (new): Cherry-pick a BitMagic fix
+    needed for modern compilers, adjusting the path appropriately.'
+    (Closes: #1097434.)
+
+ -- Aaron M. Ucko <ucko@debian.org>  Sat, 03 May 2025 22:16:44 -0400
+
 ncbi-blast+ (2.16.0+ds-6) unstable; urgency=medium
 
   * debian/control: Reinstate big-endian builds, which can be salvaged

diff --git a/debian/patches/fix_bm_for_gcc15 b/debian/patches/fix_bm_for_gcc15
new file mode 100644 (file)
index 0000000..a6d8bf4
--- /dev/null
+++ b/debian/patches/fix_bm_for_gcc15
@@ -0,0 +1,31 @@
+From fab01f43eca266bf56efb1aca659773c911a83fb Mon Sep 17 00:00:00 2001
+From: Anatoliy Kuznetsov <anatoliy.kuznetsov@gmail.com>
+Date: Tue, 3 Sep 2024 15:29:08 -0400
+Subject: [PATCH] fixed clang compilation issues
+
+---
+ c++/include/util/bitset/bm.h | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/c++/include/util/bitset/bm.h b/c++/include/util/bitset/bm.h
+index 70996e53..05bb139c 100644
+--- a/c++/include/util/bitset/bm.h
++++ b/c++/include/util/bitset/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_;

diff --git a/debian/patches/series b/debian/patches/series
index d754932eb1cc5c065cd715c3b6bab092cef4af1b..a1c9c0e946c7e3c042acaa59c293335112e64d56 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -21,3 +21,4 @@ run_perl_directly
 tune_lmdb_defaults
 2to3
 big_endian_workaround
+fix_bm_for_gcc15