From 45fd0e43e6ae3debc83b4c71ff415b4588c78fa2 Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Sat, 3 May 2025 22:16:45 -0400 Subject: [PATCH] + debian/patches/fix_bm_for_gcc15 (#1097434). Cherry-pick a BitMagic fix needed for modern compilers, adjusting the path appropriately. --- debian/changelog | 9 +++++++++ debian/patches/fix_bm_for_gcc15 | 31 +++++++++++++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 41 insertions(+) create mode 100644 debian/patches/fix_bm_for_gcc15 diff --git a/debian/changelog b/debian/changelog index 18fc12a8..cf89c7de 100644 --- 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 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 index 00000000..a6d8bf46 --- /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 +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 d754932e..a1c9c0e9 100644 --- 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 -- 2.30.2