[med-svn] [Git][med-team/ncbi-igblast][master] 3 commits: Backport upstream fix for GCC-15 failure (Closes: #1097435)

Andrius Merkys (@merkys) gitlab at salsa.debian.org
Tue Sep 30 13:38:57 BST 2025



Andrius Merkys pushed to branch master at Debian Med / ncbi-igblast


Commits:
697d2a68 by Andrius Merkys at 2025-09-30T08:08:45-04:00
Backport upstream fix for GCC-15 failure (Closes: #1097435)

- - - - -
5f101f9d by Andrius Merkys at 2025-09-30T08:14:53-04:00
Adjust debian/source/lintian-overrides.

- - - - -
2510ef5b by Andrius Merkys at 2025-09-30T08:15:10-04:00
Update changelog for 1.20.0-3 release

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/d52aea6f5599e85a0535c3f8a344aed2fa8a7e22.patch
- debian/patches/series
- debian/source/lintian-overrides


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+ncbi-igblast (1.20.0-3) unstable; urgency=medium
+
+  * Use system-provided lmdb.
+  * Backport upstream fix for GCC-15 failure (Closes: #1097435)
+  * Adjust debian/source/lintian-overrides.
+
+ -- Andrius Merkys <merkys at debian.org>  Tue, 30 Sep 2025 08:15:02 -0400
+
 ncbi-igblast (1.20.0-2) unstable; urgency=medium
 
   * Link in internal_data/ directory locally for autopkgtest, as it does not


=====================================
debian/patches/d52aea6f5599e85a0535c3f8a344aed2fa8a7e22.patch
=====================================
@@ -0,0 +1,36 @@
+From d52aea6f5599e85a0535c3f8a344aed2fa8a7e22 Mon Sep 17 00:00:00 2001
+From: Aaron Ucko <ucko at ncbi.nlm.nih.gov>
+Date: Tue, 5 Nov 2024 16:41:25 +0000
+Subject: [PATCH] bm::bulk_insert_iterator::operator=: Modernize tempblock
+ logistics.
+
+Fix compilation under recent versions of Clang.
+UPSTREAM-GIT: fab01f4.
+
+git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@103414 78c7ea69-d796-4a43-9a09-de51944f1b03
+---
+ include/util/bitset/bm.h | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/include/util/bitset/bm.h b/include/util/bitset/bm.h
+index 547b1085e26..0c59785f57c 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_;


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 avoid-gcc-crash.patch
+d52aea6f5599e85a0535c3f8a344aed2fa8a7e22.patch


=====================================
debian/source/lintian-overrides
=====================================
@@ -6,4 +6,4 @@ source-is-missing c++/src/html/ncbi_menu_dnd.js
 source-is-missing c++/src/html/ncbi_menu_dyn.js
 # JSON not evil license, related code is not present
 # Aaron M. Ucko: As this file explains, the problematic JSON license applies only to a jsonchecker subtree NCBI already doesn't redistribute
-license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson11/license.txt
+license-problem-json-evil [c++/include/misc/jsonwrapp/rapidjson11/license.txt]



View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/6594caff68688248aa42ea6745bbb81afc15b98d...2510ef5bf1b86ca6a84cb721728a658a483eff58

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/6594caff68688248aa42ea6745bbb81afc15b98d...2510ef5bf1b86ca6a84cb721728a658a483eff58
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