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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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