[med-svn] [Git][med-team/vg][debian/experimental] 3 commits: d/copyright: exclude the unused benchmarks.js from the vendored copies of atomic_queue
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Sep 14 08:44:07 BST 2024
Michael R. Crusoe pushed to branch debian/experimental at Debian Med / vg
Commits:
d765819b by Michael R. Crusoe at 2024-09-12T16:55:49+02:00
d/copyright: exclude the unused benchmarks.js from the vendored copies of atomic_queue
- - - - -
77a91624 by Michael R. Crusoe at 2024-09-14T09:43:10+02:00
d/control: update names of obsolete packages to their replacements
Closes: #1043312
- - - - -
f1ff8d66 by Michael R. Crusoe at 2024-09-14T09:43:40+02:00
update gcc patch
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/gcc-14 → debian/patches/gcc-12
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -28,7 +28,11 @@ vg (1.59.0+ds-1) UNRELEASED; urgency=medium
* d/patches/series: skip the ssw patches to use the code copy for now.
* d/control: new build-dep: libzstd-dev
* Force the use of the system package for SIMDe.
- * Added patch to fix gcc-14 issues.
+ * Added patch to fix gcc 12+ issues.
+ * d/copyright: exclude the unused benchmarks.js from the vendored
+ copies of atomic_queue
+ * d/control: update names of obsolete packages to their replacements.
+ Closes: #1043312
-- Michael R. Crusoe <crusoe at debian.org> Wed, 11 Sep 2024 17:32:18 +0200
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
pv <!nocheck>,
- bsdmainutils,
+ bsdextrautils | bsdmainutils,
zlib1g-dev,
rs,
libffi-dev,
@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13),
unzip,
librdf0-dev,
cmake,
- pkg-config,
+ pkgconf,
bc,
gtk-doc-tools,
raptor2-utils <!nocheck>,
=====================================
debian/copyright
=====================================
@@ -1,11 +1,13 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: vg
Source: https://github.com/vgteam/vg#vg
-Files-Excluded: deps/libdeflate
+Files-Excluded: deps/atomic_queue/html/benchmarks.js
+ deps/libdeflate
deps/jemalloc
deps/backward-cpp
deps/elfutils
deps/raptor
+ deps/mmmultimap/deps/atomic_queue/html/benchmarks.js
deps/snappy
deps/sonLib/externalTools/quicktree_1.1/include/buildtree.h~
deps/fermi-lite
@@ -26,6 +28,7 @@ Files-Excluded: deps/libdeflate
deps/dozeu/simde
deps/gssw/src/simde
deps/ssw/src/simde
+ deps/xg/deps/mmmulti/deps/atomic_queue/html/benchmarks.js
src/simde
#deps/ssw
=====================================
debian/patches/gcc-14 → debian/patches/gcc-12
=====================================
@@ -1,17 +1,19 @@
From: "Michael R. Crusoe" <crusoe at debian.org>
Date: Wed, 11 Sep 2024 17:58:38 +0200
-Subject: GCC 14 fix
+Subject: GCC 12+ fixes
Forwarded: not-needed
Similar to https://github.com/vgteam/vg/commit/fa824c1f5500a71ee215311e18049c46c50712b5
---
- deps/kff-cpp-api/kff_io.cpp | 1 +
- deps/kff-cpp-api/main.cpp | 1 +
- deps/libhandlegraph/src/include/handlegraph/serializable.hpp | 1 +
- .../deps/libhandlegraph/src/include/handlegraph/serializable.hpp | 1 +
- deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp | 3 ++-
- 5 files changed, 6 insertions(+), 1 deletion(-)
+ deps/kff-cpp-api/kff_io.cpp | 1 +
+ deps/kff-cpp-api/main.cpp | 1 +
+ deps/libhandlegraph/src/include/handlegraph/serializable.hpp | 1 +
+ .../deps/libhandlegraph/src/include/handlegraph/serializable.hpp | 1 +
+ deps/sublinear-Li-Stephens/src/haplotype_manager.hpp | 1 +
+ deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp | 3 ++-
+ src/multipath_mapper.cpp | 6 ++++--
+ 7 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/deps/kff-cpp-api/kff_io.cpp b/deps/kff-cpp-api/kff_io.cpp
index e23d396..76b4864 100644
@@ -61,6 +63,18 @@ index b16a753..a7f6ab8 100644
namespace handlegraph {
+diff --git a/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp b/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
+index aac6d91..eee423e 100644
+--- a/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
++++ b/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
+@@ -8,6 +8,7 @@
+ #include <vector>
+ #include <string>
+ #include <iostream>
++#include <cstdint>
+
+ using namespace std;
+
diff --git a/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp b/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp
index e4b2283..5ed35a4 100644
--- a/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp
@@ -80,3 +94,20 @@ index e4b2283..5ed35a4 100644
-#endif
\ No newline at end of file
+#endif
+diff --git a/src/multipath_mapper.cpp b/src/multipath_mapper.cpp
+index 23e52a7..fe7aa3b 100644
+--- a/src/multipath_mapper.cpp
++++ b/src/multipath_mapper.cpp
+@@ -1836,8 +1836,10 @@ namespace vg {
+ std::swap(rescued_secondaries[i], rescued_secondaries[end - 1]);
+ std::swap(rescued_distances[i], rescued_distances[end - 1]);
+ std::swap(rescued_multiplicities[i], rescued_multiplicities[end - 1]);
+- std::swap(duplicate[i], duplicate[end - 1]);
+-
++ // nb: cant std::swap bool vectors in new c++
++ bool dupe_i = duplicate[i];
++ duplicate[i] = duplicate[end - 1];
++ duplicate[end - 1] = dupe_i;
+ end--;
+ }
+ else {
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
-gcc-14
+gcc-12
use_packaged_libdeflate
use_packaged_jemalloc
use_packaged_libbackward-cpp
View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/80845a337a43f65c36f5850cbe1850f427384676...f1ff8d66e12e09011154b979f38b203c36aa53d6
--
View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/80845a337a43f65c36f5850cbe1850f427384676...f1ff8d66e12e09011154b979f38b203c36aa53d6
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240914/3467dcbf/attachment-0001.htm>
More information about the debian-med-commit
mailing list