[med-svn] [Git][med-team/snap-aligner][master] 8 commits: Refresh patches.

Santiago Vila (@sanvila) gitlab at salsa.debian.org
Sun Oct 4 20:30:17 BST 2026 


Santiago Vila pushed to branch master at Debian Med / snap-aligner


Commits:
7ddb5cd9 by Santiago Vila at 2026-10-04T20:50:00+02:00
Refresh patches.

- - - - -
4673d2fe by Santiago Vila at 2026-10-04T20:55:00+02:00
Detach threads created in StartNewThread to stop leaking thread stacks. Closes: #848589.

- - - - -
13a32fc1 by Santiago Vila at 2026-10-04T21:00:00+02:00
d/control: Drop "Rules-Requires-Root: no" (default).

- - - - -
6eba72ef by Santiago Vila at 2026-10-04T21:05:00+02:00
d/control: Drop "Priority: optional" (default).

- - - - -
219f9f70 by Santiago Vila at 2026-10-04T21:10:00+02:00
d/control: Update standards-version.

- - - - -
829b85a5 by Santiago Vila at 2026-10-04T21:15:00+02:00
Simplify debian/salsa-ci.yml.

- - - - -
ac4d0bf8 by Santiago Vila at 2026-10-04T21:20:00+02:00
d/salsa-ci.yml: Disable redundant/duplicate jobs.

- - - - -
f365099b by Santiago Vila at 2026-10-04T21:25:00+02:00
Upload for unstable as 2.0.5+dfsg-2

- - - - -


9 changed files:

- debian/changelog
- debian/control
- + debian/patches/detach-threads.patch
- debian/patches/drop-msse → debian/patches/drop-msse.patch
- debian/patches/non-x86-and-kfreebsd → debian/patches/non-x86-and-kfreebsd.patch
- debian/patches/series
- debian/patches/simde → debian/patches/simde.patch
- debian/patches/spelling → debian/patches/spelling.patch
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+snap-aligner (2.0.5+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * Detach threads created in StartNewThread to stop leaking thread stacks.
+    Closes: #848589.
+  * Drop "Rules-Requires-Root: no" (default).
+  * Drop "Priority: optional" (default).
+  * Update standards-version.
+  * Fine-tune salsa-ci.yml.
+
+ -- Santiago Vila <sanvila at debian.org>  Sun, 04 Oct 2026 21:25:00 +0200
+
 snap-aligner (2.0.5+dfsg-1) unstable; urgency=medium
 
   * d/control: simplify architecture specification via the provisions


=====================================
debian/control
=====================================
@@ -3,17 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Michael R. Crusoe <crusoe at debian.org>,
            Pranav Ballaney <ballaneypranav at gmail.com>
 Section: science
-Priority: optional
 Build-Depends: debhelper-compat (= 13),
                architecture-is-64-bit,
                help2man,
                zlib1g-dev,
                libsimde-dev
-Standards-Version: 4.7.2
+Standards-Version: 4.7.4
 Vcs-Browser: https://salsa.debian.org/med-team/snap-aligner
 Vcs-Git: https://salsa.debian.org/med-team/snap-aligner.git
 Homepage: https://snap.cs.berkeley.edu/
-Rules-Requires-Root: no
 
 Package: snap-aligner
 Architecture: any


=====================================
debian/patches/detach-threads.patch
=====================================
@@ -0,0 +1,31 @@
+From: Santiago Vila <sanvila at debian.org>
+Subject: Detach threads created in StartNewThread to stop leaking thread stacks
+Bug-Debian: https://bugs.debian.org/848589
+
+On POSIX, `StartNewThread` created joinable threads that are never
+joined or detached. `tests/EventTest.cpp` spawns ~23,700 such threads
+across the "many waiters"/"single waiters" tests; each finished thread
+keeps its ~8 MB stack until process exit, so `unit_tests` accumulates
+~190 GB of virtual memory.
+
+The codebase never joins threads (all completion is signaled via
+`SingleWaiterObject`/counters), and the Windows `StartNewThread`
+already effectively detaches (`CreateThread` + `CloseHandle`), so this
+just brings Linux in line. Detached threads run to completion exactly
+as before.
+
+--- a/SNAPLib/Compat.cpp
++++ b/SNAPLib/Compat.cpp
+@@ -1573,7 +1573,11 @@
+ {
+     ThreadInfo *info = new ThreadInfo(threadMainFunction, threadMainFunctionParameter);
+     pthread_t thread;
+-    return pthread_create(&thread, NULL, runThread, info) == 0;
++    if (0 != pthread_create(&thread, NULL, runThread, info)) {
++        return false;
++    }
++    pthread_detach(thread);
++    return true;
+ }
+ 
+ void BindThreadToProcessor(unsigned processorNumber)


=====================================
debian/patches/drop-msse → debian/patches/drop-msse.patch
=====================================
@@ -1,9 +1,9 @@
 Author: Michael R. Crusoe
-Description: drop SSE flag, not needed for AMD64 and x32 and limits portability
-according to Aaron M. Ucko <ucko at debian.org>
+Description: drop SSE flag, not needed for AMD64 and x32 and limits portability according to Aaron M. Ucko <ucko at debian.org>
 Forwarded: https://github.com/amplab/snap/pull/67
---- snap-aligner.orig/Makefile
-+++ snap-aligner/Makefile
+
+--- a/Makefile
++++ b/Makefile
 @@ -3,7 +3,7 @@
    #CXXFLAGS = -g -O0 -Wno-format -std=c++98
  endif


=====================================
debian/patches/non-x86-and-kfreebsd → debian/patches/non-x86-and-kfreebsd.patch
=====================================
@@ -1,8 +1,8 @@
-Description: Uses more liberal CPP defines to add compatibility to kfreebsd &
-non-x86 systems
+Description: Uses more liberal CPP defines to add compatibility to kfreebsd & non-x86 systems
 Author: Michael R. Crusoe <crusoe at ucdavis.edu> and Aaron M. Ucko <ucko at debian.org>
---- snap-aligner.orig/SNAPLib/Compat.cpp
-+++ snap-aligner/SNAPLib/Compat.cpp
+
+--- a/SNAPLib/Compat.cpp
++++ b/SNAPLib/Compat.cpp
 @@ -1319,7 +1319,7 @@
  _int64 timeInNanos()
  {
@@ -12,8 +12,8 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu> and Aaron M. Ucko <ucko at debian.or
      clock_gettime(CLOCK_REALTIME, &ts); // Works on Linux
  #elif defined(__MACH__)
      clock_serv_t cclock;
---- snap-aligner.orig/SNAPLib/Compat.h
-+++ snap-aligner/SNAPLib/Compat.h
+--- a/SNAPLib/Compat.h
++++ b/SNAPLib/Compat.h
 @@ -77,7 +77,7 @@
  #include <sched.h>  // For sched_setaffinity
  #endif


=====================================
debian/patches/series
=====================================
@@ -1,4 +1,5 @@
-non-x86-and-kfreebsd
-drop-msse
-simde
-spelling
+non-x86-and-kfreebsd.patch
+drop-msse.patch
+simde.patch
+spelling.patch
+detach-threads.patch


=====================================
debian/patches/simde → debian/patches/simde.patch
=====================================
@@ -1,9 +1,10 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: Enable building on non-x86 systems
 Forwarded: https://github.com/amplab/snap/pull/130
---- snap-aligner.orig/SNAPLib/Compat.h
-+++ snap-aligner/SNAPLib/Compat.h
-@@ -77,12 +77,18 @@
+
+--- a/SNAPLib/Compat.h
++++ b/SNAPLib/Compat.h
+@@ -77,11 +77,17 @@
  #include <sched.h>  // For sched_setaffinity
  #endif
  
@@ -12,7 +13,6 @@ Forwarded: https://github.com/amplab/snap/pull/130
 -#else
 -#define _mm_prefetch(...) {}
 -#include <emmintrin.h> // For vector types like __m128i
--#endif
 +#define SIMDE_ENABLE_NATIVE_ALIASES
 +#include <simde/x86/sse2.h>
 +#if !defined(SIMDE_X86_SSE_NATIVE) && !defined(SIMDE_MATH_SLEEF_ENABLE)
@@ -24,7 +24,6 @@ Forwarded: https://github.com/amplab/snap/pull/130
 +#  define _MM_HINT_T1 2
 +#  define _MM_HINT_T2 3
 +HEDLEY_DIAGNOSTIC_POP
-+#endif
+ #endif
  
  typedef int64_t _int64;
- typedef uint64_t _uint64;


=====================================
debian/patches/spelling → debian/patches/spelling.patch
=====================================
@@ -1,8 +1,9 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: Fix a typo
 Forwarded: https://github.com/amplab/snap/pull/172
---- snap-aligner.orig/SNAPLib/AlignerOptions.cpp
-+++ snap-aligner/SNAPLib/AlignerOptions.cpp
+
+--- a/SNAPLib/AlignerOptions.cpp
++++ b/SNAPLib/AlignerOptions.cpp
 @@ -142,7 +142,7 @@
              "  -h   maximum hits to consider per seed (default: %d)\n"
              "  -ms  minimum seed matches per location (default: %d)\n"


=====================================
debian/salsa-ci.yml
=====================================
@@ -1,8 +1,8 @@
 ---
 include:
-  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
-  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
 
-# Does not build on i386
 variables:
   SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
+  SALSA_CI_DISABLE_BUILD_PACKAGE_ALL: 1
+  SALSA_CI_DISABLE_BUILD_PACKAGE_ANY: 1



View it on GitLab: https://salsa.debian.org/med-team/snap-aligner/-/compare/314cd30d5ce97a356187fff67670e7448efe2942...f365099bec885f13cb02f28abee3ce6c7c69ff0b

-- 
View it on GitLab: https://salsa.debian.org/med-team/snap-aligner/-/compare/314cd30d5ce97a356187fff67670e7448efe2942...f365099bec885f13cb02f28abee3ce6c7c69ff0b
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