[med-svn] [Git][med-team/examl][master] 2 commits: fix-makefile-shuffle.patch: new: prevent spurious clean.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / examl


Commits:
5990e05e by Étienne Mollier at 2025-11-27T22:21:44+01:00
fix-makefile-shuffle.patch: new: prevent spurious clean.

Closes: #1105362

- - - - -
3808a86a by Étienne Mollier at 2025-11-27T22:32:34+01:00
d/changelog: ready for upload to unstable.

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix-makefile-shuffle.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,13 +1,14 @@
-examl (3.0.22-7) UNRELEASED; urgency=medium
+examl (3.0.22-7) unstable; urgency=medium
 
   * d/b/simd-dispatch: fix possible off-by-one error.
     The error affects automated estimation of examl cores count usage.
-    It may be related to #1087184.
+    (Closes: #1087184)
   * d/watch: convert to v5 Github template.
   * d/control: drop redundant Rules-Requires-Root: no.
   * d/control: declare compliance to standards version 4.7.2.
+  * fix-makefile-shuffle.patch: new: prevent spurious clean. (Closes: #1105362)
 
- -- Étienne Mollier <emollier at debian.org>  Thu, 27 Nov 2025 22:04:02 +0100
+ -- Étienne Mollier <emollier at debian.org>  Thu, 27 Nov 2025 22:31:56 +0100
 
 examl (3.0.22-6) unstable; urgency=medium
 


=====================================
debian/patches/fix-makefile-shuffle.patch
=====================================
@@ -0,0 +1,76 @@
+Description: fix build failure with reverse make execution.
+ This change removes invocations of the clean target from all targets.
+ This prevents deletion of build artifacts when the clean target is
+ reached after artifacts are produced.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105362
+Forwarded: no
+Last-Update: 2025-11-27
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- examl.orig/examl/Makefile.AVX.gcc
++++ examl/examl/Makefile.AVX.gcc
+@@ -18,7 +18,7 @@
+ 
+ SFX :=""
+ 
+-all : clean examl$(SFX)
++all : examl$(SFX)
+ 
+ GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
+ 
+--- examl.orig/examl/Makefile.KNL.icc
++++ examl/examl/Makefile.KNL.icc
+@@ -20,7 +20,7 @@
+ 
+ objs    = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o byteFile.o partitionAssignment.o communication.o mic_native_dna.o mic_native_aa.o quartets.o
+ 
+-all : clean examl-KNL
++all : examl-KNL
+ 
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+--- examl.orig/examl/Makefile.MIC.icc
++++ examl/examl/Makefile.MIC.icc
+@@ -17,7 +17,7 @@
+ 
+ objs    = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o byteFile.o partitionAssignment.o communication.o mic_native_dna.o mic_native_aa.o quartets.o
+ 
+-all : clean examl-MIC
++all : examl-MIC
+ 
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+--- examl.orig/examl/Makefile.OMP.SSE3.gcc
++++ examl/examl/Makefile.OMP.SSE3.gcc
+@@ -16,7 +16,7 @@
+ 
+ objs    = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o  treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o  byteFile.o partitionAssignment.o communication.o quartets.o
+ 
+-all : clean examl-OMP
++all : examl-OMP
+ 
+ GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
+ 
+--- examl.orig/examl/Makefile.SSE3.gcc
++++ examl/examl/Makefile.SSE3.gcc
+@@ -17,7 +17,7 @@
+ 
+ objs    = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o  treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o  byteFile.o partitionAssignment.o communication.o quartets.o
+ 
+-all : clean examl
++all : examl
+ 
+ GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
+ 
+--- examl.orig/parser/Makefile.SSE3.gcc
++++ examl/parser/Makefile.SSE3.gcc
+@@ -13,7 +13,7 @@
+ 
+ SFX := ""
+ 
+-all : clean parse-examl$(SFX)
++all : parse-examl$(SFX)
+ 
+ GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h 
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 hardening.patch
 simde
 fix_implicit_declaration.patch
+fix-makefile-shuffle.patch



View it on GitLab: https://salsa.debian.org/med-team/examl/-/compare/fbee5a3e20a72cc8f0003de15386f2832e7ed4dc...3808a86a7073cde4b568ca414903b23dfd9a20cc

-- 
View it on GitLab: https://salsa.debian.org/med-team/examl/-/compare/fbee5a3e20a72cc8f0003de15386f2832e7ed4dc...3808a86a7073cde4b568ca414903b23dfd9a20cc
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