[med-svn] [Git][med-team/rna-star][master] 3 commits: debian/patches/packaged_simde: Use packaged SIMDe header, not the code-copy

Sun Jan 22 15:02:59 GMT 2023


Michael R. Crusoe pushed to branch master at Debian Med / rna-star


Commits:
4592b1d5 by Michael R. Crusoe at 2023-01-22T15:32:51+01:00
debian/patches/packaged_simde: Use packaged SIMDe header, not the code-copy

- - - - -
9a40b48e by Michael R. Crusoe at 2023-01-22T15:33:12+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
284513a5 by Michael R. Crusoe at 2023-01-22T15:33:29+01:00
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/patches/do-not-enforce-avx2.patch
- debian/patches/donotuse_own_htslib.patch
- + debian/patches/packaged_simde
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+rna-star (2.7.10b+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * debian/patches/packaged_simde: Use packaged SIMDe header, not the
+    code-copy.
+  * Standards-Version: 4.6.2 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Sun, 22 Jan 2023 15:33:29 +0100
+
 rna-star (2.7.10b+dfsg-1) unstable; urgency=medium
 
   * New upstream release.


=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
                xxd,
                zlib1g-dev,
                libsimde-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/rna-star
 Vcs-Git: https://salsa.debian.org/med-team/rna-star.git
 Homepage: https://github.com/alexdobin/STAR/


=====================================
debian/copyright
=====================================
@@ -5,6 +5,7 @@ Source: https://github.com/alexdobin/STAR/releases
 Files-Excluded: bin/*
                 source/htslib
                 source/parametersDefault.xxd
+                source/opal/simde_avx2.h
                 .gitignore
 
 Files: *


=====================================
debian/patches/do-not-enforce-avx2.patch
=====================================
@@ -3,8 +3,8 @@ Author: Nilesh Patra <nilesh at debian.org>
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=992270
 Forwarded: not-needed
 Last-Update: 2021-08-18
---- a/source/Makefile
-+++ b/source/Makefile
+--- rna-star.orig/source/Makefile
++++ rna-star/source/Makefile
 @@ -40,7 +40,6 @@
  # Defaults, can be overridden by make arguments or environment
  CXXFLAGS ?= -pipe -Wall -Wextra
@@ -13,7 +13,7 @@ Last-Update: 2021-08-18
  
  # Unconditionally set essential flags and optimization options
  CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add)
-@@ -103,7 +102,7 @@
+@@ -104,7 +103,7 @@
  
  opal/opal.o : opal/opal.cpp opal/opal.h
  	cd opal && \


=====================================
debian/patches/donotuse_own_htslib.patch
=====================================
@@ -2,8 +2,8 @@ Author: Steffen Moeller <moeller at debian.org>,
 Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
 Description: Use Debian packaged htslib
 Forwarded: not-needed
---- a/source/Makefile
-+++ b/source/Makefile
+--- rna-star.orig/source/Makefile
++++ rna-star/source/Makefile
 @@ -12,8 +12,8 @@
  CXX ?= g++
  
@@ -24,7 +24,7 @@ Forwarded: not-needed
  CXXFLAGS_main := -O3 $(CXXFLAGS_common)
  CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
  
-@@ -96,10 +96,10 @@
+@@ -97,10 +97,10 @@
  
  
  %.o : %.cpp
@@ -37,7 +37,7 @@ Forwarded: not-needed
  
  all: cleanCompileInfo STAR$(SFX)
  
-@@ -113,8 +113,6 @@
+@@ -114,8 +114,6 @@
  
  .PHONY: CLEAN
  CLEAN: clean
@@ -46,7 +46,7 @@ Forwarded: not-needed
  
  .PHONY: clean_solo
  clean_solo:
-@@ -130,7 +128,7 @@
+@@ -131,7 +129,7 @@
  ifneq ($(MAKECMDGOALS),clean_solo)
  ifneq ($(MAKECMDGOALS),STARforMac)
  ifneq ($(MAKECMDGOALS),STARforMacGDB)
@@ -55,7 +55,7 @@ Forwarded: not-needed
  	echo $(SOURCES)
  	'rm' -f ./Depend.list
  	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -142,11 +140,6 @@
+@@ -143,11 +141,6 @@
  endif
  endif
  
@@ -67,8 +67,8 @@ Forwarded: not-needed
  parametersDefault.xxd: parametersDefault
  	xxd -i parametersDefault > parametersDefault.xxd
  
---- a/source/bamRemoveDuplicates.cpp
-+++ b/source/bamRemoveDuplicates.cpp
+--- rna-star.orig/source/bamRemoveDuplicates.cpp
++++ rna-star/source/bamRemoveDuplicates.cpp
 @@ -1,7 +1,7 @@
  #include <unordered_map>
  #include "bamRemoveDuplicates.h"
@@ -78,8 +78,8 @@ Forwarded: not-needed
  #include "IncludeDefine.h"
  #include SAMTOOLS_BGZF_H
  #include "ErrorWarning.h"
---- a/source/bam_cat.c
-+++ b/source/bam_cat.c
+--- rna-star.orig/source/bam_cat.c
++++ rna-star/source/bam_cat.c
 @@ -52,8 +52,8 @@
  #include <stdlib.h>
  #include <unistd.h>
@@ -91,8 +91,8 @@ Forwarded: not-needed
  #include <cstring>
  
  #define BUF_SIZE 0x10000
---- a/source/signalFromBAM.h
-+++ b/source/signalFromBAM.h
+--- rna-star.orig/source/signalFromBAM.h
++++ rna-star/source/signalFromBAM.h
 @@ -1,6 +1,6 @@
  #ifndef CODE_signalFromBAM
  #define CODE_signalFromBAM
@@ -101,8 +101,8 @@ Forwarded: not-needed
  #include  <fstream>
  #include <string>
  #include "Stats.h"
---- a/source/IncludeDefine.h
-+++ b/source/IncludeDefine.h
+--- rna-star.orig/source/IncludeDefine.h
++++ rna-star/source/IncludeDefine.h
 @@ -30,8 +30,8 @@
  #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
  
@@ -114,8 +114,8 @@ Forwarded: not-needed
  
  using namespace std;
  
---- a/source/BAMfunctions.cpp
-+++ b/source/BAMfunctions.cpp
+--- rna-star.orig/source/BAMfunctions.cpp
++++ rna-star/source/BAMfunctions.cpp
 @@ -1,5 +1,5 @@
  #include "BAMfunctions.h"
 -#include "htslib/htslib/kstring.h"
@@ -123,9 +123,9 @@ Forwarded: not-needed
  
  
  string bam_cigarString (bam1_t *b) {//output CIGAR string
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
-@@ -29,7 +29,7 @@
+--- rna-star.orig/source/STAR.cpp
++++ rna-star/source/STAR.cpp
+@@ -30,7 +30,7 @@
  
  #include "twoPassRunPass1.h"
  
@@ -134,8 +134,8 @@ Forwarded: not-needed
  #include "parametersDefault.xxd"
  
  void usage(int usageType) {
---- a/source/bam_cat.h
-+++ b/source/bam_cat.h
+--- rna-star.orig/source/bam_cat.h
++++ rna-star/source/bam_cat.h
 @@ -1,7 +1,7 @@
  #ifndef CODE_bam_cat
  #define CODE_bam_cat
@@ -145,8 +145,8 @@ Forwarded: not-needed
  
  int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
  
---- a/source/Parameters.cpp
-+++ b/source/Parameters.cpp
+--- rna-star.orig/source/Parameters.cpp
++++ rna-star/source/Parameters.cpp
 @@ -376,7 +376,6 @@
  
      inOut->logMain << "STAR version=" << STAR_VERSION << "\n";


=====================================
debian/patches/packaged_simde
=====================================
@@ -0,0 +1,14 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Use packaged SIMDe header, not the code-copy
+Forwarded: not-needed
+--- rna-star.orig/source/opal/opal.cpp
++++ rna-star/source/opal/opal.cpp
+@@ -7,7 +7,7 @@
+ 
+ extern "C" {
+ #define SIMDE_ENABLE_NATIVE_ALIASES
+-#include <simde_avx2.h> // AVX2 and lower
++#include <simde/x86/avx2.h> // AVX2 and lower
+ }
+ 
+ #include "opal.h"


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ reproducible.patch
 mathRoutinesNotInScope.patch
 do-not-enforce-avx2.patch
 gcc-12.patch
+packaged_simde



View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/a880cfe0460e2d53a0f6861b8bcbad3794c2ac8f...284513a5269cd895732c0fe01614eecbd84d9ed5

-- 
View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/a880cfe0460e2d53a0f6861b8bcbad3794c2ac8f...284513a5269cd895732c0fe01614eecbd84d9ed5
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