[med-svn] [Git][med-team/rna-star][master] 4 commits: debian/{rules, clean: specify the source directory, and simplify

[Michael R. Crusoe]

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


Commits:
4abc9eac by Michael R. Crusoe at 2021-03-01T12:18:10+01:00
debian/{rules,clean: specify the source directory, and simplify

- - - - -
b6ca7250 by Michael R. Crusoe at 2021-03-01T12:18:10+01:00
document Nilesh's work

- - - - -
70e0d4dd by Michael R. Crusoe at 2021-03-01T12:18:59+01:00
some patches don't need forwarding

- - - - -
b411154c by Michael R. Crusoe at 2021-03-01T12:33:23+01:00
debian/patches/reproducible.patch: Reproducibly include the build time using SOURCE_DATE_EPOCH

- - - - -


6 changed files:

- debian/changelog
- + debian/clean
- debian/patches/donotuse_own_htslib.patch
- debian/patches/reproducible.patch
- debian/patches/simde.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+rna-star (2.7.8a+dfsg-2) UNRELEASED; urgency=high
+
+  [ Michael R. Crusoe ]
+  * Team upload.
+  * debian/{rules,clean: specify the source directory, and simplify
+
+  [ Nilesh Patra ]
+  * debian/{rules,control,patches/simde.patch}: use libsimde-dev to enable
+    building on non-x86 systems.
+    Removed "-march=native" architecture baseline violation. Closes: #983723
+
+  [ Michael R. Crusoe ]
+  * debian/patches/reproducible.patch: Reproducibly include the build
+    time using SOURCE_DATE_EPOCH
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 01 Mar 2021 12:10:42 +0100
+
 rna-star (2.7.8a+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/clean
=====================================
@@ -0,0 +1,2 @@
+source/parametersDefault.xxd
+opal/opal.o


=====================================
debian/patches/donotuse_own_htslib.patch
=====================================
@@ -1,7 +1,7 @@
 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
 Index: rna-star/source/Makefile
 ===================================================================
 --- rna-star.orig/source/Makefile


=====================================
debian/patches/reproducible.patch
=====================================
@@ -1,16 +1,21 @@
 Description: make build reproducible
  Stops build hostname and directory from being recorded in the artifact.
 Author: Sascha Steinbiss <sascha at steinbiss.name>
-Index: rna-star/source/Makefile
-===================================================================
 --- rna-star.orig/source/Makefile
 +++ rna-star/source/Makefile
-@@ -18,7 +18,7 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts
+@@ -18,7 +18,14 @@
  LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
  LDFLAGS_gdb := $(LDFLAGS_shared)
  
 -COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
-+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="<not set in Debian>"'
++DATE_FMT = --iso-8601=seconds
++ifdef SOURCE_DATE_EPOCH
++    BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")
++else
++    BUILD_DATE ?= $(shell date "$(DATE_FMT)")
++endif
++
++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) <place not set in Debian package>"
  
  # Defaults, can be overridden by make arguments or environment
  CXXFLAGS ?= -pipe -Wall -Wextra


=====================================
debian/patches/simde.patch
=====================================
@@ -1,8 +1,9 @@
 Description: Use simde instead of intel intrinsics
 Author: Nilesh Patra <nilesh at debian.org>
 Last-Update: 2021-02-26
---- a/source/opal/opal.cpp
-+++ b/source/opal/opal.cpp
+Forwarded: https://github.com/alexdobin/STAR/issues/1160
+--- rna-star.orig/source/opal/opal.cpp
++++ rna-star/source/opal/opal.cpp
 @@ -6,7 +6,8 @@
  #include <vector>
  
@@ -13,14 +14,14 @@ Last-Update: 2021-02-26
  }
  
  #include "opal.h"
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -84,7 +84,7 @@
+--- rna-star.orig/source/Makefile
++++ rna-star/source/Makefile
+@@ -91,7 +91,7 @@
  
  opal/opal.o : opal/opal.cpp opal/opal.h
  	cd opal && \
 -	$(CXX) -c -O3 -std=c++11 -march=native opal.cpp
-+	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) -std=c++11 opal.cpp
++	$(CXX) -c -O3 $(CPPFLAGS) $(CXXFLAGS) -std=c++11 opal.cpp
  
  .PHONY: clean
  clean:


=====================================
debian/rules
=====================================
@@ -14,15 +14,13 @@ export DEB_CFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
 export DEB_CXXFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
 
 %:
-	dh $@
+	dh $@ --sourcedirectory=source
 
 override_dh_auto_build:
-	dh_auto_build --sourcedirectory=source -- CCFLAGS_common_add="-flto $(CCFLAGS)" CCFLAGS="$(CCFLAGS)" LDFLAGS_add="$(LDFLAGS)"
+	dh_auto_build -- CCFLAGS_common_add="-flto $(CCFLAGS)" CCFLAGS="$(CCFLAGS)" LDFLAGS_add="$(LDFLAGS)"
 
 override_dh_auto_clean:
-	cd source && $(MAKE) clean
-	rm -f source/parametersDefault.xxd
-	rm -f opal/opal.o
+	cd source && ${MAKE} clean
 
 override_dh_compress:
 	dh_compress --exclude=.pdf



View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d

-- 
View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d
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