[med-svn] [Git][med-team/minimap2][master] 7 commits: Fix non-x86 build.

Michael R. Crusoe (@crusoe) gitlab at salsa.debian.org
Sun Nov 7 16:07:51 GMT 2021 


Michael R. Crusoe pushed to branch master at Debian Med / minimap2


Commits:
ab668582 by Michael R. Crusoe at 2021-10-14T14:30:13+02:00
Fix non-x86 build.

- - - - -
6e773cd2 by Michael R. Crusoe at 2021-10-14T14:30:13+02:00
mark do_not_use_natbib.bst.patch as not needing forwarding

- - - - -
f3d6f049 by Michael R. Crusoe at 2021-10-14T14:42:34+02:00
non x86 fixup

- - - - -
bf81a7df by Michael R. Crusoe at 2021-11-07T17:04:24+01:00
Revive SIMDe patch

- - - - -
7ff3586a by Michael R. Crusoe at 2021-11-07T17:04:24+01:00
debian/copyright: exclude sse2neon in favor of libsimde-dev

- - - - -
be58275b by Michael R. Crusoe at 2021-11-07T17:04:24+01:00
fix typo

- - - - -
7f672ad5 by Michael R. Crusoe at 2021-11-07T17:06:56+01:00
release 2.22+dfsg-2

- - - - -


8 changed files:

- debian/changelog
- debian/copyright
- debian/patches/ar.patch
- debian/patches/do_not_use_natbib.bst.patch
- debian/patches/python-sse4-arch.patch
- debian/patches/series
- + debian/patches/simde
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+minimap2 (2.22+dfsg-2) unstable; urgency=medium
+
+  * Team upload
+  * Fix non-x86 build.
+  * mark do_not_use_natbib.bst.patch as not needing forwarding
+  * Revive SIMDe patch
+  * debian/copyright: exclude sse2neon in favor of libsimde-dev
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Sun, 07 Nov 2021 17:06:42 +0100
+
 minimap2 (2.22+dfsg-1) unstable; urgency=medium
 
   * Team upload


=====================================
debian/copyright
=====================================
@@ -2,7 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: minimap2
 Upstream-Contact: Heng Li <hengli at broadinstitute.org>
 Source: https://github.com/lh3/minimap2
-Files-Excluded: */natbib.*
+Files-Excluded: */natbib.*, sse2neon/*
 
 Files: *
 Copyright: © 2018-     Dana-Farber Cancer Institute


=====================================
debian/patches/ar.patch
=====================================
@@ -1,6 +1,6 @@
 Author: Steffen Moeller
 Last-Update: 2020-03-15 04:06:20 +0100
-Descriptio: Fix ar call to support debugging symbols properly
+Description: Fix ar call to support debugging symbols properly
 
 --- minimap2.orig/Makefile
 +++ minimap2/Makefile


=====================================
debian/patches/do_not_use_natbib.bst.patch
=====================================
@@ -1,7 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: Fri, 09 Nov 2018 23:36:05 +0100
 Description: Natbib style is only for non-profit use
-
+Forwarded: not-needed
 --- a/tex/bioinfo.cls
 +++ b/tex/bioinfo.cls
 @@ -824,7 +824,8 @@


=====================================
debian/patches/python-sse4-arch.patch
=====================================
@@ -5,12 +5,12 @@ Description: Only pass -msse4.1 to the compiler on amd64
 
 --- minimap2.orig/setup.py
 +++ minimap2/setup.py
-@@ -16,7 +16,7 @@
+@@ -16,8 +16,6 @@
  if platform.machine() in ["aarch64", "arm64"]:
  	include_dirs.append("sse2neon/")
  	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
 -else:
-+elif platform.machine() == "x86_64":
- 	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
+-	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
  
  def readme():
+ 	with open('python/README.rst') as f:


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ do_not_use_natbib.bst.patch
 ar.patch
 link_mappy_to_libminimap.patch
 python-sse4-arch.patch
+simde


=====================================
debian/patches/simde
=====================================
@@ -0,0 +1,69 @@
+--- minimap2.orig/Makefile.simde
++++ minimap2/Makefile.simde
+@@ -1,8 +1,9 @@
+-CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
+-CPPFLAGS=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
+-INCLUDES=	-Ilib/simde
+-OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \
+-			ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
++CFLAGS+=		-g -Wall -O2 -Wc++-compat #-Wextra
++CPPFLAGS+=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
++INCLUDES=
++OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
++			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
++			ksw2_ll_sse.o ksw2_extz2.o ksw2_extd2.o ksw2_exts2.o
+ PROG=		minimap2
+ PROG_EXTRA=	sdust minimap2-lite
+ LIBS=		-lm -lz -lpthread
+@@ -37,28 +38,27 @@
+ extra:all $(PROG_EXTRA)
+ 
+ minimap2:main.o libminimap2.a
+-		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
++		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)
+ 
+ minimap2-lite:example.o libminimap2.a
+-		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
++		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)
+ 
+ libminimap2.a:$(OBJS)
+-		$(AR) -csru $@ $(OBJS)
++		rm -f $@
++		$(AR) csrD $@ $(OBJS)
+ 
+-sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
+-		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
++ksw2_extz2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+ 
+-ksw2_ll_simde.o:ksw2_ll_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
++ksw2_extd2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+ 
+-ksw2_extz2_simde.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
++ksw2_exts2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+ 
+-ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
++sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
++		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz $(LDFLAGS)
+ 
+-ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+-		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+ 
+ # other non-file targets
+ 
+@@ -80,10 +80,6 @@
+ index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h
+ index.o: ksort.h
+ kalloc.o: kalloc.h
+-ksw2_extd2_sse.o: ksw2.h kalloc.h
+-ksw2_exts2_sse.o: ksw2.h kalloc.h
+-ksw2_extz2_sse.o: ksw2.h kalloc.h
+-ksw2_ll_sse.o: ksw2.h kalloc.h
+ kthread.o: kthread.h
+ main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
+ map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h


=====================================
debian/rules
=====================================
@@ -1,10 +1,7 @@
 #!/usr/bin/make -f
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-# from minimap 1
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 include /usr/share/dpkg/architecture.mk
-export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
 
 RANLIB ?= ranlib
 
@@ -18,13 +15,13 @@ override_dh_auto_clean:
 	rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf
 	rm -f libminimap2.a
 
-ifneq (,$(filter $(DEB_HOST_ARCH_CPU),amd64))
-build_vars += amd64=1
-else ifneq (,$(filter $(DEB_HOST_ARCH_CPU),amd64))
-build_vars += i386=1
-else ifneq (,$(filter $(DEB_HOST_ARCH_CPU),arm64))
-build_vars += aarch64=1
+ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64))
+build_vars = -f Makefile.simde
+export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
 endif
+# ifneq (,$(filter $(DEB_HOST_ARCH_CPU),arm64))
+# build_vars += aarch64=1
+# endif
 
 override_dh_auto_build:
 	dh_auto_build -- $(build_vars)



View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/compare/dcc5929a37635e276c038cff118a12ff388ddd81...7f672ad55aeec73bef7a32475022a89246c16a48

-- 
View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/compare/dcc5929a37635e276c038cff118a12ff388ddd81...7f672ad55aeec73bef7a32475022a89246c16a48
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