[med-svn] [Git][med-team/skesa][master] 5 commits: Build against ncbi-vdb 3.x and sra-sdk 3.x (which subsumed ngs-sdk).

Fri Jan 20 23:04:58 GMT 2023


Aaron M. Ucko pushed to branch master at Debian Med / skesa


Commits:
a2e6de79 by Aaron M. Ucko at 2023-01-20T18:01:38-05:00
Build against ncbi-vdb 3.x and sra-sdk 3.x (which subsumed ngs-sdk).

- - - - -
3431efa7 by Aaron M. Ucko at 2023-01-20T18:02:20-05:00
link_boost_dynamically.patch (new): Drop upstream linkage override.

- - - - -
313a05c3 by Aaron M. Ucko at 2023-01-20T18:03:00-05:00
Add myself to Uploaders.

- - - - -
6151fe45 by Aaron M. Ucko at 2023-01-20T18:03:27-05:00
routine-update: Standards-Version: 4.6.2

- - - - -
5208d721 by Aaron M. Ucko at 2023-01-20T18:03:43-05:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/patches/hardening.patch
- + debian/patches/link_boost_dynamically.patch
- debian/patches/series
- debian/patches/use_debian_packaged_ngs-sdk.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,15 @@
-skesa (2.4.0-5) UNRELEASED; urgency=medium
+skesa (2.4.0-5) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Cleanup d/rules
 
- -- Andreas Tille <tille at debian.org>  Tue, 17 Jan 2023 16:57:58 +0100
+  [ Aaron M. Ucko ]
+  * Build against ncbi-vdb 3.x and sra-sdk 3.x (which subsumed ngs-sdk).
+  * link_boost_dynamically.patch (new): Drop upstream linkage override.
+  * Add myself to Uploaders.
+  * Standards-Version: 4.6.2 (routine-update)
+
+ -- Aaron M. Ucko <ucko at debian.org>  Fri, 20 Jan 2023 18:03:43 -0500
 
 skesa (2.4.0-4) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -1,6 +1,6 @@
 Source: skesa
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Aaron M. Ucko <ucko at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
@@ -11,9 +11,9 @@ Build-Depends: debhelper-compat (= 13),
                libboost-regex-dev,
                libboost-system-dev,
                libboost-timer-dev,
-               libncbi-vdb-dev (>= 2.11.2+dfsg-2),
-               libngs-sdk-dev
-Standards-Version: 4.6.1
+               libncbi-vdb-dev (>= 3),
+               libngs-c++-dev
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/skesa
 Vcs-Git: https://salsa.debian.org/med-team/skesa.git
 Homepage: https://github.com/ncbi/SKESA


=====================================
debian/patches/hardening.patch
=====================================
@@ -2,24 +2,20 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Wed, 17 Jul 2019 10:54:03 +0200
 Description: Propagate hardening options
 
-Index: skesa/Makefile
+Index: b/Makefile
 ===================================================================
---- skesa.orig/Makefile
-+++ skesa/Makefile
-@@ -40,10 +40,10 @@ NGS_INCL := -I $(NGS_PATH)/include
- NGS_LIB := -L $(NGS_PATH)/lib64
- 
- CC = c++ -std=c++11 -fdiagnostics-color=never
--CFLAGS = -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
-+CFLAGS += -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
+--- a/Makefile
++++ b/Makefile
+@@ -43,7 +43,7 @@ CC = c++ -std=c++11 -fdiagnostics-color=
+ CFLAGS = -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
           -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
  
--LIBS = $(VDB_LIB) -lncbi-ngs-c++ -lncbi-vdb \
-+LIBS += $(VDB_LIB) -lncbi-ngs-c++ -lncbi-vdb \
-        $(NGS_LIB) -lngs-c++ -lzstd \
+-LIBS = -lngs-c++ -lncbi-vdb -lzstd \
++LIBS += -lngs-c++ -lncbi-vdb -lzstd \
         -Wl,-Bstatic $(BOOST_LIB) \
         -lboost_program_options \
-@@ -70,7 +70,7 @@ glb_align.o: glb_align.hpp Makefile
+        -lboost_iostreams \
+@@ -69,7 +69,7 @@ glb_align.o: glb_align.hpp Makefile
  
  skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
  skesa: skesa.o glb_align.o


=====================================
debian/patches/link_boost_dynamically.patch
=====================================
@@ -0,0 +1,21 @@
+Index: b/Makefile
+===================================================================
+--- a/Makefile
++++ b/Makefile
+@@ -44,14 +44,14 @@ CFLAGS = -Wall -Wno-format-y2k  -pthread
+          -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
+ 
+ LIBS += -lngs-c++ -lncbi-vdb -lzstd \
+-       -Wl,-Bstatic $(BOOST_LIB) \
++       $(BOOST_LIB) \
+        -lboost_program_options \
+        -lboost_iostreams \
+        -lboost_regex \
+        -lboost_timer \
+        -lboost_chrono \
+        -lboost_system \
+-       -Wl,-Bdynamic -lrt -ldl -lm  -lpthread -lz
++       -lrt -ldl -lm  -lpthread -lz
+ 
+ %.o: %.cpp
+ 	$(CC) -c -o $@ $< $(CFLAGS)


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 use_debian_packaged_ngs-sdk.patch
 hardening.patch
+link_boost_dynamically.patch


=====================================
debian/patches/use_debian_packaged_ngs-sdk.patch
=====================================
@@ -2,22 +2,21 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Wed, 17 Jul 2019 10:54:03 +0200
 Description: Use Debian packaged ngs-sdk
 
-Index: skesa/Makefile
+Index: b/Makefile
 ===================================================================
---- skesa.orig/Makefile
-+++ skesa/Makefile
-@@ -43,8 +43,8 @@ CC = c++ -std=c++11 -fdiagnostics-color=
+--- a/Makefile
++++ b/Makefile
+@@ -43,8 +43,7 @@ CC = c++ -std=c++11 -fdiagnostics-color=
  CFLAGS = -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
           -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
  
 -LIBS = $(VDB_LIB) -lncbi-ngs-c++-static -lncbi-vdb-static \
 -       $(NGS_LIB) -lngs-c++-static \
-+LIBS = $(VDB_LIB) -lncbi-ngs-c++ -lncbi-vdb \
-+       $(NGS_LIB) -lngs-c++ -lzstd \
++LIBS = -lngs-c++ -lncbi-vdb -lzstd \
         -Wl,-Bstatic $(BOOST_LIB) \
         -lboost_program_options \
         -lboost_iostreams \
-@@ -68,15 +68,15 @@ clean:
+@@ -68,15 +67,15 @@ clean:
  
  glb_align.o: glb_align.hpp Makefile
  
@@ -36,16 +35,3 @@ Index: skesa/Makefile
  kmercounter: kmercounter.o glb_align.o
  	$(CC) -o $@ $^ $(LIBS)
  
-Index: skesa/ngs_includes.hpp
-===================================================================
---- skesa.orig/ngs_includes.hpp
-+++ skesa/ngs_includes.hpp
-@@ -24,7 +24,7 @@
- *
- */
- 
--#include <ncbi-vdb/NGS.hpp>
-+#include <ncbi-vdb/ngs/ncbi/NGS.hpp>
- #include <ngs/ErrorMsg.hpp>
- #include <ngs/ReadCollection.hpp>
- #include <ngs/ReadIterator.hpp>



View it on GitLab: https://salsa.debian.org/med-team/skesa/-/compare/228b7d5337a9a555aa9a75cc9eea9865ed8a2002...5208d7218d3c5043c6950f140981271f4bcc6467

-- 
View it on GitLab: https://salsa.debian.org/med-team/skesa/-/compare/228b7d5337a9a555aa9a75cc9eea9865ed8a2002...5208d7218d3c5043c6950f140981271f4bcc6467
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