[med-svn] [Git][med-team/ncbi-vdb][master] 3 commits: zstd.patch: Adopt dynamic system zstd more fully.

[Aaron M. Ucko (@ucko)]

Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb


Commits:
545d1b2f by Aaron M. Ucko at 2021-11-22T22:34:52-05:00
zstd.patch: Adopt dynamic system zstd more fully.

* Comment out ZSTD_STATIC_LINKING_ONLY to enforce use of stable APIs.
* Actually link libncbi-(w)vdb and libvdb-sqlite against libzstd.

- - - - -
c4a37fff by Aaron M. Ucko at 2021-11-22T22:38:25-05:00
Have libncbi-vdb2 break sra-toolkit (<< 2.11) anyway.

Even with zstd linkage fixed, sra-toolkit 2.10.x's autopkgtest will
still fail over dropped support for protected repository configuration.

- - - - -
6566a485 by Aaron M. Ucko at 2021-11-22T22:39:27-05:00
Finalize ncbi-vdb 2.11.2+dfsg-4 for unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/patches/zstd.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+ncbi-vdb (2.11.2+dfsg-4) unstable; urgency=medium
+
+  * zstd.patch: Adopt dynamic system zstd more fully.
+    - Comment out ZSTD_STATIC_LINKING_ONLY to enforce use of stable APIs.
+    - Actually link libncbi-(w)vdb and libvdb-sqlite against libzstd.
+  * Have libncbi-vdb2 break sra-toolkit (<< 2.11) anyway -- even with zstd
+    linkage fixed, sra-toolkit 2.10.x's autopkgtest will still fail over
+    dropped support for protected repository configuration.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Mon, 22 Nov 2021 22:39:27 -0500
+
 ncbi-vdb (2.11.2+dfsg-3) unstable; urgency=medium
 
   * Leave mbedtls quirk handling to d-shlibs (>= 0.104).  (Closes: #999788.)


=====================================
debian/control
=====================================
@@ -28,6 +28,7 @@ Architecture: amd64 arm64 i386 x32
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Breaks: sra-toolkit (<< 2.11~)
 Description: libraries for using data in the INSDC Sequence Read Archives
  NGS is a new, domain-specific API for accessing reads, alignments and
  pileups produced from Next Generation Sequencing. The API itself is


=====================================
debian/patches/zstd.patch
=====================================
@@ -1,14 +1,16 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 11 Oct 2021 11:37:20 +0200
+Author: Andreas Tille <tille at debian.org>, Aaron Ucko <ucko at debian.org>
+Last-Update: Mon, 22 Nov 2021 22:14:57 -0500
 Description: Use Debian packaged libzstd
 
 --- a/libs/vxf/zstd.c
 +++ b/libs/vxf/zstd.c
-@@ -32,7 +32,7 @@
+@@ -31,8 +31,8 @@
+ #include <klib/log.h>
  #include <vdb/xform.h>
  
- #define ZSTD_STATIC_LINKING_ONLY
+-#define ZSTD_STATIC_LINKING_ONLY
 -#include <ext/zstd.h>
++/* #define ZSTD_STATIC_LINKING_ONLY */
 +#include <zstd.h>
  
  #ifndef ZSTD_MIN_LEVEL
@@ -24,3 +26,34 @@ Description: Use Debian packaged libzstd
  
  #include <klib/rc.h>
  #include <vdb/xform.h>
+--- a/libs/ncbi-vdb/Makefile
++++ b/libs/ncbi-vdb/Makefile
+@@ -152,7 +152,7 @@ VDB_OBJ = \
+ 	$(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))
+ 
+ VDB_LIB = \
+-	$(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto
++	$(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto -lzstd
+ 
+ $(LIBDIR)/libncbi-vdb.$(LIBX): $(VDB_OBJ)
+ 	$(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB)
+@@ -178,7 +178,7 @@ WVDB_OBJ = \
+ 	$(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RDWR)))
+ 
+ WVDB_LIB = \
+-	$(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto
++	$(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto -lzstd
+ 
+ $(LIBDIR)/libncbi-wvdb.$(LIBX): $(WVDB_OBJ)
+ 	$(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(WVDB_LIB)
+--- a/libs/vdb-sqlite/Makefile
++++ b/libs/vdb-sqlite/Makefile
+@@ -85,7 +85,7 @@ VDB_SQLITE_OBJ = \
+ 	$(addsuffix .$(LOBX),$(VDB_SQLITE_SRC))
+ 
+ VDB_SQLITE_LIB = \
+-	-sncbi-vdb -lmbedx509 -lmbedtls -lmbedcrypto -lz -lbz2
++	-sncbi-vdb -lmbedx509 -lmbedtls -lmbedcrypto -lzstd -lz -lbz2
+ 
+ VDB_SQLITE_VERS = \
+ 	$(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers



View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/182e49d87c8912f3311376f0455ce968ce8a9a40...6566a48576b6eafaf1cbd15c6b3b36363a066c50

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/182e49d87c8912f3311376f0455ce968ce8a9a40...6566a48576b6eafaf1cbd15c6b3b36363a066c50
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20211123/ad98be37/attachment-0001.htm>