[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on ncbi-blast+ 2.17.0-ds3 for 1117022 and 1117023.

[Aaron M. Ucko (@ucko)]

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


Commits:
90383e12 by Aaron M. Ucko at 2025-10-16T15:54:57-04:00
Start work on ncbi-blast+ 2.17.0-ds3 for 1117022 and 1117023.

- - - - -
f8a96fcd by Aaron M. Ucko at 2025-10-16T16:10:18-04:00
Stick with software CRC-32C on 32-bit ARM (#1117022).

* debian/control: Restrict armv8crc-support dependency to arm64.
* debian/patches/zcf-simde-crc32c: Leave CFLAGS alone on 32-bit ARM;
  adjustments aren't actually worthwhile there and would have needed to
  go further on armhf, on which (at least under GCC) ARMv8 targets
  additionally need +simd.  (Closes: #1117022.)

- - - - -
1aa65de7 by Aaron M. Ucko at 2025-10-16T16:13:35-04:00
d/p/support_x32: Slightly broaden VDB allow-list (#1117023)

... in configure(.ac).

- - - - -
36649aa9 by Aaron M. Ucko at 2025-10-16T16:15:13-04:00
Finalize ncbi-blast+ 2.17.0+ds-3 for unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/support_x32
- debian/patches/zcf-simde-crc32c


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+ncbi-blast+ (2.17.0+ds-3) unstable; urgency=medium
+
+  * debian/control: Restrict armv8crc-support dependency to arm64.
+  * debian/patches/support_x32: Slightly broaden configure(.ac)'s VDB
+    allow-list.  (Closes: #1117023.)
+  * debian/patches/zcf-simde-crc32c: Leave CFLAGS alone on 32-bit ARM;
+    adjustments aren't actually worthwhile there and would have needed to
+    go further on armhf, on which (at least under GCC) ARMv8 targets
+    additionally need +simd.  (Closes: #1117022.)
+
+ -- Aaron M. Ucko <ucko at debian.org>  Thu, 16 Oct 2025 16:15:12 -0400
+
 ncbi-blast+ (2.17.0+ds-2) unstable; urgency=medium
 
   * debian/control:


=====================================
debian/control
=====================================
@@ -35,7 +35,7 @@ Package: ncbi-blast+
 Architecture: any
 Multi-Arch: foreign
 Depends:
- armv8crc-support [any-arm arm64],
+ armv8crc-support [arm64],
  ncbi-data,
  python3,
  sse4.2-support [any-amd64 any-i386 any-x32],


=====================================
debian/patches/support_x32
=====================================
@@ -14,3 +14,25 @@ Avoid picking up wrong inline assembly.
  #    define NCBI_COUNTER_64_BIT
  #  endif
  #  ifdef NCBI_COUNTER_64_BIT
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -28265,7 +28265,7 @@ $as_echo "$as_me: WARNING: $message" >&2
+             darwin*:*86*:64 ) vdb_libpath=mac/$vdb_mode/x86_64/lib   ;;
+             darwin*:*86*:* )  vdb_libpath=mac/$vdb_mode/fat86/lib    ;;
+             darwin*:arm*   )  vdb_libpath=mac/$vdb_mode/arm64/lib    ;;
+-            linux*:*86*:64 )  vdb_libpath=linux/$vdb_mode/x86_64/lib ;;
++            linux*:*86*64  )  vdb_libpath=linux/$vdb_mode/x86_64/lib ;;
+             linux*:aarch64* ) vdb_libpath=linux/$vdb_mode/arm64/lib  ;;
+             * )
+                if test -n "$with_vdb"; then
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -7837,7 +7837,7 @@ if test "$with_vdb" != "no" ; then
+             darwin*:*86*:64 ) vdb_libpath=mac/$vdb_mode/x86_64/lib   ;;
+             darwin*:*86*:* )  vdb_libpath=mac/$vdb_mode/fat86/lib    ;;
+             darwin*:arm*   )  vdb_libpath=mac/$vdb_mode/arm64/lib    ;;
+-            linux*:*86*:64 )  vdb_libpath=linux/$vdb_mode/x86_64/lib ;;
++            linux*:*86*64  )  vdb_libpath=linux/$vdb_mode/x86_64/lib ;;
+             linux*:aarch64* ) vdb_libpath=linux/$vdb_mode/arm64/lib  ;;
+             * )
+                if test -n "$with_vdb"; then


=====================================
debian/patches/zcf-simde-crc32c
=====================================
@@ -30,3 +30,13 @@
  /* ===========================================================================
   * Insert string str in the dictionary and return the previous head
   * of the hash chain (the most recent string with same hash key).
+--- a/c++/src/util/compress/zlib_cloudflare/Makefile.zlib_cf.lib.unix
++++ b/c++/src/util/compress/zlib_cloudflare/Makefile.zlib_cf.lib.unix
+@@ -1,6 +1,6 @@
+ # $Id: Makefile.zlib_cf.lib.unix 677587 2024-01-18 20:07:53Z ivanov $
+ 
+-ifneq "" "$(findstring --arm,$(signature))$(findstring --aarch64,$(signature))"
++ifneq "" "$(findstring --arm64,$(signature))$(findstring --aarch64,$(signature))"
+   crc32.o:   CFLAGS += -march=armv8-a+crc
+   deflate.o: CFLAGS += -march=armv8-a+crc
+ endif



View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/8583d2dbeb911fe85599c7097f49f2270e8689fd...36649aa9ff049e56e2be8b4d4e06325dec7d4de9

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/8583d2dbeb911fe85599c7097f49f2270e8689fd...36649aa9ff049e56e2be8b4d4e06325dec7d4de9
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