[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on ncbi-blast+ 2.16.0+ds-6 (yet more arch tuneups).

[Aaron M. Ucko (@ucko)]

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


Commits:
d00524e8 by Aaron M. Ucko at 2024-08-06T21:35:42-04:00
Start work on ncbi-blast+ 2.16.0+ds-6 (yet more arch tuneups).

- - - - -
aba12722 by Aaron M. Ucko at 2024-08-06T21:44:20-04:00
Reinstate big-endian builds, with default blastdb_version 4.

* debian/control: Reinstate big-endian builds, which can be salvaged
  adequately well.
* debian/patches/big_endian_workaround (new): On big-endian
  architectures, roll makeblastdb's and makeprofiledb's default
  blastdb_version back to 4 pending a proper fix.  Some things,
  including in particular q2-feature-classifier, will still explicitly
  request version 5, but everything else should be OK.  (See #1077777.)

- - - - -
56f72ef1 by Aaron M. Ucko at 2024-08-06T21:44:53-04:00
debian/rules: Try disabling optimization altogether on sh4.

- - - - -
5f9892c6 by Aaron M. Ucko at 2024-08-06T21:45:10-04:00
Finalize ncbi-blast+ 2.16.0+ds-6 for unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/big_endian_workaround
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+ncbi-blast+ (2.16.0+ds-6) unstable; urgency=medium
+
+  * debian/control: Reinstate big-endian builds, which can be salvaged
+    adequately well.
+  * debian/patches/big_endian_workaround (new): On big-endian
+    architectures, roll makeblastdb's and makeprofiledb's default
+    blastdb_version back to 4 pending a proper fix.  Some things,
+    including in particular q2-feature-classifier, will still explicitly
+    request version 5, but everything else should be OK.  (See #1077777.)
+  * debian/rules: Try disabling optimization altogether on sh4.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Tue, 06 Aug 2024 21:45:09 -0400
+
 ncbi-blast+ (2.16.0+ds-5) unstable; urgency=medium
 
   * debian/control: Forbid builds for big-endian architectures, at least


=====================================
debian/control
=====================================
@@ -6,7 +6,6 @@ Uploaders: Olivier Sallou <osallou at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               architecture-is-little-endian,
                autoconf2.69
 Build-Depends-Arch: libboost-test-dev,
                     libbz2-dev,


=====================================
debian/patches/big_endian_workaround
=====================================
@@ -0,0 +1,34 @@
+--- a/c++/src/app/blastdb/makeblastdb.cpp
++++ b/c++/src/app/blastdb/makeblastdb.cpp
+@@ -293,7 +293,13 @@ void CMakeBlastDBApp::Init()
+     arg_desc->AddDefaultKey("blastdb_version", "version",
+                              "Version of BLAST database to be created",
+                              CArgDescriptions::eInteger,
+-                             NStr::NumericToString(static_cast<int>(eBDB_Version5)));
++                             NStr::NumericToString(static_cast<int>
++#ifdef WORDS_BIGENDIAN
++						   (eBDB_Version4)
++#else
++						   (eBDB_Version5)
++#endif
++						   ));
+     arg_desc->SetConstraint("blastdb_version",
+                             new CArgAllow_Integers(eBDB_Version4, eBDB_Version5));
+     arg_desc->AddDefaultKey("max_file_sz", "number_of_bytes",
+--- a/c++/src/app/blastdb/makeprofiledb.cpp
++++ b/c++/src/app/blastdb/makeprofiledb.cpp
+@@ -420,7 +420,13 @@ void CMakeProfileDBApp::x_SetupArgDescri
+     arg_desc->AddDefaultKey("blastdb_version", "version",
+                              "Version of BLAST database to be created",
+                              CArgDescriptions::eInteger,
+-                             NStr::NumericToString(static_cast<int>(eBDB_Version5)));
++                             NStr::NumericToString(static_cast<int>
++#ifdef WORDS_BIGENDIAN
++						   (eBDB_Version4)
++#else
++						   (eBDB_Version5)
++#endif
++						   ));
+     arg_desc->SetConstraint("blastdb_version",
+                             new CArgAllow_Integers(eBDB_Version4, eBDB_Version5));
+ 


=====================================
debian/patches/series
=====================================
@@ -20,3 +20,4 @@ support_gcc10
 run_perl_directly
 tune_lmdb_defaults
 2to3
+big_endian_workaround


=====================================
debian/rules
=====================================
@@ -54,10 +54,13 @@ endif
 
 include /usr/share/dpkg/buildflags.mk
 
-ifneq (,$(filter mips% sh4,$(DEB_HOST_ARCH)))
+ifneq (,$(filter mips%,$(DEB_HOST_ARCH)))
 CXXFLAGS := $(CXXFLAGS:-O%=-O)
 DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
 endif
+ifeq (sh4,$(DEB_HOST_ARCH))
+DEB_CONFIGURE_COMMON_FLAGS += --without-optimization
+endif
 
 export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
 



View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/66da03abfe7a40c0dd64c70ca3339a8f179f0225...5f9892c67b474913eaf0d9b5f9261a8d771dbd28

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/66da03abfe7a40c0dd64c70ca3339a8f179f0225...5f9892c67b474913eaf0d9b5f9261a8d771dbd28
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