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 <[email protected]> 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 <[email protected]>, 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 You're receiving this email because of your account on salsa.debian.org.
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