[med-svn] [Git][med-team/ncbi-blastplus][master] 5 commits: Start work on ncbi-blast+ 2.16.0+ds5 (more arch tuneups).

[Aaron M. Ucko (@ucko)]

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


Commits:
43e1771a by Aaron M. Ucko at 2024-08-04T15:52:26-04:00
Start work on ncbi-blast+ 2.16.0+ds5 (more arch tuneups).

- - - - -
32585817 by Aaron M. Ucko at 2024-08-04T15:58:14-04:00
d/control: Forbid builds for big-endian archs, at least for now.

They nominally succeed, but two dependent autopkgtests (for cct and
kleborate) have started failing on s390x, and there's no evidence that
other BE architectures fare any better.  (See #1077777.)

- - - - -
55470f19 by Aaron M. Ucko at 2024-08-04T16:00:50-04:00
debian/rules: Try building with -fsection-anchors on alpha

... in hopes of satisfying the GOT size limit there too.

- - - - -
17b63f36 by Aaron M. Ucko at 2024-08-04T16:04:02-04:00
Extend -O1 cap to sh4, which still encountered VM exhaustion.

- - - - -
66da03ab by Aaron M. Ucko at 2024-08-04T16:04:33-04:00
Finalize ncbi-blast+ 2.16.0+ds-5 for unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+ncbi-blast+ (2.16.0+ds-5) unstable; urgency=medium
+
+  * debian/control: Forbid builds for big-endian architectures, at least
+    for now.  They nominally succeed, but two dependent autopkgtests (for
+    cct and kleborate) have started failing on s390x, and there's no
+    evidence that other BE architectures fare any better.  (See #1077777.)
+  * debian/rules:
+    - Try building with -fsection-anchors on alpha in hopes of satisfying
+      the GOT size limit there too.
+    - Extend -O1 cap to sh4, which still encountered VM exhaustion.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Sun, 04 Aug 2024 16:04:32 -0400
+
 ncbi-blast+ (2.16.0+ds-4) unstable; urgency=medium
 
   * debian/rules:


=====================================
debian/control
=====================================
@@ -6,6 +6,7 @@ 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/rules
=====================================
@@ -38,6 +38,10 @@ ifeq ($(DEB_HOST_ARCH_BITS),32)
   endif
 endif
 
+ifeq (alpha,$(DEB_HOST_ARCH))
+  export DEB_CFLAGS_MAINT_APPEND   += -fsection-anchors
+  export DEB_CXXFLAGS_MAINT_APPEND += -fsection-anchors
+endif
 ifeq (hppa,$(DEB_HOST_ARCH))
   export DEB_CFLAGS_MAINT_APPEND   += -ffunction-sections
   export DEB_CXXFLAGS_MAINT_APPEND += -ffunction-sections
@@ -50,7 +54,7 @@ endif
 
 include /usr/share/dpkg/buildflags.mk
 
-ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
+ifneq (,$(filter mips% sh4,$(DEB_HOST_ARCH)))
 CXXFLAGS := $(CXXFLAGS:-O%=-O)
 DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
 endif



View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/52c39a81773b4fd6326a51d10183dbb44e296ae1...66da03abfe7a40c0dd64c70ca3339a8f179f0225

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/52c39a81773b4fd6326a51d10183dbb44e296ae1...66da03abfe7a40c0dd64c70ca3339a8f179f0225
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/20240804/a82b885d/attachment-0001.htm>