[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on ncbi-blast+ 2.16.0+ds-2 to fix FTBFS on some archs.

[Aaron M. Ucko (@ucko)]

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


Commits:
accc7d00 by Aaron M. Ucko at 2024-07-26T14:28:02-04:00
Start work on ncbi-blast+ 2.16.0+ds-2 to fix FTBFS on some archs.

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14aea822 by Aaron M. Ucko at 2024-07-26T14:43:38-04:00
debian/rules: Link with -latomic on most 32-bit architectures

... excepting only x86 and armhf, which succeed as is.

- - - - -
c0f41780 by Aaron M. Ucko at 2024-07-26T14:54:31-04:00
debian/patches/hurd_fixes: Extend to ncbi_localip.c.

It otherwise accommodates PATH_MAX's absence only under Windows.

- - - - -
31d0b479 by Aaron M. Ucko at 2024-07-26T14:54:56-04:00
Finalize ncbi-blast+ 2.16.0+ds-2 for unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/patches/hurd_fixes
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+ncbi-blast+ (2.16.0+ds-2) unstable; urgency=medium
+
+  * debian/patches/hurd_fixes: Extend to ncbi_localip.c, which otherwise
+    accommodates PATH_MAX's absence only under Windows.
+  * debian/rules: Link with -latomic on most 32-bit architectures
+    (excepting only x86 and armhf, which succeed as is).
+
+ -- Aaron M. Ucko <ucko at debian.org>  Fri, 26 Jul 2024 14:54:55 -0400
+
 ncbi-blast+ (2.16.0+ds-1) unstable; urgency=medium
 
   * New upstream release, which should be (more than) new enough for


=====================================
debian/patches/hurd_fixes
=====================================
@@ -40,3 +40,14 @@ Last-Update: 2020-09-19
  #  define PATH_MAX 512                  // will actually use less than 32 chars
  #endif // NCBI_OS_MSWIN && !PATH_MAX
  
+--- a/c++/src/connect/ncbi_localip.c
++++ b/c++/src/connect/ncbi_localip.c
+@@ -67,7 +67,7 @@
+ #  define INADDR_LOOPBACK  0x7F000001
+ #endif /*!INADDR_LOOPBACK*/
+ 
+-#if defined(NCBI_OS_MSWIN)  &&  !defined(PATH_MAX)
++#if /* defined(NCBI_OS_MSWIN)  && */ !defined(PATH_MAX)
+ #  ifdef _MAX_PATH
+ #    define PATH_MAX  _MAX_PATH
+ #else


=====================================
debian/rules
=====================================
@@ -28,6 +28,12 @@ DEB_CONFIGURE_EXTRA_FLAGS += --without-strip --with-symbols
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie reproducible=-timeless
 export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
 
+ifeq ($(DEB_HOST_ARCH_BITS),32)
+  ifeq (,$(filter armhf %i386 x32,$(DEB_HOST_ARCH))
+    export LIBS=-latomic
+  endif
+endif
+
 include /usr/share/dpkg/architecture.mk
 include /usr/share/dpkg/buildflags.mk
 



View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/1411bc81806aad716ae2e204821a73378587bf88...31d0b4795bf0f8056948bd455ef1bae5915a85c5

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