[med-svn] [Git][med-team/ncbi-vdb][master] 7 commits: Start work on ncbi-vdb 3.0.0+dfsg2-3 to fix non-amd64 builds.

Aaron M. Ucko (@ucko) gitlab at salsa.debian.org
Fri Sep 2 04:04:53 BST 2022 


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


Commits:
547c2352 by Aaron M. Ucko at 2022-09-01T21:39:39-04:00
Start work on ncbi-vdb 3.0.0+dfsg2-3 to fix non-amd64 builds.

- - - - -
981b371a by Aaron M. Ucko at 2022-09-01T21:41:35-04:00
debian/rules: Unhardcode architecture component in chrpath call.

- - - - -
f15ca4ad by Aaron M. Ucko at 2022-09-01T22:19:11-04:00
d/rules: Address arm64/aarch64 header path mismatch with a symlink.

* .gitignore: Ignore it.

- - - - -
f55d9739 by Aaron M. Ucko at 2022-09-01T22:20:10-04:00
debian/patches/detect_BITS.patch (new): Base BITS on sizeof(void *).

This change is particularly helpful on x32, which the build system
otherwise conflates with x86_64.

- - - - -
8e74a5d1 by Aaron M. Ucko at 2022-09-01T22:25:46-04:00
debian/patches/fix_x32.patch (new): Fully fix x32 builds.

In particular, don't try to build test-wvdb-slow when the address
space is only 32 bits wide.

- - - - -
a33e1527 by Aaron M. Ucko at 2022-09-01T22:30:04-04:00
d/patches/fix_cmake.patch: Explicitly link mbedtls's dependencies.

They see some direct usage.

- - - - -
7090c8b8 by Aaron M. Ucko at 2022-09-01T23:01:22-04:00
Finalize ncbi-vdb 3.0.0+dfsg2-3 for upload to experimental (still).

- - - - -


7 changed files:

- .gitignore
- debian/changelog
- + debian/patches/detect_BITS.patch
- debian/patches/fix_cmake.patch
- + debian/patches/fix_x32.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
.gitignore
=====================================
@@ -44,6 +44,7 @@ test/vfs/user-settings.mkfg
 test/vxf/local_config/user-settings.mkfg
 libs/cipher/cipher-1.7/cipher.egg-info
 
+interfaces/cc/gcc/aarch64
 libs/ngs-jni/jni.h
 libs/ngs-jni/jni_md.h
 obj-*


=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+ncbi-vdb (3.0.0+dfsg2-3) experimental; urgency=medium
+
+  * .gitignore: Ignore temporary interfaces/cc/gcc/aarch64 symlink.
+  * debian/patches/detect_BITS.patch (new): Base BITS on sizeof(void *).
+    This change is particularly helpful on x32, which the build system
+    otherwise conflates with x86_64.
+  * debian/patches/fix_cmake.patch: Explicitly link mbedtls's dependencies.
+    They see some direct usage.
+  * debian/patches/fix_x32.patch (new): Fully fix x32 builds.
+    In particular, don't try to build test-wvdb-slow when the address
+    space is only 32 bits wide.
+  * debian/rules:
+    - Unhardcode architecture component in chrpath call.
+    - Address arm64/aarch64 header path mismatch with a symlink.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Thu, 01 Sep 2022 23:01:22 -0400
+
 ncbi-vdb (3.0.0+dfsg2-2) experimental; urgency=medium
 
   * debian/.gitignore: Also ignore common-install-stamp.


=====================================
debian/patches/detect_BITS.patch
=====================================
@@ -0,0 +1,21 @@
+--- a/build/env.cmake
++++ b/build/env.cmake
+@@ -26,6 +26,8 @@
+ # Calculation of the global settings for the CMake build.
+ #
+ 
++include(CheckTypeSize)
++
+ # allow implicit source file extensions
+ if ( ${CMAKE_VERSION} VERSION_EQUAL "3.20" OR
+      ${CMAKE_VERSION} VERSION_GREATER "3.20")
+@@ -105,6 +107,9 @@ elseif ("x86_64" STREQUAL ${ARCH} )
+     endif()
+ endif()
+ 
++check_type_size("void *" SIZEOF_VOID_P)
++math(EXPR BITS "8 * ${SIZEOF_VOID_P}")
++
+ # now any unique combinations of OS and ARCH
+ if     ( "mac-x86_84" STREQUAL ${OS}-${ARCH})
+ elseif ( "linux-x86_64" STREQUAL ${OS}-${ARCH})


=====================================
debian/patches/fix_cmake.patch
=====================================
@@ -3,8 +3,6 @@ Last-Update: 2022-02-21 09:28:30 +0100
 Origin: https://lists.debian.org/debian-med/2022/02/msg00094.html
 Description: Set linker flags properly
 
-Index: ncbi-vdb/libs/CMakeLists.txt
-===================================================================
 --- ncbi-vdb.orig/libs/CMakeLists.txt
 +++ ncbi-vdb/libs/CMakeLists.txt
 @@ -32,7 +32,6 @@ add_subdirectory(axf) # sra tools depend
@@ -24,8 +22,6 @@ Index: ncbi-vdb/libs/CMakeLists.txt
      foreach( h IN ITEMS ${HEADERS} )
          install( DIRECTORY ${CMAKE_SOURCE_DIR}/interfaces/${h} DESTINATION ${INST_INCDIR} )
      endforeach()
-Index: ncbi-vdb/test/CMakeLists.txt
-===================================================================
 --- ncbi-vdb.orig/test/CMakeLists.txt
 +++ ncbi-vdb/test/CMakeLists.txt
 @@ -38,13 +38,12 @@ if( WIN32 )
@@ -44,8 +40,6 @@ Index: ncbi-vdb/test/CMakeLists.txt
  add_subdirectory(judy_test)
  add_subdirectory(klib)
  add_subdirectory(kfs)
-Index: ncbi-vdb/libs/ncbi-vdb/CMakeLists.txt
-===================================================================
 --- ncbi-vdb.orig/libs/ncbi-vdb/CMakeLists.txt
 +++ ncbi-vdb/libs/ncbi-vdb/CMakeLists.txt
 @@ -30,9 +30,6 @@ set( VDB_LIB_CMN_TARGETS
@@ -68,23 +62,23 @@ Index: ncbi-vdb/libs/ncbi-vdb/CMakeLists.txt
  )
  
  if( LibXml2_FOUND  )
-Index: ncbi-vdb/libs/ncbi-vdb/CMakeLists.posix.txt
-===================================================================
 --- ncbi-vdb.orig/libs/ncbi-vdb/CMakeLists.posix.txt
 +++ ncbi-vdb/libs/ncbi-vdb/CMakeLists.posix.txt
-@@ -32,7 +32,7 @@ endforeach()
+@@ -32,7 +32,8 @@ endforeach()
  
  add_library( ncbi-vdb STATIC "${VDB_LIB_RD}" )
  ExportStatic( ncbi-vdb true )
 -ExportShared( ncbi-vdb true "${LIBXML2};m;dl;pthread")
-+ExportShared( ncbi-vdb true "${LIBXML2};mbedtls;z;bz2;zstd;m;dl;pthread")
++ExportShared( ncbi-vdb true
++  "${LIBXML2};mbedtls;mbedx509;mbedcrypto;z;bz2;zstd;m;dl;pthread")
  
  ################################
  set( VDB_LIB_RDWR "" )
-@@ -42,5 +42,5 @@ endforeach()
+@@ -42,5 +43,6 @@ endforeach()
  
  add_library( ncbi-wvdb STATIC "${VDB_LIB_RDWR}" )
  ExportStatic( ncbi-wvdb true )
 -ExportShared( ncbi-wvdb true "${LIBXML2};m;dl;pthread")
-+ExportShared( ncbi-wvdb true "${LIBXML2};mbedtls;z;bz2;zstd;m;dl;pthread")
++ExportShared( ncbi-wvdb true
++  "${LIBXML2};mbedtls;mbedx509;mbedcrypto;z;bz2;zstd;m;dl;pthread")
  


=====================================
debian/patches/fix_x32.patch
=====================================
@@ -0,0 +1,12 @@
+--- a/test/vdb/CMakeLists.txt
++++ b/test/vdb/CMakeLists.txt
+@@ -54,7 +54,9 @@ AddExecutableTest( Test_VDB_VDB-4156 "te
+ 
+ # Slow tests
+ AddExecutableTest( SlowTest_VDB_vdb-slow "test-vdb-slow" "${COMMON_LIBS_READ}" )
++if (${BITS} GREATER 32)
+ AddExecutableTest( SlowTest_VDB_wvdb-slow "test-wvdb-slow" "${COMMON_LIBS_WRITE};${ADDITIONAL_LIBS}" )
++endif()
+ 
+ # TODO: make sure runs are not cached in the user repository when running tests
+ 


=====================================
debian/patches/series
=====================================
@@ -8,3 +8,5 @@ fix_build.patch
 fix_cmake.patch
 soversion.patch
 libsam-extract_shared.patch
+detect_BITS.patch
+fix_x32.patch


=====================================
debian/rules
=====================================
@@ -40,6 +40,7 @@ override_dh_auto_clean:
 	rm -f libs/ngs-jni/jni_md.h
 	rm -f build/ld.linux.exe_cmd.sh
 	rm -f debian/common-install-stamp
+	rm -f interfaces/cc/gcc/aarch64
 	rm -f test/cloud/cloud-kfg/.aws/c*
 	rm -f test/kdb/root/sra/SRR600096.sra.cache
 	rm -f test/kdb/user-settings.mkfg
@@ -52,6 +53,7 @@ override_dh_auto_clean:
 override_dh_auto_configure-indep:;
 
 override_dh_auto_build-arch:
+	ln -s arm64 interfaces/cc/gcc/aarch64
 	dh_auto_build --no-parallel -- NO_VDB3=1
 	# we need to make really sure that no 'vdb_'-prefixed functions will remain ...
 	if find . \( -name "*.so" -o -name "*.a" \) -exec strings \{\} \; | tee | grep -q vdb_mbedtls ; then \
@@ -125,6 +127,6 @@ override_dh_auto_install-arch: debian/common-install-stamp
 	d-shlibmove $(DSLMFLAGS) \
 		    $(LIBINSTALLDIR)/libsam-extract.so
 	find debian/lib* -name .gitignore -delete
-	chrpath --delete debian/libkdf5-3/usr/lib/x86_64-linux-gnu/libkdf5.so.3.0.0
+	chrpath --delete debian/libkdf5-3/usr/lib/$(MULTIARCH)/libkdf5.so.3.0.0
 
 override_dh_auto_install-indep: debian/common-install-stamp



View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/00144c55e75284c7dc3fb3152e6306fbc6a1e318...7090c8b87b8a9b01c33fd15d85ec1767a13d3ff9

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/00144c55e75284c7dc3fb3152e6306fbc6a1e318...7090c8b87b8a9b01c33fd15d85ec1767a13d3ff9
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