CMakeLists.txt

@@ -189,7 +189,8 @@ endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3")
     PCL_CHECK_FOR_AVX()
-    if(${HAVE_AVX_EXTENSIONS})
+
+    if(${HAVE_AVX_EXTENSIONS} AND NOT ${NOAVX})
         set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")
         add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
         PCL_CHECK_FOR_FMA3()
@@ -197,7 +198,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
             set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mfma")
             add_definitions (-D_SLKP_USE_FMA3_INTRINSICS)
         endif (${HAVE_FMA3})
-    else(${HAVE_AVX_EXTENSIONS})
+    else(${HAVE_AVX_EXTENSIONS} AND NOT ${NOAVX})
         PCL_CHECK_FOR_SSE3()
         if(${HAVE_SSE3_EXTENSIONS})
             add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
@@ -290,7 +291,7 @@ if(NOT NODE)
     message("Node not installed; API documentation will not be generated")
 else(NOT NODE)
     add_custom_target(
-        docs ALL
+        docs
         rm -rf ./docs && npm install -g documentation@4 && documentation build --polyglot -f md ./res/TemplateBatchFiles/libv3/**/*.bf -o ./docs.md
     )
 endif(NOT NODE)

debian/changelog

-hyphy (2.5.0+dfsg-1) UNRELEASED; urgency=medium
+hyphy (2.5.1+dfsg-1) UNRELEASED; urgency=medium
 
+  [ Helmut Grohne ]
+  * Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross
+    compilation. (Closes: #943311)
+
+  [ Andreas Tille ]
   * New upstream version
   * debhelper-compat 12
-  * Standards-Version: 4.4.0
   * Secure URI in copyright format
   * Remove trailing whitespace in debian/changelog
+  * New upstream version
+  * Standards-Version: 4.4.1
+  * Use secure URI in Homepage field.
+  * Remove patches msse_option_only_if_available.patch that are missing
+    from debian/patches/series.
   TODO: Fix build failure
 
- -- Andreas Tille <tille@debian.org>  Sun, 28 Jul 2019 01:08:15 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Dec 2019 13:30:30 +0100
 
 hyphy (2.3.14+dfsg-2) unstable; urgency=medium
 

debian/control

@@ -8,11 +8,12 @@ Build-Depends: debhelper-compat (= 12),
                mpi-default-dev,
                libcurl4-gnutls-dev | libcurl4-dev,
                libssl-dev,
-               libsqlite3-dev
-Standards-Version: 4.4.0
+               libsqlite3-dev,
+               pkg-config
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/hyphy
 Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
-Homepage: http://hyphy.org/
+Homepage: https://hyphy.org/
 
 Package: hyphy-pt
 Architecture: any

debian/patches/msse_option_only_if_available.patch

-Description: Make sure that also in tests the existence of SSE3 extension is done
- --> deactivated
-Bug-Debian: http://bugs.debian.org/793344
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 23 Jul 2015 13:12:54 +0200
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -438,12 +438,23 @@ set_property(
-     TARGET HYPHYGTEST
-     APPEND PROPERTY COMPILE_DEFINITIONS __UNITTEST__
- )
-+
-+PCL_CHECK_FOR_SSE3()
-+if(${HAVE_SSE3_EXTENSIONS})
- set_target_properties(
-     HYPHYGTEST
-     PROPERTIES
-     COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3"
-     LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3"
- )
-+else(${HAVE_SSE3_EXTENSIONS})
-+set_target_properties(
-+    HYPHYGTEST
-+    PROPERTIES
-+    COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
-+    LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
-+)
-+endif(${HAVE_SSE3_EXTENSIONS})
- 
- 
- #-------------------------------------------------------------------------------

src/core/global_things.cpp

@@ -119,7 +119,7 @@ namespace hy_global {
                      kErrorStringDatasetRefIndexError ("Dataset index reference out of range"),
                      kErrorStringMatrixExportError    ("Export matrix called with a non-polynomial matrix argument"),
                      kErrorStringNullOperand          ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
-                      kHyPhyVersion  = _String ("2.5.0"),
+                      kHyPhyVersion  = _String ("2.5.1"),
     
                     kNoneToken = "None",
                     kNullToken = "null",

src/core/strings.cpp

@@ -52,7 +52,7 @@
 
 
 _String   compileDate = __DATE__,
-          __HYPHY__VERSION__ = _String ("2.5.0");
+          __HYPHY__VERSION__ = _String ("2.5.1");
 
 using namespace hy_global;