[med-svn] [Git][med-team/hyphy][master] 8 commits: Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross compilation
Andreas Tille
gitlab at salsa.debian.org
Fri Dec 6 12:41:02 GMT 2019
Andreas Tille pushed to branch master at Debian Med / hyphy
Commits:
58f5e817 by Andreas Tille at 2019-12-06T12:28:25Z
Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross compilation
- - - - -
35e8076f by Andreas Tille at 2019-12-06T12:30:30Z
routine-update: New upstream version
- - - - -
a6bb7eb3 by Andreas Tille at 2019-12-06T12:30:31Z
New upstream version 2.5.1+dfsg
- - - - -
f45f6fbd by Andreas Tille at 2019-12-06T12:30:43Z
Update upstream source from tag 'upstream/2.5.1+dfsg'
Update to upstream version '2.5.1+dfsg'
with Debian dir c3fee3e619e5bea520e22044ed8e607b83fd5876
- - - - -
1d09f1f8 by Andreas Tille at 2019-12-06T12:30:47Z
routine-update: Standards-Version: 4.4.1
- - - - -
e00bf264 by Andreas Tille at 2019-12-06T12:30:50Z
Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
- - - - -
850fca6c by Andreas Tille at 2019-12-06T12:30:51Z
Remove patches msse_option_only_if_available.patch that are missing from debian/patches/series.
Fixes lintian: patch-file-present-but-not-mentioned-in-series
See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details.
- - - - -
df335440 by Andreas Tille at 2019-12-06T12:40:40Z
Build keeps on failing - needs time to investigate
- - - - -
6 changed files:
- CMakeLists.txt
- debian/changelog
- debian/control
- − debian/patches/msse_option_only_if_available.patch
- src/core/global_things.cpp
- src/core/strings.cpp
Changes:
=====================================
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 at 4 && documentation build --polyglot -f md ./res/TemplateBatchFiles/libv3/**/*.bf -o ./docs.md
)
endif(NOT NODE)
=====================================
debian/changelog
=====================================
@@ -1,13 +1,22 @@
-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 at debian.org> Sun, 28 Jul 2019 01:08:15 +0200
+ -- Andreas Tille <tille at 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 deleted
=====================================
@@ -1,32 +0,0 @@
-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 at 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;
View it on GitLab: https://salsa.debian.org/med-team/hyphy/compare/62e35b115323a53d000bdac86c68ca50ece84c5d...df335440535562f7c62290cfdf726ced74abcdd8
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/compare/62e35b115323a53d000bdac86c68ca50ece84c5d...df335440535562f7c62290cfdf726ced74abcdd8
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