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@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 <[email protected]> Sun, 28 Jul 2019 01:08:15 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> -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 You're receiving this email because of your account on salsa.debian.org.
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