[med-svn] [Git][med-team/hyphy][upstream] New upstream version 2.5.57+dfsg
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Nov 24 11:33:03 GMT 2023
Étienne Mollier pushed to branch upstream at Debian Med / hyphy
Commits:
39b2a0ec by Étienne Mollier at 2023-11-24T12:26:19+01:00
New upstream version 2.5.57+dfsg
- - - - -
3 changed files:
- CMakeLists.txt
- res/TemplateBatchFiles/MSS-selector.bf
- src/core/global_things.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -183,9 +183,9 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
endif()
if(${GCC_VERSION} VERSION_LESS 6.0)
- set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=gnu++14 -g ")
+ set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=gnu++14")
else(${GCC_VERSION} VERSION_LESS 6.0)
- set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -g")
+ set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14")
endif(${GCC_VERSION} VERSION_LESS 6.0)
#set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fopt-info")
@@ -492,11 +492,11 @@ if(${MPI_FOUND})
HYPHYMPI
PROPERTIES
if(${OPENMP_FOUND})
- COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g"
- LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS} -g"
+ COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
+ LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
else(${OPENMP_FOUND})
- COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} -g"
- LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} -g"
+ COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS}"
+ LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS}"
endif(${OPENMP_FOUND})
)
endif(${MPI_FOUND})
@@ -631,11 +631,11 @@ set_target_properties(
hyphy
PROPERTIES
if(${OPENMP_FOUND})
- COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -g "
- LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS} -g "
+ COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
+ LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
else(${OPENMP_FOUND})
- COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} -g "
- LINK_FLAGS "${DEFAULT_LINK_FLAGS} -g "
+ COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS}"
+ LINK_FLAGS "${DEFAULT_LINK_FLAGS}"
endif(${OPENMP_FOUND})
)
=====================================
res/TemplateBatchFiles/MSS-selector.bf
=====================================
@@ -69,7 +69,7 @@ mss.ic_score = io.SelectAnOption ({"AIC-c" : "Small Sample AIC score",
mss.is_bic = mss.ic_score == "BIC";
KeywordArgument ("classes", "How many rate classes should be considered", "2");
-mss.rate_classes = io.PromptUser ("How many rate classes should be considered?", 2, 2, 5, TRUE);
+mss.rate_classes = io.PromptUser ("How many rate classes should be considered?", 2, 2, 6, TRUE);
mss.file_records = {};
=====================================
src/core/global_things.cpp
=====================================
@@ -122,7 +122,7 @@ namespace hy_global {
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"),
kErrorNumerical ("To treat numerical errors as warnings, please specify \"ENV=TOLERATE_NUMERICAL_ERRORS=1;\" as the command line argument. This often resolves the issue, which is indicative of numerical instability."),
- kHyPhyVersion = _String ("2.5.56"),
+ kHyPhyVersion = _String ("2.5.57"),
kNoneToken = "None",
kNullToken = "null",
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/commit/39b2a0ecbed9e57d460f94e22dee214d46300852
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/commit/39b2a0ecbed9e57d460f94e22dee214d46300852
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