I am trying to build manta from source but I have a wall of error such as:
ERROR manta-1.5.0: manta-1.5.0/src/c++/lib/applications/GenerateSVCandidates/SVFinder.cpp:630:1: error: style:The scope of the variable 'readSuppBp' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
FINE manta-1.5.0: void f(int x)
FINE manta-1.5.0: {
FINE manta-1.5.0: int i = 0;
FINE manta-1.5.0: if (x) {
FINE manta-1.5.0: // it's safe to move 'int i = 0;' here
FINE manta-1.5.0: for (int n = 0; n < 10; ++n) {
FINE manta-1.5.0: // it is possible but not safe to move 'int i = 0;' here
FINE manta-1.5.0: do_something(&i);
FINE manta-1.5.0: }
FINE manta-1.5.0: }
FINE manta-1.5.0: }
FINE manta-1.5.0: When you see this message it is always safe to reduce the variable scope 1 level.
ERROR manta-1.5.0: manta-1.5.0/src/c++/lib/applications/GenerateSVCandidates/SVScorer.cpp:81:1: error: style:Consider using std::count_if algorithm instead of a raw loop.
ERROR manta-1.5.0: manta-1.5.0/src/c++/lib/applications/GenerateSVCandidates/test/EdgeRetrieverBinTest.cpp:29:1: error: error:There is an unknown macro here somewhere. Configuration is required. If BOOST_AUTO_TEST_SUITE is a macro then please configure it.
I tried to fix the second error with BOOST_AUTO_TEST_SUITE applying boost guideline as follow:
for testFile in $(find src/c++ -type f -name '*Test.cpp' ); do
testFileBasename=$(basename "${testFile}" .cpp)
sed -i "/\"boost\/test\/unit_test.hpp\"/c\#define BOOST_TEST_MODULE ${testFileBasename}\n#include <boost/test/included/unit_test.hpp>" "${testFile}"
done
Which gave as example for src/c++/lib/alignment/test/AlignmentUtilTest.cpp:
Anyway it would be welcome to be able to build manta offline and used our already built samtools release
maybe for this purpose commenting add_subdirectory (redist) line from CMakeLists.txt is enough
sed -i 's/add_subdirectory (redist)/# &/' CMakeLists.txt
Dear,
I am trying to build manta from source but I have a wall of error such as:
I tried to fix the second error with BOOST_AUTO_TEST_SUITE applying boost guideline as follow:
Which gave as example for
src/c++/lib/alignment/test/AlignmentUtilTest.cpp
:But that do not fix this error
Anyway it would be welcome to be able to build manta offline and used our already built samtools release maybe for this purpose commenting
add_subdirectory (redist)
line from CMakeLists.txt is enoughThanks for your help best regards