search

jonassibbesen / rpvg

Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
MIT License
47 stars 6 forks source link

build rpvg failed #40

Closed hailingfang closed 1 year ago

hailingfang commented 1 year ago

-- The C compiler identification is GNU 12.2.1 -- The CXX compiler identification is GNU 12.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- Found Protobuf: /usr/lib64/libprotobuf.so (found version "3.19.4") -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.0") -- Checking for module 'htslib' -- Found htslib, version 1.13 -- Configuring done -- Generating done -- Build files have been written to: /home/fanghl/rpvg/build

===============================

[ 84%] Building CXX object CMakeFiles/rpvg-tests.dir/src/tests/main_test.cpp.o In file included from /usr/include/signal.h:328, from /home/fanghl/rpvg/deps/Catch2/single_include/catch2/catch.hpp:8034, from /home/fanghl/rpvg/src/tests/main_test.cpp:4: /home/fanghl/rpvg/deps/Catch2/single_include/catch2/catch.hpp:10822:58: error: call to non-‘constexpr’ function ‘long int sysconf(int)’ 10822 | static constexpr std::size_t sigStackSize = 32768 >= MINSIGSTKSZ ? 32768 : MINSIGSTKSZ; | ^~~ In file included from /usr/include/bits/sigstksz.h:24: /usr/include/unistd.h:640:17: note: ‘long int sysconf(int)’ declared here 640 | extern long int sysconf (int name) THROW; | ^~~ /home/fanghl/rpvg/deps/Catch2/single_include/catch2/catch.hpp:10881:45: error: size of array ‘altStackMem’ is not an integral constant-expression 10881 | char FatalConditionHandler::altStackMem[sigStackSize] = {}; | ^~~~ make[2]: [CMakeFiles/rpvg-tests.dir/build.make:76: CMakeFiles/rpvg-tests.dir/src/tests/main_test.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:256: CMakeFiles/rpvg-tests.dir/all] Error 2 make: *** [Makefile:101: all] Error 2

===============================

I checkout Catch2 to v2.13.9 and the problem solved.

Hope this is helpful.

jonassibbesen commented 1 year ago

Hi, Thanks for letting me know. I just merged a PR that updates the Catch2 version used.