Hi Jose,
I got some problem in install st_viewer, the detail message are as belows. Could you help me to check the error? Thanks!
Best
Fuqing
When I run cmake command, it's work well and success.
cjx@9QLQZJL1QJJK014:~/st_viewer_build$ cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="/opt/QCustomPlot/qcustomplot" ../st_viewer
-- The CXX compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
--
-- Building a release version...
-- Performing Test COMPILER_SUPPORTS_PIC
-- Performing Test COMPILER_SUPPORTS_PIC - Success
-- Found Armadillo: /usr/lib/libarmadillo.so (found version "8.400.0")
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Configuring done
-- Generating done
-- Build files have been written to: /home/cjx/st_viewer_build
When I run make -j4, it's report this error as belows.(I just paste the error part)
Part I
/home/cjx/st_viewer/src/data/STData.cpp:298:34: error: no matching function for call to ‘log1p(arma::vec&)’
values = log1p(values);
^
In file included from /usr/include/features.h:424:0,
from /usr/include/x86_64-linux-gnu/c++/7/bits/os_defines.h:39,
from /usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h:533,
from /usr/include/c++/7/type_traits:38,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:45,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:43,
from /usr/include/x86_64-linux-gnu/qt5/QtCore/QSharedPointer:1,
from /home/cjx/st_viewer/src/data/STData.h:4,
from /home/cjx/st_viewer/src/data/STData.cpp:1:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: note: candidate: double log1p(double)
MATHCALL (log1p,, (Mdoublex));
^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: note: no known conversion for argument 1 from ‘arma::vec {aka arma::Col}’ to ‘double’
In file included from /usr/include/armadillo:26:0,
from /home/cjx/st_viewer/src/data/STData.h:17,
from /home/cjx/st_viewer/src/data/STData.cpp:1:
/usr/include/c++/7/cmath:1566:3: note: candidate: constexpr float std::log1p(float)
log1p(float x)
^~~~~
/usr/include/c++/7/cmath:1566:3: note: no known conversion for argument 1 from ‘arma::vec {aka arma::Col}’ to ‘float’
/usr/include/c++/7/cmath:1570:3: note: candidate: constexpr long double std::log1p(long double)
log1p(long double x)
^~~~~
/usr/include/c++/7/cmath:1570:3: note: no known conversion for argument 1 from ‘arma::vec {aka arma::Col}’ to ‘long double’
/usr/include/c++/7/cmath:1578:5: note: candidate: template constexpr typename gnu_cxx::__enable_if<std::is_integer<_Tp>::value, double>::type std::log1p(_Tp)
log1p(_Tp x)
^~~~~
/usr/include/c++/7/cmath:1578:5: note: template argument deduction/substitution failed:
/usr/include/c++/7/cmath: In substitution of ‘template constexpr typename __gnu_cxx::enable_if<std::is_integer<_Tp>::value, double>::type std::log1p(_Tp) [with _Tp = arma::Col]’:
/home/cjx/st_viewer/src/data/STData.cpp:298:34: required from here
/usr/include/c++/7/cmath:1578:5: error: no type named ‘type’ in ‘struct gnu_cxx::enable_if<false, double>’
/home/cjx/st_viewer/src/data/STData.cpp: In static member function ‘static STData::STDataFrame STData::aggregate(const QList&)’:
/home/cjx/st_viewer/src/data/STData.cpp:552:75: error: no matching function for call to ‘QSet::QSet(QList::const_iterator, QList::const_iterator)’
merged_genes += QSet(data.genes.begin(), data.genes.end());
Part II
At global scope:
cc1plus: error: unrecognized command line option ‘-Wno-unused-lambda-capture’ [-Werror]
cc1plus: error: unrecognized command line option ‘-Wno-unused-local-typedef’ [-Werror]
cc1plus: all warnings being treated as errors
src/data/CMakeFiles/data.dir/build.make:143: recipe for target 'src/data/CMakeFiles/data.dir/STData.cpp.o' failed
make[2]: [src/data/CMakeFiles/data.dir/STData.cpp.o] Error 1
make[2]: Leaving directory '/home/cjx/st_viewer_build'
CMakeFiles/Makefile2:473: recipe for target 'src/data/CMakeFiles/data.dir/all' failed
make[1]: [src/data/CMakeFiles/data.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Hi Jose, I got some problem in install st_viewer, the detail message are as belows. Could you help me to check the error? Thanks! Best Fuqing
When I run cmake command, it's work well and success.
cjx@9QLQZJL1QJJK014:~/st_viewer_build$ cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="/opt/QCustomPlot/qcustomplot" ../st_viewer -- The CXX compiler identification is GNU 7.5.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done
-- Building Spatial Transcriptomics Viewer ..... -- Change a configuration variable with: cmake -D=
-- CMAKE_INSTALL_PREFIX = /usr/local
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = /opt/QCustomPlot/qcustomplot
-- CMAKE_CXX_COMPILER = /usr/bin/c++
-- TARGET_ARCH =
-- VERSION = 0.8.7
-- CONFIGURATION FILE = /home/cjx/st_viewer/assets/stviewer.conf
-- -- Building a release version... -- Performing Test COMPILER_SUPPORTS_PIC -- Performing Test COMPILER_SUPPORTS_PIC - Success -- Found Armadillo: /usr/lib/libarmadillo.so (found version "8.400.0") -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Configuring done -- Generating done -- Build files have been written to: /home/cjx/st_viewer_build
When I run make -j4, it's report this error as belows.(I just paste the error part)
Part I
/home/cjx/st_viewer/src/data/STData.cpp:298:34: error: no matching function for call to ‘log1p(arma::vec&)’ values = log1p(values); ^ In file included from /usr/include/features.h:424:0, from /usr/include/x86_64-linux-gnu/c++/7/bits/os_defines.h:39, from /usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h:533, from /usr/include/c++/7/type_traits:38, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qsharedpointer.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QSharedPointer:1, from /home/cjx/st_viewer/src/data/STData.h:4, from /home/cjx/st_viewer/src/data/STData.cpp:1: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: note: candidate: double log1p(double) MATHCALL (log1p,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: note: no known conversion for argument 1 from ‘arma::vec {aka arma::Col}’ to ‘double’
In file included from /usr/include/armadillo:26:0,
from /home/cjx/st_viewer/src/data/STData.h:17,
from /home/cjx/st_viewer/src/data/STData.cpp:1:
/usr/include/c++/7/cmath:1566:3: note: candidate: constexpr float std::log1p(float)
log1p(float x)
^~~~~
/usr/include/c++/7/cmath:1566:3: note: no known conversion for argument 1 from ‘arma::vec {aka arma::Col}’ to ‘float’
/usr/include/c++/7/cmath:1570:3: note: candidate: constexpr long double std::log1p(long double)
log1p(long double x)
^~~~~
/usr/include/c++/7/cmath:1570:3: note: no known conversion for argument 1 from ‘arma::vec {aka arma::Col}’ to ‘long double’
/usr/include/c++/7/cmath:1578:5: note: candidate: template constexpr typename gnu_cxx::__enable_if<std::is_integer<_Tp>::value, double>::type std::log1p(_Tp)
log1p(_Tp x)
^~~~~
/usr/include/c++/7/cmath:1578:5: note: template argument deduction/substitution failed:
/usr/include/c++/7/cmath: In substitution of ‘template constexpr typename __gnu_cxx:: enable_if<std::is_integer<_Tp>::value, double>::type std::log1p(_Tp) [with _Tp = arma::Col]’:
/home/cjx/st_viewer/src/data/STData.cpp:298:34: required from here
/usr/include/c++/7/cmath:1578:5: error: no type named ‘type’ in ‘struct gnu_cxx:: enable_if<false, double>’
/home/cjx/st_viewer/src/data/STData.cpp: In static member function ‘static STData::STDataFrame STData::aggregate(const QList&)’:
/home/cjx/st_viewer/src/data/STData.cpp:552:75: error: no matching function for call to ‘QSet::QSet(QList::const_iterator, QList::const_iterator)’
merged_genes += QSet(data.genes.begin(), data.genes.end());
Part II
At global scope: cc1plus: error: unrecognized command line option ‘-Wno-unused-lambda-capture’ [-Werror] cc1plus: error: unrecognized command line option ‘-Wno-unused-local-typedef’ [-Werror] cc1plus: all warnings being treated as errors src/data/CMakeFiles/data.dir/build.make:143: recipe for target 'src/data/CMakeFiles/data.dir/STData.cpp.o' failed make[2]: [src/data/CMakeFiles/data.dir/STData.cpp.o] Error 1 make[2]: Leaving directory '/home/cjx/st_viewer_build' CMakeFiles/Makefile2:473: recipe for target 'src/data/CMakeFiles/data.dir/all' failed make[1]: [src/data/CMakeFiles/data.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs....
Part III
cd /home/cjx/st_viewer_build/src/viewPages && /usr/bin/c++ -DNO_QT_PRIVATE_HEADERS -DQT_CHARTS_LIB -DQT_CONCURRENT_LIB -DQT_CORE_LIB -DQT_DBUS_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_NO_DEBUG_OUTPUT -DQT_OPENGL_LIB -DQT_PRINTSUPPORT_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -I/home/cjx/st_viewer_build/src/viewPages -I/home/cjx/st_viewer/src/viewPages -I/home/cjx/st_viewer_build/src/viewPages/viewPages_autogen/include -I/home/cjx/st_viewer_build -I/home/cjx/st_viewer/src -I/home/cjx/st_viewer_build/src -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -I/usr/include/x86_64-linux-gnu/qt5/QtPrintSupport -I/usr/include/x86_64-linux-gnu/qt5/QtOpenGL -I/usr/include/x86_64-linux-gnu/qt5/QtConcurrent -I/usr/include/x86_64-linux-gnu/qt5/QtCharts -I/usr/include/x86_64-linux-gnu/qt5/QtDBus -I/usr/include/x86_64-linux-gnu/qt5/QtSvg -I/opt/QCustomPlot/qcustomplot -std=c++17 -Woverloaded-virtual -Wundef -Wall -Wextra -Wformat -Wunused-variable -Wreturn-type -Wempty-body -Wdisabled-optimization -Wredundant-decls -Wpacked -Wuninitialized -Wswitch -pedantic-errors -fuse-cxa-atexit -ffast-math -funroll-loops -Wno-unused-parameter -Wno-unused-function -Wno-undef -Wno-missing-declarations -Wno-unknown-pragmas -Wno-sign-compare -Wno-cast-qual -Wno-cast-align -Wno-redundant-decls -Wno-implicit-fallthrough -Wno-unused-local-typedef -Wno-unused-lambda-capture -Wno-pedantic -Wno-deprecated -Wno-parentheses -Werror -fopenmp -O3 -DNDEBUG -fPIC -std=gnu++1z -o CMakeFiles/viewPages.dir/ClustersWidget.cpp.o -c /home/cjx/st_viewer/src/viewPages/ClustersWidget.cpp make[2]: Leaving directory '/home/cjx/st_viewer_build' [ 57%] Built target viewPages make[1]: Leaving directory '/home/cjx/st_viewer_build' Makefile:154: recipe for target 'all' failed make: *** [all] Error 2