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AutoFlowResearch / SmartPeak

Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
MIT License
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Scripting issues during make #462

Open oligegilo opened 2 years ago

oligegilo commented 2 years ago

Hi all, after I managed to get cmake working, make ran into some scripting issues - I guess it's because I'm working on a RedHat system which sometimes needs a special treatment. The output of make is like below. Would be great if that could be adjusted so that make succeeds. Thank you!

[ 1%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 1%] Building CXX object src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/CastValue.cpp.o [ 2%] Building CXX object src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ApplicationProcessor.cpp.o [ 3%] Building CXX object src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ConsoleHandler.cpp.o /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp: In member function ‘bool SmartPeak::CastValue::is_lessthan(const SmartPeak::CastValue&, bool) const’: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:217:16: error: ‘transform’ is not a member of ‘std’ std::transform(s.begin(), s_.end(), alowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:218:16: error: ‘transform’ is not a member of ‘std’ std::transform(other.s.begin(), other.s_.end(), b_lowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp: In member function ‘bool SmartPeak::CastValue::is_greaterthan(const SmartPeak::CastValue&, bool) const’: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:252:14: error: ‘transform’ is not a member of ‘std’ std::transform(s.begin(), s_.end(), alowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:253:14: error: ‘transform’ is not a member of ‘std’ std::transform(other.s.begin(), other.s_.end(), b_lowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp: In member function ‘bool SmartPeak::CastValue::is_equalto(const SmartPeak::CastValue&, bool) const’: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:287:14: error: ‘transform’ is not a member of ‘std’ std::transform(s.begin(), s_.end(), alowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:288:14: error: ‘transform’ is not a member of ‘std’ std::transform(other.s.begin(), other.s_.end(), b_lowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp: In lambda function: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:314:16: error: ‘transform’ is not a member of ‘std’ std::transform(l.begin(), l.end(), a_lowercase.begin(), ::tolower); ^~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:315:16: error: ‘transform’ is not a member of ‘std’ std::transform(r.begin(), r.end(), b_lowercase.begin(), ::tolower); ^~~~~ make[2]: [src/smartpeak/CMakeFiles/SmartPeak.dir/build.make:90: src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/CastValue.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:23: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:176:27: error: ‘RollingFileAppender’ is not a member of ‘plog’ std::shared_ptr<plog::RollingFileAppender> m_file_appender; ^~~~~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:176:27: note: suggested alternative: ‘ConsoleAppender’ std::shared_ptr<plog::RollingFileAppender> m_file_appender; ^~~~~~~ ConsoleAppender /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:176:53: error: ‘CsvFormatter’ is not a member of ‘plog’ std::shared_ptr<plog::RollingFileAppender> m_file_appender; ^~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:176:53: error: template argument 1 is invalid /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:176:65: error: expected unqualified-id before ‘>’ token std::shared_ptr<plog::RollingFileAppender> m_file_appender; ^~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:177:49: error: ‘TxtFormatter’ is not a member of ‘plog’ std::shared_ptr<plog::ConsoleAppender> m_console_appender; ^~~~ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:177:49: error: template argument 1 is invalid /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:177:61: error: template argument 1 is invalid std::shared_ptr<plog::ConsoleAppender> m_console_appender; ^~ In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationHandler.h:26, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h:26, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:24: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/Filenames.h:89:18: warning: class ‘SmartPeak::Filenames’ is implicitly friends with itself friend class Filenames; ^~~~~ In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/RawDataProcessor.h:27, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationHandler.h:27, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h:26, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:24: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/MetaDataHandler.h:125:69: warning: missing initializer for member ‘tm::tm_gmtoff’ [-Wmissing-field-initializers] std::tm acquisition_date_and_time = { 0, 0, 0, 1, 0, 0, 0, 0, 0 }; // Need to start at Day 1 of the month ^ /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/MetaDataHandler.h:125:69: warning: missing initializer for member ‘tm::tm_zone’ [-Wmissing-field-initializers] In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/Utilities.h:45, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:25: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: In member function ‘virtual int io::detail::OwningStdIOByteSourceBase::read(char*, int)’: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:152:50: warning: conversion from ‘size_t’ {aka ‘long unsigned int’} to ‘int’ may change value [-Wconversion] return std::fread(buffer, 1, size, file);

/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: In member function ‘virtual int io::detail::NonOwningIStreamByteSource::read(char*, int)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:169:49: warning: conversion from ‘std::streamsize’ {aka ‘long int’} to ‘int’ may change value [-Wconversion]
                                 return in.gcount();
                                        ~~~~~~~~~^~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: In member function ‘virtual int io::detail::NonOwningStringByteSource::read(char*, int)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:185:62: warning: conversion from ‘long long int’ to ‘int’ may change value [-Wconversion]
                                         to_copy_byte_count = remaining_byte_count;
                                                              ^~~~~~~~~~~~~~~~~~~~
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/Utilities.h:45,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:25:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: At global scope:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:1099:22: warning: unnecessary parentheses in declaration of ‘row’ [-Wparentheses]
                 char*(row[column_count]);
                      ^
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp: In member function ‘virtual void SmartPeak::ConsoleHandler::initialize(const string&)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:47:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
         if (m_logdir_created) LOG_DEBUG << "Log directory created: " << m_log_filepath;
            ^
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp: In member function ‘virtual void SmartPeak::ConsoleHandler::_initialize_log_console(bool)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:111:20: error: ‘m_file_appender’ was not declared in this scope
     if (nullptr == m_file_appender && init_file_appender)
                    ^~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:111:20: note: suggested alternative: ‘init_file_appender’
     if (nullptr == m_file_appender && init_file_appender)
                    ^~~~~~~~~~~~~~~
                    init_file_appender
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:115:19: error: ‘RollingFileAppender’ is not a member of ‘plog’
             plog::RollingFileAppender<plog::CsvFormatter>>(
                   ^~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:115:19: note: suggested alternative: ‘ConsoleAppender’
             plog::RollingFileAppender<plog::CsvFormatter>>(
                   ^~~~~~~~~~~~~~~~~~~
                   ConsoleAppender
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:115:45: error: ‘CsvFormatter’ is not a member of ‘plog’
             plog::RollingFileAppender<plog::CsvFormatter>>(
                                             ^~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:116:53: warning: right operand of comma operator has no effect [-Wunused-value]
                 m_log_filepath.c_str(), 1024 * 1024 * 32, 100);
                                         ~~~~~~~~~~~~^~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:115:57: error: invalid operands of types ‘<unresolved overloaded function type>’ and ‘int’ to binary ‘operator>’
         m_file_appender = std::make_shared<
         plog::RollingFileAppender<plog::CsvFormatter>>(
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
             m_log_filepath.c_str(), 1024 * 1024 * 32, 100);
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:118:17: error: invalid operands of types ‘std::nullptr_t’ and ‘int’ to binary ‘operator==’ if (nullptr == m_console_appender)


/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:123:50: error: ‘TxtFormatter’ is not a member of ‘plog’
                 plog::ColorConsoleAppender<plog::TxtFormatter>>();
                                                  ^~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:123:50: error: template argument 1 is invalid
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:123:65: error: no matching function for call to ‘make_shared<<expression error> >()’
                 plog::ColorConsoleAppender<plog::TxtFormatter>>();
                                                                 ^
In file included from /usr/include/c++/8/memory:81,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:27,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:23:
/usr/include/c++/8/bits/shared_ptr.h:718:5: note: candidate: ‘template<class _Tp, class ... _Args> std::shared_ptr<_Tp> std::make_shared(_Args&& ...)’
     make_shared(_Args&&... __args)
     ^~~~~~~~~~~
/usr/include/c++/8/bits/shared_ptr.h:718:5: note:   template argument deduction/substitution failed:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:123:65: error: template argument 1 is invalid
                 plog::ColorConsoleAppender<plog::TxtFormatter>>();
                                                                 ^
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:128:45: error: ‘TxtFormatter’ is not a member of ‘plog’
                 plog::ConsoleAppender<plog::TxtFormatter>>();
                                             ^~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:128:45: error: template argument 1 is invalid
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:128:60: error: no matching function for call to ‘make_shared<<expression error> >()’
                 plog::ConsoleAppender<plog::TxtFormatter>>();
                                                            ^
In file included from /usr/include/c++/8/memory:81,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:27,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:23:
/usr/include/c++/8/bits/shared_ptr.h:718:5: note: candidate: ‘template<class _Tp, class ... _Args> std::shared_ptr<_Tp> std::make_shared(_Args&& ...)’
     make_shared(_Args&&... __args)
     ^~~~~~~~~~~
/usr/include/c++/8/bits/shared_ptr.h:718:5: note:   template argument deduction/substitution failed:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:128:60: error: template argument 1 is invalid
                 plog::ConsoleAppender<plog::TxtFormatter>>();
                                                            ^
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:131:20: error: ‘m_file_appender’ was not declared in this scope
     if (nullptr == m_file_appender)
                    ^~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:131:20: note: suggested alternative: ‘init_file_appender’
     if (nullptr == m_file_appender)
                    ^~~~~~~~~~~~~~~
                    init_file_appender
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:133:15: error: ‘init’ is not a member of ‘plog’
         plog::init(plog::debug, m_console_appender.get());
               ^~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:133:15: note: suggested alternative: ‘info’
         plog::init(plog::debug, m_console_appender.get());
               ^~~~
               info
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:133:52: error: request for member ‘get’ in ‘((SmartPeak::ConsoleHandler*)this)->SmartPeak::ConsoleHandler::m_console_appender’, which is of non-class type ‘int’
         plog::init(plog::debug, m_console_appender.get());
                                                    ^~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:137:15: error: ‘init’ is not a member of ‘plog’
         plog::init(plog::debug, m_file_appender.get()).addAppender(m_console_appender.get());
               ^~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:137:15: note: suggested alternative: ‘info’
         plog::init(plog::debug, m_file_appender.get()).addAppender(m_console_appender.get());
               ^~~~
               info
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:137:87: error: request for member ‘get’ in ‘((SmartPeak::ConsoleHandler*)this)->SmartPeak::ConsoleHandler::m_console_appender’, which is of non-class type ‘int’
         plog::init(plog::debug, m_file_appender.get()).addAppender(m_console_appender.get());
                                                                                       ^~~
make[2]: *** [src/smartpeak/CMakeFiles/SmartPeak.dir/build.make:104: src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ConsoleHandler.cpp.o] Error 1
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationHandler.h:27,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h:26,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:24:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/RawDataProcessor.h: In member function ‘virtual void SmartPeak::RawDataProcessor::getFilenames(SmartPeak::Filenames&) const’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/RawDataProcessor.h:65:42: warning: unused parameter ‘filenames’ [-Wunused-parameter]
     virtual void getFilenames(Filenames& filenames) const override { };
                               ~~~~~~~~~~~^~~~~~~~~
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationHandler.h:29,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h:26,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:24:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessor.h: In member function ‘virtual void SmartPeak::SequenceSegmentProcessor::getFilenames(SmartPeak::Filenames&) const’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceSegmentProcessor.h:77:42: warning: unused parameter ‘filenames’ [-Wunused-parameter]
     virtual void getFilenames(Filenames& filenames) const override { };
                               ~~~~~~~~~~~^~~~~~~~~
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationHandler.h:30,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h:26,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:24:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SampleGroupProcessor.h: In member function ‘virtual void SmartPeak::SampleGroupProcessor::getFilenames(SmartPeak::Filenames&) const’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SampleGroupProcessor.h:44:42: warning: unused parameter ‘filenames’ [-Wunused-parameter]
     virtual void getFilenames(Filenames& filenames) const override { };
                               ~~~~~~~~~~~^~~~~~~~~
[  3%] Linking CXX static library ../../../lib/libgtestd.a
[  3%] Built target gtest
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:27:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h: In constructor ‘SmartPeak::SequenceSegmentProcessorMultithread::SequenceSegmentProcessorMultithread(std::vector<SmartPeak::SequenceSegmentHandler>&, SmartPeak::SequenceHandler&, std::vector<std::shared_ptr<SmartPeak::SequenceSegmentProcessor> >&, std::map<std::__cxx11::basic_string<char>, SmartPeak::Filenames>&, SmartPeak::SequenceSegmentProcessorObservable*)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:149:61: warning: ‘SmartPeak::SequenceSegmentProcessorMultithread::sequence_segment_processing_methods_’ will be initialized after [-Wreorder]
     std::vector<std::shared_ptr<SequenceSegmentProcessor>>& sequence_segment_processing_methods_;
                                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:146:39: warning:   ‘std::map<std::__cxx11::basic_string<char>, SmartPeak::Filenames>& SmartPeak::SequenceSegmentProcessorMultithread::filenames_’ [-Wreorder]
     std::map<std::string, Filenames>& filenames_; ///< mapping from injections names to the associated filenames
                                       ^~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:111:5: warning:   when initialized here [-Wreorder]
     SequenceSegmentProcessorMultithread(
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h: In constructor ‘SmartPeak::SampleGroupProcessorMultithread::SampleGroupProcessorMultithread(std::vector<SmartPeak::SampleGroupHandler>&, SmartPeak::SequenceHandler&, std::vector<std::shared_ptr<SmartPeak::SampleGroupProcessor> >&, std::map<std::__cxx11::basic_string<char>, SmartPeak::Filenames>&, SmartPeak::SampleGroupProcessorObservable*)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:196:57: warning: ‘SmartPeak::SampleGroupProcessorMultithread::sample_group_processing_methods_’ will be initialized after [-Wreorder]
     std::vector<std::shared_ptr<SampleGroupProcessor>>& sample_group_processing_methods_;
                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:193:39: warning:   ‘std::map<std::__cxx11::basic_string<char>, SmartPeak::Filenames>& SmartPeak::SampleGroupProcessorMultithread::filenames_’ [-Wreorder]
     std::map<std::string, Filenames>& filenames_; ///< mapping from injections names to the associated filenames
                                       ^~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:158:5: warning:   when initialized here [-Wreorder]
     SampleGroupProcessorMultithread(
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h: In member function ‘virtual void SmartPeak::SequenceProcessor::getFilenames(SmartPeak::Filenames&) const’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:249:42: warning: unused parameter ‘filenames’ [-Wunused-parameter]
     virtual void getFilenames(Filenames& filenames) const override {};
                               ~~~~~~~~~~~^~~~~~~~~
[  4%] Building CXX object _deps/googletest-build/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o
[  5%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:27:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h: In member function ‘virtual void SmartPeak::ProcessSequence::getFilenames(SmartPeak::Filenames&) const’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/SequenceProcessor.h:309:42: warning: unused parameter ‘filenames’ [-Wunused-parameter]
     virtual void getFilenames(Filenames& filenames) const override {};
                               ~~~~~~~~~~~^~~~~~~~~
[  6%] Linking CXX static library ../../../lib/libgtest_maind.a
[  6%] Built target gtest_main
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/Utilities.h:45,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/SequenceParser.h:29,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:29:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: In member function ‘virtual int io::detail::OwningStdIOByteSourceBase::read(char*, int)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:152:50: warning: conversion from ‘size_t’ {aka ‘long unsigned int’} to ‘int’ may change value [-Wconversion]
                                 return std::fread(buffer, 1, size, file);
                                        ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: In member function ‘virtual int io::detail::NonOwningIStreamByteSource::read(char*, int)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:169:49: warning: conversion from ‘std::streamsize’ {aka ‘long int’} to ‘int’ may change value [-Wconversion]
                                 return in.gcount();
                                        ~~~~~~~~~^~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: In member function ‘virtual int io::detail::NonOwningStringByteSource::read(char*, int)’:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:185:62: warning: conversion from ‘long long int’ to ‘int’ may change value [-Wconversion]
                                         to_copy_byte_count = remaining_byte_count;
                                                              ^~~~~~~~~~~~~~~~~~~~
In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/Utilities.h:45,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/SequenceParser.h:29,
                 from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:29:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h: At global scope:
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/io/csv.h:1099:22: warning: unnecessary parentheses in declaration of ‘row’ [-Wparentheses]
                 char*(row[column_count]);
                      ^
[  6%] Linking CXX static library ../../../lib/libgmockd.a
[  6%] Built target gmock
[  7%] Building CXX object _deps/googletest-build/googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o
[  7%] Linking CXX static library ../../../lib/libgmock_maind.a
[  7%] Built target gmock_main
make[1]: *** [CMakeFiles/Makefile2:1097: src/smartpeak/CMakeFiles/SmartPeak.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
dmccloskey commented 2 years ago

Thanks for spotting this. My first guess is that this is a compiler issue as it looks like some of the basic C++ library methods are missing or have different signatures from what would be expected. What is the compiler and version that you are currently using?

oligegilo commented 2 years ago

Alright, there you go: gcc (GCC) 8.3.1 20191121 (Red Hat 8.3.1-5)

dmccloskey commented 2 years ago

Thanks for the information. I am thinking that it is not using the C++17 library. Can you try compiling using the flag -std=c++17?