Scripting issues during make

[oligegilo]

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_less_than(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(), a_lowercase.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_greater_than(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(), a_lowercase.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_equal_to(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(), a_lowercase.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::RollingFileAppenderplog::CsvFormatter> 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::RollingFileAppenderplog::CsvFormatter> 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::RollingFileAppenderplog::CsvFormatter> 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::RollingFileAppenderplog::CsvFormatter> 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::ConsoleAppenderplog::TxtFormatter> 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::ConsoleAppenderplog::TxtFormatter> 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::RollingFileAppenderplog::CsvFormatter>(
^~~~~~~~~~~~~~~~~~~
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:115:19: note: suggested alternative: ‘ConsoleAppender’
plog::RollingFileAppenderplog::CsvFormatter>(
^~~~~~~~~~~~~~~~~~~
ConsoleAppender
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:115:45: error: ‘CsvFormatter’ is not a member of ‘plog’
plog::RollingFileAppenderplog::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 ‘’ and ‘int’ to binary ‘operator>’
m_file_appender = std::make_shared<
~~~~~~~~~~~~~~~~~
plog::RollingFileAppenderplog::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::ColorConsoleAppenderplog::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< >()’
plog::ColorConsoleAppenderplog::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::ColorConsoleAppenderplog::TxtFormatter>();
^
/home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:128:45: error: ‘TxtFormatter’ is not a member of ‘plog’
plog::ConsoleAppenderplog::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< >()’
plog::ConsoleAppenderplog::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::ConsoleAppenderplog::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::vectorSmartPeak::SequenceSegmentHandler&, SmartPeak::SequenceHandler&, std::vector<std::shared_ptrSmartPeak::SequenceSegmentProcessor >&, std::map<std::cxx11::basic_string, 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>& 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, 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::vectorSmartPeak::SampleGroupHandler&, SmartPeak::SequenceHandler&, std::vector<std::shared_ptrSmartPeak::SampleGroupProcessor >&, std::map<std::cxx11::basic_string, 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>& 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, 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]

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]

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

[dmccloskey]

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?