[Octave-bug-tracker] [bug #65461] Can't install MVApack package

[anonyme]

Follow-up Comment #7, bug #65461 (group octave):

This is the full error :

lib/input.cpp: In function 'ScanOPs scans_from_file(const Path&, Int32)':
lib/input.cpp:109:21: error: invalid initialization of reference of type
'const String&' {aka 'const std::__cxx11::ba
sic_string<char>&'} from expression of type 'const Path' {aka 'const
std::filesystem::__cxx11::path'}
  109 |     if(!file_exists(path)) {
      |                     ^~~~
In file included from include/datastructures.h:8,
                 from lib/input.cpp:7:
include/util.h:39:14: note: in passing argument 1 of 'bool file_exists(const
String&)'
   39 | file_exists( String const& );
      |              ^~~~~~~~~~~~~
lib/input.cpp:113:49: error: invalid initialization of reference of type
'const String&' {aka 'const std::__cxx11::ba
sic_string<char>&'} from expression of type 'const Path' {aka 'const
std::filesystem::__cxx11::path'}
  113 |     const String ext = lowercase(file_extension(path));
      |                                                 ^~~~
In file included from include/datastructures.h:8,
                 from lib/input.cpp:7:
include/util.h:45:16: note: in passing argument 1 of 'String
file_extension(const String&)'
   45 | file_extension(String const &);
      |                ^~~~~~~~~~~~~~
lib/input.cpp:124:63: error: invalid initialization of reference of type
'const String&' {aka 'const std::__cxx11::ba
sic_string<char>&'} from expression of type 'const Path' {aka 'const
std::filesystem::__cxx11::path'}
  124 |         std::cout<<"Unknown file extension: "<<file_extension(path)<<"
for file " <<path<<"\n";
      |                                                               ^~~~
In file included from include/datastructures.h:8,
                 from lib/input.cpp:7:
include/util.h:45:16: note: in passing argument 1 of 'String
file_extension(const String&)'
   45 | file_extension(String const &);
      |                ^~~~~~~~~~~~~~
In file included from lib/octave-connect.cpp:4:
include/octave-connect.h:11:10: fatal error: octave/oct.h: No such file or
directory
   11 | #include <octave/oct.h>
      |          ^~~~~~~~~~~~~~
compilation terminated.
lib/peak.cc:3:10: fatal error: octave/oct.h: No such file or directory
    3 | #include <octave/oct.h>
      |          ^~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:63: lcms_lib.a] Error 1
make: Entering directory '/tmp/oct-mBiogM/mvapack-Micah/src'
g++ -std=c++17 -Iinclude/ -Iexternal/   -DPSAPI_VERSION=1
-IC:\Users\JUGUIB~1\Desktop\OCTAVE~1.0-W\OCTAVE~1.0-W\mingw
64\/include 
-IC:\Users\JUGUIB~1\Desktop\OCTAVE~1.0-W\OCTAVE~1.0-W\mingw64\include\octave-6.3.0\octave\..
-IC:\Users\
JUGUIB~1\Desktop\OCTAVE~1.0-W\OCTAVE~1.0-W\mingw64\include\octave-6.3.0\octave
-IC:\Users\JUGUIB~1\Desktop\OCTAVE~1.0
-W\OCTAVE~1.0-W\mingw64\include   -fopenmp -g -O2     -Iexternal/  
-DPSAPI_VERSION=1 -IC:\Users\JUGUIB~1\Desktop\OCT
AVE~1.0-W\OCTAVE~1.0-W\mingw64\/include 
-IC:\Users\JUGUIB~1\Desktop\OCTAVE~1.0-W\OCTAVE~1.0-W\mingw64\include\octave
-6.3.0\octave\..
-IC:\Users\JUGUIB~1\Desktop\OCTAVE~1.0-W\OCTAVE~1.0-W\mingw64\include\octave-6.3.0\octave
-IC:\Users
\JUGUIB~1\Desktop\OCTAVE~1.0-W\OCTAVE~1.0-W\mingw64\include   -fopenmp -g -O2 
   -c lib/datastructures.cpp lib/filte
r.cpp lib/input.cpp lib/octave-connect.cpp lib/peak.cc lib/scan.cpp
lib/smooth.cpp lib/types.cpp lib/util.cpp lib/zli
b.cpp lib/types.cpp external/base64/base64.cpp external/tinyxml/tinyxml2.cpp
make: Leaving directory '/tmp/oct-mBiogM/mvapack-Micah/src'

error: pkg: error running 'make' for the mvapack package.
error: called from
    configure_make at line 110 column 9
    install at line 196 column 7
    pkg at line 568 column 9


And this is the file, the error stems from :

//
// Created by cjurich on 1/25/21.
//
#ifndef MVAPACK_LCMS_INPUT_H
#define MVAPACK_LCMS_INPUT_H

#include <regex>
#include <memory>
#include <fstream>
#include <iostream>

#include <util.h>
#include <types.h>
#include <datastructures.h>

#include <base64/base64.h>
#include <tinyxml/tinyxml2.h>

ScanOPs
scans_from_file(Path const &, Int32);

ScanOP
get_scan(Path const &, const Int32, Int16);

Peaks
peaks_from_csv(Path const &);

void
clusters_to_csv(Path const&, Clusters const&);

Clusters
clusters_from_csv(Path const&);

void
mzsamples_to_csv(Path const&, MZSamples const & );

std::pair<Strings,Strings>
load_mappings(Path const &);


class Reader {
    public:
        enum FILETYPE {
            PWIZ,
            MZXML,
            MZML
        };

    private:
        FILETYPE curr_type_; 
        std::ifstream fh_;
        String filename_;
        Int32 scans_left_;
    
    public:
        Reader() {} 
    
    public:
        ScanOP
        get_scan( Int32 level=1 ) ;
   
    public:
        void
        set_input( String const & );

    public:
        bool 
        scans_remaining() ;
    
    public:
        bool
        eof() const {
            return fh_.eof();
        }

    private:
        String
        get_line_();

    private: 
        ScanOP
        _get_scan_pwiz( Int32 );

    private: 
        ScanOP
        _get_scan_mzxml( Int32 );
   
    private: 
        ScanOP
        _get_scan_mzml( Int32 );
    
    private:
        void
        _pwiz_init();
    
    private:
        void
        _mzxml_init();

    private:
        void
        _mzml_init();

};


void
save_slices( MZSamples const&, String const& ); 

using ReaderOP = std::shared_ptr< Reader >;


#endif //MVAPACK_LCMS_INPUT_H

Help!



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