Issues installing MethPipe

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Hallvard

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Mar 23, 2021, 11:08:37 AM3/23/21

to MethPipe and MethBase Users

Hi,

I am trying to install MethPipe 4.1.1 on a linux server running Red Hat Enterprise 7.9.

I am following the installation instructions as written here https://github.com/smithlabcode/methpipe, and use a specified prefix directory as I do not have admin privileges.

However, when I run make in the build directory I get the same error message every time. Is there a solution to this problem? I am primarily interested in using the methcounts program.

Is it possible to compile this independently from the rest of MethPipe and use it for the quantification of cytosine methylation levels in case that MethPipe cannot be installed?

This is the error message:

-bash-4.2$ make

make all-recursive

make[1]: Entering directory `/data/hallvaaw/software/methpipe-4.1.1/build'

Making all in src/smithlab_cpp

make[2]: Entering directory `/data/hallvaaw/software/methpipe-4.1.1/build/src/smithlab_cpp'

make all-am

make[3]: Entering directory `/data/hallvaaw/software/methpipe-4.1.1/build/src/smithlab_cpp'

CXX GenomicRegion.lo

CXX MappedRead.lo

CXX OptionParser.lo

../../../src/smithlab_cpp/OptionParser.cpp: In function ‘void read_config_file(const string&, std::vector<std::basic_string<char> >&)’:

../../../src/smithlab_cpp/OptionParser.cpp:371:54: error: no matching function for call to ‘regex_replace(std::string&, std::regex, const char [1])’

line = regex_replace(line, regex(outer_space), "");

../../../src/smithlab_cpp/OptionParser.cpp:371:54: note: candidates are:

In file included from /usr/include/c++/4.8.2/regex:62:0,

from ../../../src/smithlab_cpp/OptionParser.cpp:35:

/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)

regex_replace(const basic_string<_Ch_type>& __s,

/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template argument deduction/substitution failed:

../../../src/smithlab_cpp/OptionParser.cpp:371:54: note: mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [1]’

line = regex_replace(line, regex(outer_space), "");

In file included from /usr/include/c++/4.8.2/regex:62:0,

from ../../../src/smithlab_cpp/OptionParser.cpp:35:

/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)

regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,

/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template argument deduction/substitution failed:

../../../src/smithlab_cpp/OptionParser.cpp:371:54: note: deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)

line = regex_replace(line, regex(outer_space), "");

../../../src/smithlab_cpp/OptionParser.cpp:372:55: error: no matching function for call to ‘regex_replace(std::string&, std::regex, const char [2])’

line = regex_replace(line, regex(inner_space), " ");

../../../src/smithlab_cpp/OptionParser.cpp:372:55: note: candidates are:

In file included from /usr/include/c++/4.8.2/regex:62:0,

from ../../../src/smithlab_cpp/OptionParser.cpp:35:

regex_replace(const basic_string<_Ch_type>& __s,

/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template argument deduction/substitution failed:

../../../src/smithlab_cpp/OptionParser.cpp:372:55: note: mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [2]’

line = regex_replace(line, regex(inner_space), " ");

In file included from /usr/include/c++/4.8.2/regex:62:0,

from ../../../src/smithlab_cpp/OptionParser.cpp:35:

regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,

/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template argument deduction/substitution failed:

../../../src/smithlab_cpp/OptionParser.cpp:372:55: note: deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)

line = regex_replace(line, regex(inner_space), " ");

../../../src/smithlab_cpp/OptionParser.cpp:389:64: error: no matching function for call to ‘regex_replace(std::string&, std::regex, const char [1])’

option_value = regex_replace(line, regex(outer_space), "");

../../../src/smithlab_cpp/OptionParser.cpp:389:64: note: candidates are:

In file included from /usr/include/c++/4.8.2/regex:62:0,

from ../../../src/smithlab_cpp/OptionParser.cpp:35:

regex_replace(const basic_string<_Ch_type>& __s,

/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template argument deduction/substitution failed:

../../../src/smithlab_cpp/OptionParser.cpp:389:64: note: mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [1]’

option_value = regex_replace(line, regex(outer_space), "");

In file included from /usr/include/c++/4.8.2/regex:62:0,

from ../../../src/smithlab_cpp/OptionParser.cpp:35:

regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,

/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template argument deduction/substitution failed:

../../../src/smithlab_cpp/OptionParser.cpp:389:64: note: deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)

option_value = regex_replace(line, regex(outer_space), "");

make[3]: *** [OptionParser.lo] Error 1

make[3]: Leaving directory `/data/hallvaaw/software/methpipe-4.1.1/build/src/smithlab_cpp'

make[2]: *** [all] Error 2

make[2]: Leaving directory `/data/hallvaaw/software/methpipe-4.1.1/build/src/smithlab_cpp'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/data/hallvaaw/software/methpipe-4.1.1/build'

make: *** [all] Error 2

Best regards,

Hallvard A.W.

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