Trouble updating Signac

[Jeron1996]

Thanks for this great single-cell ATAC analysis package.

I have some trouble updating Signac version 1.0.0 to 1.1.0. I am trying to install it using a windows 10 laptop, CRAN and compiling from source. After I run install.packages("Signac") I get a bunch of errors, that appear to originate from the compiler. I have checked my Rtools version and it is the version associated with R3.6.3. Do you have any suggestions to solve this issue?

Console output

Installing package into ‘C:/Users/Jeron/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
       binary source needs_compilation
Signac  1.0.0  1.1.0              TRUE

installing the source package ‘Signac’

trying URL 'https://cran.rstudio.com/src/contrib/Signac_1.1.0.tar.gz'
Content type 'application/x-gzip' length 720211 bytes (703 KB)
downloaded 703 KB

* installing *source* package 'Signac' ...
** package 'Signac' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.3/include" -DNDEBUG  -I"C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include"        -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.3/include" -DNDEBUG  -I"C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include"        -O2 -Wall  -mtune=core2 -c filter.cpp -o filter.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.3/include" -DNDEBUG  -I"C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include"        -O2 -Wall  -mtune=core2 -c group.cpp -o group.o
group.cpp: In function 'SEXPREC* groupCommand(std::string, Rcpp::Nullable<Rcpp::Vector<16> >, std::size_t, bool)':
group.cpp:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<whitelist_cells.size(); i++) {
                       ^
group.cpp:91:31: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
     uint8_t nuc_free_inc = end-start < 147 ? 1: 0;
                               ^
group.cpp:91:31: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.3/include" -DNDEBUG  -I"C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include"        -O2 -Wall  -mtune=core2 -c split.cpp -o split.o
split.cpp: In function 'int splitFragments(std::string, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::string, std::string, int, bool, bool)':
split.cpp:125:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < streams.size(); i++) {
                     ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/i686-w64-mingw32/bits/c++allocator.h:33:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/allocator.h:46,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:41,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/stdexcept:39,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/array:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tuple:39,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/unordered_map:41,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp/r/headers.h:67,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ext/new_allocator.h: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::basic_ofstream<char>; _Args = {std::basic_ofstream<char, std::char_traits<char> >}; _Tp = std::basic_ofstream<char>]':
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/alloc_traits.h:253:4:   required from 'static std::_Require<typename std::allocator_traits<_Alloc>::__construct_helper<_Tp, _Args>::type> std::allocator_traits<_Alloc>::_S_construct(_Alloc&, _Tp*, _Args&& ...) [with _Tp = std::basic_ofstream<char>; _Args = {std::basic_ofstream<char, std::char_traits<char> >}; _Alloc = std::allocator<std::basic_ofstream<char> >; std::_Require<typename std::allocator_traits<_Alloc>::__construct_helper<_Tp, _Args>::type> = void]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/alloc_traits.h:399:57:   required from 'static decltype (_S_construct(__a, __p, (forward<_Args>)(std::allocator_traits::construct::__args)...)) std::allocator_traits<_Alloc>::construct(_Alloc&, _Tp*, _Args&& ...) [with _Tp = std::basic_ofstream<char>; _Args = {std::basic_ofstream<char, std::char_traits<char> >}; _Alloc = std::allocator<std::basic_ofstream<char> >; decltype (_S_construct(__a, __p, (forward<_Args>)(std::allocator_traits::construct::__args)...)) = <type error>]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/vector.tcc:97:40:   required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::basic_ofstream<char, std::char_traits<char> >}; _Tp = std::basic_ofstream<char>; _Alloc = std::allocator<std::basic_ofstream<char> >]'
split.cpp:39:72:   required from here
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ext/new_allocator.h:120:4: error: use of deleted function 'std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)'
  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
    ^
In file included from split.cpp:4:0:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:602:11: note: 'std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)' is implicitly deleted because the default definition would be ill-formed:
     class basic_ofstream : public basic_ostream<_CharT,_Traits>
           ^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:602:11: error: use of deleted function 'std::basic_ostream<char>::basic_ostream(const std::basic_ostream<char>&)'
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64:0,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:49,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:58:11: note: 'std::basic_ostream<char>::basic_ostream(const std::basic_ostream<char>&)' is implicitly deleted because the default definition would be ill-formed:
     class basic_ostream : virtual public basic_ios<_CharT, _Traits>
           ^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:58:11: error: use of deleted function 'std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)'
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:44:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:49,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_ios.h:66:11: note: 'std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)' is implicitly deleted because the default definition would be ill-formed:
     class basic_ios : public ios_base
           ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:49,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:786:5: error: 'std::ios_base::ios_base(const std::ios_base&)' is private
     ios_base(const ios_base&);
     ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:44:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:49,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_ios.h:66:11: error: within this context
     class basic_ios : public ios_base
           ^
In file included from split.cpp:4:0:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:602:11: error: use of deleted function 'std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)'
     class basic_ofstream : public basic_ostream<_CharT,_Traits>
           ^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:602:11: error: use of deleted function 'std::basic_filebuf<char>::basic_filebuf(const std::basic_filebuf<char>&)'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:72:11: note: 'std::basic_filebuf<char>::basic_filebuf(const std::basic_filebuf<char>&)' is implicitly deleted because the default definition would be ill-formed:
     class basic_filebuf : public basic_streambuf<_CharT, _Traits>
           ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:43:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:49,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/streambuf:802:7: error: 'std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]' is private
       basic_streambuf(const basic_streambuf& __sb)
       ^
In file included from split.cpp:4:0:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:72:11: error: within this context
     class basic_filebuf : public basic_streambuf<_CharT, _Traits>
           ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/vector:62:0,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/RcppCommon.h:59,
                 from C:/Users/Jeron/Documents/R/win-library/3.6/Rcpp/include/Rcpp.h:27,
                 from split.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_construct.h: In instantiation of 'void std::_Construct(_T1*, _Args&& ...) [with _T1 = std::basic_ofstream<char>; _Args = {std::basic_ofstream<char, std::char_traits<char> >}]':
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_uninitialized.h:75:53:   required from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<std::basic_ofstream<char>*>; _ForwardIterator = std::basic_ofstream<char>*; bool _TrivialValueTypes = false]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_uninitialized.h:126:41:   required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<std::basic_ofstream<char>*>; _ForwardIterator = std::basic_ofstream<char>*]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_uninitialized.h:279:63:   required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<std::basic_ofstream<char>*>; _ForwardIterator = std::basic_ofstream<char>*; _Tp = std::basic_ofstream<char>]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_uninitialized.h:302:69:   required from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = std::basic_ofstream<char>*; _ForwardIterator = std::basic_ofstream<char>*; _Allocator = std::allocator<std::basic_ofstream<char> >]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/vector.tcc:423:43:   required from 'void std::vector<_Tp, _Alloc>::_M_emplace_back_aux(_Args&& ...) [with _Args = {std::basic_ofstream<char, std::char_traits<char> >}; _Tp = std::basic_ofstream<char>; _Alloc = std::allocator<std::basic_ofstream<char> >]'
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/vector.tcc:101:54:   required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::basic_ofstream<char, std::char_traits<char> >}; _Tp = std::basic_ofstream<char>; _Alloc = std::allocator<std::basic_ofstream<char> >]'
split.cpp:39:72:   required from here
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_construct.h:75:7: error: use of deleted function 'std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)'
     { ::new(static_cast<void*>(__p)) _T1(std::forward<_Args>(__args)...); }
       ^
make: *** [C:/PROGRA~1/R/R-36~1.3/etc/i386/Makeconf:215: split.o] Error 1
ERROR: compilation failed for package 'Signac'
* removing 'C:/Users/Jeron/Documents/R/win-library/3.6/Signac'
* restoring previous 'C:/Users/Jeron/Documents/R/win-library/3.6/Signac'
Warning in install.packages :
  installation of package ‘Signac’ had non-zero exit status

SessionInfo()

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3   

[timoast]

This appears to be an issue with the g++ compiler version <5. We've pushed an update to the develop branch that should solve this, so you should be able to successfully build from the develop branch. See the website for install instructions: https://satijalab.org/signac/articles/install.html#development-version-1

[Jeron1996]

That fixed it, thanks a lot.