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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
The text was updated successfully, but these errors were encountered:
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
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
SessionInfo()
The text was updated successfully, but these errors were encountered: