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davipatti/serosolver-1.0.1-compilation-error.txt

Created July 27, 2022 15:43
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Compilation error trying to install serosolver 1.0.1
Raw
serosolver-1.0.1-compilation-error.txt
> devtools::install_github("seroanalytics/serosolver")
Downloading GitHub repo seroanalytics/serosolver@HEAD
✔ checking for file ‘/tmp/Rtmpw3v9xS/remotes52ad50a06bda/seroanalytics-serosolver-4b632c4/DESCRIPTION’ ...
─ preparing ‘serosolver’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘serosolver_1.0.1.tar.gz’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘serosolver’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boosting_functions_fast.cpp -o boosting_functions_fast.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c helpers.cpp -o helpers.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c infection_model_fast.cpp -o infection_model_fast.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c likelihood_funcs.cpp -o likelihood_funcs.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c proposal.cpp -o proposal.o
proposal.cpp: In function ‘Rcpp::List inf_hist_prop_prior_v2_and_v4(Rcpp::NumericVector, Rcpp::IntegerMatrix, Rcpp::DataFrame, Rcpp::IntegerMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::NumericMatrix, double, int, bool, double, double, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)’:
proposal.cpp:829:41: error: no match for ‘operator>’ (operand types are ‘std::vector<int, std::allocator<int> >’ and ‘int’)
829 | indices = new_infection_history > 0;
| ~~~~~~~~~~~~~~~~~~~~~ ^ ~
| | |
| | int
| std::vector<int, std::allocator<int> >
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/operators.h:29,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/sugar.h:30,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:78,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__Vector.h:55:1: note: candidate: ‘template<int RTYPE, bool LHS_NA, class LHS_T, bool RHS_NA, class RHS_T> Rcpp::sugar::Comparator<RTYPE, Rcpp::sugar::greater<RTYPE>, LHS_NA, LHS_T, RHS_NA, RHS_T> operator>(const Rcpp::VectorBase<RTYPE, NA, VECTOR>&, const Rcpp::VectorBase<RTYPE, RHS_NA, RHS_T>&)’
55 | operator>(
| ^~~~~~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__Vector.h:55:1: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const Rcpp::VectorBase<RTYPE, NA, VECTOR>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/operators.h:30,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/sugar.h:30,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:78,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:54:1: note: candidate: ‘template<int RTYPE, bool NA, class T> Rcpp::sugar::Comparator_With_One_Value<RTYPE, Rcpp::sugar::less<RTYPE>, NA, T> operator>(typename Rcpp::traits::storage_type<RTYPE>::type, const Rcpp::VectorBase<RTYPE, NA, VECTOR>&)’
54 | operator>(
| ^~~~~~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:54:1: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: mismatched types ‘const Rcpp::VectorBase<RTYPE, NA, VECTOR>’ and ‘int’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/operators.h:30,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/sugar.h:30,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:78,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:78:1: note: candidate: ‘template<int RTYPE, bool NA, class T> Rcpp::sugar::Comparator_With_One_Value<RTYPE, Rcpp::sugar::greater<RTYPE>, NA, T> operator>(const Rcpp::VectorBase<RTYPE, NA, VECTOR>&, typename Rcpp::traits::storage_type<RTYPE>::type)’
78 | operator>(
| ^~~~~~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:78:1: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const Rcpp::VectorBase<RTYPE, NA, VECTOR>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/array:40,
from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_iterator.h:1168:5: note: candidate: ‘template<class _IteratorL, class _IteratorR, class _Container> bool __gnu_cxx::operator>(const __gnu_cxx::__normal_iterator<_IteratorL, _Container>&, const __gnu_cxx::__normal_iterator<_IteratorR, _Container>&)’
1168 | operator>(const __normal_iterator<_IteratorL, _Container>& __lhs,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_iterator.h:1168:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const __gnu_cxx::__normal_iterator<_IteratorL, _Container>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/array:40,
from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_iterator.h:1176:5: note: candidate: ‘template<class _Iterator, class _Container> bool __gnu_cxx::operator>(const __gnu_cxx::__normal_iterator<_Iterator, _Container>&, const __gnu_cxx::__normal_iterator<_Iterator, _Container>&)’
1176 | operator>(const __normal_iterator<_Iterator, _Container>& __lhs,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_iterator.h:1176:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const __gnu_cxx::__normal_iterator<_Iterator, _Container>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/unordered_map:43,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_pair.h:502:5: note: candidate: ‘template<class _T1, class _T2> constexpr bool std::operator>(const std::pair<_T1, _T2>&, const std::pair<_T1, _T2>&)’
502 | operator>(const pair<_T1, _T2>& __x, const pair<_T1, _T2>& __y)
| ^~~~~~~~
/usr/include/c++/11/bits/stl_pair.h:502:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::pair<_T1, _T2>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/array:40,
from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_iterator.h:437:5: note: candidate: ‘template<class _Iterator> bool std::operator>(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_Iterator>&)’
437 | operator>(const reverse_iterator<_Iterator>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_iterator.h:437:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::reverse_iterator<_Iterator>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/array:40,
from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_iterator.h:476:5: note: candidate: ‘template<class _IteratorL, class _IteratorR> bool std::operator>(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_IteratorR>&)’
476 | operator>(const reverse_iterator<_IteratorL>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_iterator.h:476:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::reverse_iterator<_Iterator>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/array:40,
from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_iterator.h:1575:5: note: candidate: ‘template<class _IteratorL, class _IteratorR> bool std::operator>(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorR>&)’
1575 | operator>(const move_iterator<_IteratorL>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_iterator.h:1575:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::move_iterator<_IteratorL>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/array:40,
from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_iterator.h:1625:5: note: candidate: ‘template<class _Iterator> bool std::operator>(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorL>&)’
1625 | operator>(const move_iterator<_Iterator>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_iterator.h:1625:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::move_iterator<_IteratorL>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/tuple:39,
from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/array:320:5: note: candidate: ‘template<class _Tp, long unsigned int _Nm> bool std::operator>(const std::array<_Tp, _Nm>&, const std::array<_Tp, _Nm>&)’
320 | operator>(const array<_Tp, _Nm>& __one, const array<_Tp, _Nm>& __two)
| ^~~~~~~~
/usr/include/c++/11/array:320:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::array<_Tp, _Nm>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/hashtable_policy.h:34,
from /usr/include/c++/11/bits/hashtable.h:35,
from /usr/include/c++/11/unordered_map:46,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/tuple:1589:5: note: candidate: ‘template<class ... _TElements, class ... _UElements> constexpr bool std::operator>(const std::tuple<_Tps ...>&, const std::tuple<_Types ...>&)’
1589 | operator>(const tuple<_TElements...>& __t,
| ^~~~~~~~
/usr/include/c++/11/tuple:1589:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::tuple<_Tps ...>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/string:55,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/macros/macros.h:25,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:64,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/basic_string.h:6378:5: note: candidate: ‘template<class _CharT, class _Traits, class _Alloc> bool std::operator>(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&, const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&)’
6378 | operator>(const basic_string<_CharT, _Traits, _Alloc>& __lhs,
| ^~~~~~~~
/usr/include/c++/11/bits/basic_string.h:6378:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/string:55,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/macros/macros.h:25,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:64,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/basic_string.h:6391:5: note: candidate: ‘template<class _CharT, class _Traits, class _Alloc> bool std::operator>(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&, const _CharT*)’
6391 | operator>(const basic_string<_CharT, _Traits, _Alloc>& __lhs,
| ^~~~~~~~
/usr/include/c++/11/bits/basic_string.h:6391:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/string:55,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/macros/macros.h:25,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/r/headers.h:64,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:30,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/basic_string.h:6403:5: note: candidate: ‘template<class _CharT, class _Traits, class _Alloc> bool std::operator>(const _CharT*, const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&)’
6403 | operator>(const _CharT* __lhs,
| ^~~~~~~~
/usr/include/c++/11/bits/basic_string.h:6403:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: mismatched types ‘const _CharT*’ and ‘std::vector<int, std::allocator<int> >’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:53,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:846:5: note: candidate: ‘template<class _Tp, class _Dp, class _Up, class _Ep> bool std::operator>(const std::unique_ptr<_Tp, _Dp>&, const std::unique_ptr<_Up, _Ep>&)’
846 | operator>(const unique_ptr<_Tp, _Dp>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/unique_ptr.h:846:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::unique_ptr<_Tp, _Dp>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:53,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:853:5: note: candidate: ‘template<class _Tp, class _Dp> bool std::operator>(const std::unique_ptr<_Tp, _Dp>&, std::nullptr_t)’
853 | operator>(const unique_ptr<_Tp, _Dp>& __x, nullptr_t)
| ^~~~~~~~
/usr/include/c++/11/bits/unique_ptr.h:853:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::unique_ptr<_Tp, _Dp>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:53,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:862:5: note: candidate: ‘template<class _Tp, class _Dp> bool std::operator>(std::nullptr_t, const std::unique_ptr<_Tp, _Dp>&)’
862 | operator>(nullptr_t, const unique_ptr<_Tp, _Dp>& __x)
| ^~~~~~~~
/usr/include/c++/11/bits/unique_ptr.h:862:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: mismatched types ‘const std::unique_ptr<_Tp, _Dp>’ and ‘int’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/list:63,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:56,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_list.h:2063:5: note: candidate: ‘template<class _Tp, class _Alloc> bool std::operator>(const std::__cxx11::list<_Tp, _Alloc>&, const std::__cxx11::list<_Tp, _Alloc>&)’
2063 | operator>(const list<_Tp, _Alloc>& __x, const list<_Tp, _Alloc>& __y)
| ^~~~~~~~
/usr/include/c++/11/bits/stl_list.h:2063:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::__cxx11::list<_Tp, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/map:61,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:57,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_map.h:1515:5: note: candidate: ‘template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator>(const std::map<_Key, _Tp, _Compare, _Alloc>&, const std::map<_Key, _Tp, _Compare, _Alloc>&)’
1515 | operator>(const map<_Key, _Tp, _Compare, _Alloc>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_map.h:1515:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::map<_Key, _Tp, _Compare, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/map:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:57,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_multimap.h:1180:5: note: candidate: ‘template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator>(const std::multimap<_Key, _Tp, _Compare, _Alloc>&, const std::multimap<_Key, _Tp, _Compare, _Alloc>&)’
1180 | operator>(const multimap<_Key, _Tp, _Compare, _Alloc>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_multimap.h:1180:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::multimap<_Key, _Tp, _Compare, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/set:61,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:58,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_set.h:1037:5: note: candidate: ‘template<class _Key, class _Compare, class _Alloc> bool std::operator>(const std::set<_Key, _Compare, _Alloc>&, const std::set<_Key, _Compare, _Alloc>&)’
1037 | operator>(const set<_Key, _Compare, _Alloc>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_set.h:1037:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::set<_Key, _Compare, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/set:62,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:58,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_multiset.h:1023:5: note: candidate: ‘template<class _Key, class _Compare, class _Alloc> bool std::operator>(const std::multiset<_Key, _Compare, _Alloc>&, const std::multiset<_Key, _Compare, _Alloc>&)’
1023 | operator>(const multiset<_Key,_Compare,_Alloc>& __x,
| ^~~~~~~~
/usr/include/c++/11/bits/stl_multiset.h:1023:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::multiset<_Key, _Compare, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/vector:67,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:60,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_vector.h:1943:5: note: candidate: ‘template<class _Tp, class _Alloc> bool std::operator>(const std::vector<_Tp, _Alloc>&, const std::vector<_Tp, _Alloc>&)’
1943 | operator>(const vector<_Tp, _Alloc>& __x, const vector<_Tp, _Alloc>& __y)
| ^~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1943:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: mismatched types ‘const std::vector<_Tp, _Alloc>’ and ‘int’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/include/c++/11/deque:67,
from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:61,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/include/c++/11/bits/stl_deque.h:2297:5: note: candidate: ‘template<class _Tp, class _Alloc> bool std::operator>(const std::deque<_Tp, _Alloc>&, const std::deque<_Tp, _Alloc>&)’
2297 | operator>(const deque<_Tp, _Alloc>& __x, const deque<_Tp, _Alloc>& __y)
| ^~~~~~~~
/usr/include/c++/11/bits/stl_deque.h:2297:5: note: template argument deduction/substitution failed:
proposal.cpp:829:43: note: ‘std::vector<int, std::allocator<int> >’ is not derived from ‘const std::deque<_Tp, _Alloc>’
829 | indices = new_infection_history > 0;
| ^
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/date_datetime/date_datetime.h:25,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:64,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/date_datetime/Date.h:166:19: note: candidate: ‘bool Rcpp::operator>(const Rcpp::Date&, const Rcpp::Date&)’
166 | inline bool operator>( const Date &d1, const Date& d2) { return d1.m_d > d2.m_d; }
| ^~~~~~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/date_datetime/Date.h:166:42: note: no known conversion for argument 1 from ‘std::vector<int, std::allocator<int> >’ to ‘const Rcpp::Date&’
166 | inline bool operator>( const Date &d1, const Date& d2) { return d1.m_d > d2.m_d; }
| ~~~~~~~~~~~~^~
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/date_datetime/date_datetime.h:29,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:64,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25,
from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
from proposal.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/date_datetime/Datetime.h:160:20: note: candidate: ‘bool Rcpp::operator>(const Rcpp::Datetime&, const Rcpp::Datetime&)’
160 | inline bool operator>(const Datetime &d1, const Datetime& d2) { return d1.m_dt > d2.m_dt; }
| ^~~~~~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/date_datetime/Datetime.h:160:46: note: no known conversion for argument 1 from ‘std::vector<int, std::allocator<int> >’ to ‘const Rcpp::Datetime&’
160 | inline bool operator>(const Datetime &d1, const Datetime& d2) { return d1.m_dt > d2.m_dt; }
| ~~~~~~~~~~~~~~~~^~
proposal.cpp:840:43: error: invalid initialization of reference of type ‘const double&’ from expression of type ‘Rcpp::IntegerVector’ {aka ‘Rcpp::Vector<13>’}
840 | infection_strain_indices_tmp,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from proposal.cpp:2:
boosting_functions_fast.h:11:52: note: in passing argument 7 of ‘void titre_data_fast_individual_base(Rcpp::NumericVector&, const double&, const double&, const double&, const double&, const bool&, const double&, const double&, const double&, const double&, Rcpp::NumericVector, Rcpp::IntegerVector, const NumericVector&, const IntegerVector&, const NumericVector&, const IntegerVector&, const NumericVector&, const int&, const int&, const int&, const IntegerVector&, const int&, const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, bool)’
11 | const double &mu_vac,
| ~~~~~~~~~~~~~~^~~~~~
proposal.cpp:904:43: error: invalid initialization of reference of type ‘const double&’ from expression of type ‘Rcpp::IntegerVector’ {aka ‘Rcpp::Vector<13>’}
904 | infection_strain_indices_tmp,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from proposal.cpp:2:
boosting_functions_fast.h:11:52: note: in passing argument 7 of ‘void titre_data_fast_individual_base(Rcpp::NumericVector&, const double&, const double&, const double&, const double&, const bool&, const double&, const double&, const double&, const double&, Rcpp::NumericVector, Rcpp::IntegerVector, const NumericVector&, const IntegerVector&, const NumericVector&, const IntegerVector&, const NumericVector&, const int&, const int&, const int&, const IntegerVector&, const int&, const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, bool)’
11 | const double &mu_vac,
| ~~~~~~~~~~~~~~^~~~~~
proposal.cpp:930:7: error: expected primary-expression before ‘if’
930 | if(solve_likelihood && lik_changed)
| ^~
proposal.cpp:1168:2: error: expected ‘}’ at end of input
1168 | }
| ^
proposal.cpp:213:37: note: to match this ‘{’
213 | ){
| ^
proposal.cpp:1168:2: warning: control reaches end of non-void function [-Wreturn-type]
1168 | }
| ^
make: *** [/usr/lib/R/etc/Makeconf:177: proposal.o] Error 1
ERROR: compilation failed for package ‘serosolver’
* removing ‘/usr/local/lib/R/site-library/serosolver’
* restoring previous ‘/usr/local/lib/R/site-library/serosolver’
Error: Failed to install 'serosolver' from GitHub:
(converted from warning) installation of package ‘/tmp/Rtmpw3v9xS/file52adb5c19d3/serosolver_1.0.1.tar.gz’ had non-zero exit status
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