############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL scrapper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘scrapper’ ... ** this is package ‘scrapper’ version ‘1.5.2’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c adt_quality_control.cpp -o adt_quality_control.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c aggregate_across_cells.cpp -o aggregate_across_cells.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c aggregate_across_genes.cpp -o aggregate_across_genes.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c build_snn_graph.cpp -o build_snn_graph.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c center_size_factors.cpp -o center_size_factors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c choose_pseudo_count.cpp -o choose_pseudo_count.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cluster_graph.cpp -o cluster_graph.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cluster_kmeans.cpp -o cluster_kmeans.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c combine_factors.cpp -o combine_factors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c compute_block_weights.cpp -o compute_block_weights.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c correct_mnn.cpp -o correct_mnn.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c crispr_quality_control.cpp -o crispr_quality_control.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_variance_trend.cpp -o fit_variance_trend.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c model_gene_variances.cpp -o model_gene_variances.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c normalize_counts.cpp -o normalize_counts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rna_quality_control.cpp -o rna_quality_control.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c run_pca.cpp -o run_pca.o In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/Core:335, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/Dense:1, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/utils.hpp:9, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/compute.hpp:10, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/scran_pca/simple_pca.hpp:10, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/scran_pca/scran_pca.hpp:4, from run_pca.cpp:10: In destructor ‘Eigen::internal::DenseStorage_impl::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’, inlined from ‘Eigen::DenseStorage::~DenseStorage()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7, inlined from ‘Eigen::PlainObjectBase >::~PlainObjectBase()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7, inlined from ‘Eigen::Matrix::~Matrix()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:287:35, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:318:14, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:315:7, inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix; bool _Copy = false; bool _Move = false]’ at /usr/include/c++/13/optional:441:65, inlined from ‘std::_Optional_base, false, false>::~_Optional_base()’ at /usr/include/c++/13/optional:512:12, inlined from ‘std::optional >::~optional()’ at /usr/include/c++/13/optional:707:11, inlined from ‘irlba::Options >::~Options()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/Options.hpp:20:8, inlined from ‘scran_pca::SimplePcaOptions::~SimplePcaOptions()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/scran_pca/simple_pca.hpp:27:8, inlined from ‘Rcpp::List run_pca(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, bool, int, int, int, int)’ at run_pca.cpp:98:5: /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:368:85: warning: ‘*(Eigen::internal::DenseStorage_impl*)((char*)&opt + offsetof(scran_pca::SimplePcaOptions, scran_pca::SimplePcaOptions::irlba_options.irlba::Options >::initial.std::optional >::.std::_Optional_base, false, false>::)).Eigen::internal::DenseStorage_impl::m_data’ may be used uninitialized [-Wmaybe-uninitialized] 368 | EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto(m_data, size()); } | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ run_pca.cpp: In function ‘Rcpp::List run_pca(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, bool, int, int, int, int)’: run_pca.cpp:81:37: note: ‘opt’ declared here 81 | scran_pca::SimplePcaOptions opt; | ^~~ In destructor ‘Eigen::internal::DenseStorage_impl::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’, inlined from ‘Eigen::DenseStorage::~DenseStorage()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7, inlined from ‘Eigen::PlainObjectBase >::~PlainObjectBase()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7, inlined from ‘Eigen::Matrix::~Matrix()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:287:35, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:318:14, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:315:7, inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix; bool _Copy = false; bool _Move = false]’ at /usr/include/c++/13/optional:441:65, inlined from ‘std::_Optional_base, false, false>::~_Optional_base()’ at /usr/include/c++/13/optional:512:12, inlined from ‘std::optional >::~optional()’ at /usr/include/c++/13/optional:707:11, inlined from ‘irlba::Options >::~Options()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/Options.hpp:20:8, inlined from ‘scran_pca::SimplePcaOptions::~SimplePcaOptions()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/scran_pca/simple_pca.hpp:27:8, inlined from ‘Rcpp::List run_pca(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, bool, int, int, int, int)’ at run_pca.cpp:98:5: /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:368:85: warning: ‘*(Eigen::internal::DenseStorage_impl*)((char*)&opt + offsetof(scran_pca::SimplePcaOptions, scran_pca::SimplePcaOptions::irlba_options.irlba::Options >::initial.std::optional >::.std::_Optional_base, false, false>::)).Eigen::internal::DenseStorage_impl::m_data’ may be used uninitialized [-Wmaybe-uninitialized] 368 | EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto(m_data, size()); } | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ run_pca.cpp: In function ‘Rcpp::List run_pca(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, bool, int, int, int, int)’: run_pca.cpp:81:37: note: ‘opt’ declared here 81 | scran_pca::SimplePcaOptions opt; | ^~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c run_tsne.cpp -o run_tsne.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c run_umap.cpp -o run_umap.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sanitize_size_factors.cpp -o sanitize_size_factors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c scale_by_neighbors.cpp -o scale_by_neighbors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c score_gene_set.cpp -o score_gene_set.o In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/Core:335, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/Dense:1, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/utils.hpp:9, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/compute.hpp:10, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/gsdecon/compute.hpp:8, from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/gsdecon/gsdecon.hpp:4, from score_gene_set.cpp:7: In destructor ‘Eigen::internal::DenseStorage_impl::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’, inlined from ‘Eigen::DenseStorage::~DenseStorage()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7, inlined from ‘Eigen::PlainObjectBase >::~PlainObjectBase()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7, inlined from ‘Eigen::Matrix::~Matrix()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:287:35, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:318:14, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:315:7, inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix; bool _Copy = false; bool _Move = false]’ at /usr/include/c++/13/optional:441:65, inlined from ‘std::_Optional_base, false, false>::~_Optional_base()’ at /usr/include/c++/13/optional:512:12, inlined from ‘std::optional >::~optional()’ at /usr/include/c++/13/optional:707:11, inlined from ‘irlba::Options >::~Options()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/Options.hpp:20:8, inlined from ‘gsdecon::Options::~Options()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/gsdecon/Options.hpp:18:8, inlined from ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, int, int, int, int)’ at score_gene_set.cpp:63:1: /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:368:85: warning: ‘*(Eigen::internal::DenseStorage_impl*)((char*)&opt + offsetof(gsdecon::Options, gsdecon::Options::irlba_options.irlba::Options >::initial.std::optional >::.std::_Optional_base, false, false>::)).Eigen::internal::DenseStorage_impl::m_data’ may be used uninitialized [-Wmaybe-uninitialized] 368 | EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto(m_data, size()); } | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ score_gene_set.cpp: In function ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, int, int, int, int)’: score_gene_set.cpp:31:22: note: ‘opt’ declared here 31 | gsdecon::Options opt; | ^~~ In destructor ‘Eigen::internal::DenseStorage_impl::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’, inlined from ‘Eigen::DenseStorage::~DenseStorage()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7, inlined from ‘Eigen::PlainObjectBase >::~PlainObjectBase()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7, inlined from ‘Eigen::Matrix::~Matrix()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:287:35, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:318:14, inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix]’ at /usr/include/c++/13/optional:315:7, inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix; bool _Copy = false; bool _Move = false]’ at /usr/include/c++/13/optional:441:65, inlined from ‘std::_Optional_base, false, false>::~_Optional_base()’ at /usr/include/c++/13/optional:512:12, inlined from ‘std::optional >::~optional()’ at /usr/include/c++/13/optional:707:11, inlined from ‘irlba::Options >::~Options()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/Options.hpp:20:8, inlined from ‘gsdecon::Options::~Options()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/gsdecon/Options.hpp:18:8, inlined from ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, int, int, int, int)’ at score_gene_set.cpp:63:1: /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:368:85: warning: ‘*(Eigen::internal::DenseStorage_impl*)((char*)&opt + offsetof(gsdecon::Options, gsdecon::Options::irlba_options.irlba::Options >::initial.std::optional >::.std::_Optional_base, false, false>::)).Eigen::internal::DenseStorage_impl::m_data’ may be used uninitialized [-Wmaybe-uninitialized] 368 | EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto(m_data, size()); } | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ score_gene_set.cpp: In function ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable >, std::string, Rcpp::NumericVector, bool, bool, int, int, int, int)’: score_gene_set.cpp:31:22: note: ‘opt’ declared here 31 | gsdecon::Options opt; | ^~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c score_markers.cpp -o score_markers.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c set_executor.cpp -o set_executor.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c summarize_effects.cpp -o summarize_effects.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c test_enrichment.cpp -o test_enrichment.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.o aggregate_across_genes.o build_snn_graph.o center_size_factors.o choose_highly_variable_genes.o choose_pseudo_count.o cluster_graph.o cluster_kmeans.o combine_factors.o compute_block_weights.o compute_clrm1_factors.o correct_mnn.o crispr_quality_control.o fit_variance_trend.o model_gene_variances.o normalize_counts.o rna_quality_control.o run_pca.o run_tsne.o run_umap.o sanitize_size_factors.o scale_by_neighbors.o score_gene_set.o score_markers.o set_executor.o subsample_by_neighbors.o summarize_effects.o test_enrichment.o /home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/lib/libigraph.a -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-scrapper/00new/scrapper/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scrapper)