############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL scrapper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’ * installing *source* package ‘scrapper’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c adt_quality_control.cpp -o adt_quality_control.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c aggregate_across_cells.cpp -o aggregate_across_cells.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c build_snn_graph.cpp -o build_snn_graph.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c center_size_factors.cpp -o center_size_factors.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c choose_pseudo_count.cpp -o choose_pseudo_count.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cluster_graph.cpp -o cluster_graph.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cluster_kmeans.cpp -o cluster_kmeans.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c combine_factors.cpp -o combine_factors.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c correct_mnn.cpp -o correct_mnn.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c crispr_quality_control.cpp -o crispr_quality_control.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fit_variance_trend.cpp -o fit_variance_trend.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c model_gene_variances.cpp -o model_gene_variances.o In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:5, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_variances/scran_variances.hpp:5, from model_gene_variances.cpp:8: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:272:60: required from ‘void scran_variances::internal::compute_variances_sparse_row(const tatami::Matrix&, const std::vector >&, const Block_*, const std::vector >&, int) [with Value_ = double; Index_ = int; Stat_ = double; Block_ = int]’ 272 | auto stat = tatami_stats::variances::direct(range.value, range.number, NC, false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:392:41: required from ‘void scran_variances::internal::compute_variances(const tatami::Matrix&, const std::vector >&, const Block_*, const std::vector >&, int) [with Value_ = double; Index_ = int; Stat_ = double; Block_ = int]’ 392 | compute_variances_sparse_row(mat, buffers, block, block_size, num_threads); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:474:36: required from ‘void scran_variances::model_gene_variances_blocked(const tatami::Matrix&, const Block_*, const ModelGeneVariancesBlockedBuffers&, const ModelGeneVariancesOptions&) [with Value_ = double; Index_ = int; Block_ = int; Stat_ = double]’ 474 | internal::compute_variances(mat, buffers.per_block, block, block_size, options.num_threads); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model_gene_variances.cpp:76:54: required from here 76 | scran_variances::model_gene_variances_blocked(*mat, ptr, bbuffers, opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp:95:29: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | std::pair direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) { | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c normalize_counts.cpp -o normalize_counts.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rna_quality_control.cpp -o rna_quality_control.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/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/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/irlba/irlba.hpp:4, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:6, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/scran_pca.hpp:4, from run_pca.cpp:10: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:5: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:200:63: required from ‘void scran_pca::internal::run_sparse(const tatami::Matrix&, const scran_pca::SimplePcaOptions&, EigenMatrix_&, EigenMatrix_&, EigenVector_&, EigenVector_&, EigenVector_&, typename EigenVector_::Scalar&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix; EigenVector_ = Eigen::Matrix; typename EigenVector_::Scalar = double]’ 200 | auto results = tatami_stats::variances::direct(values.data() + offset, num_nonzero, ncells, /* skip_nan = */ false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:359:29: required from ‘void scran_pca::simple_pca(const tatami::Matrix&, const SimplePcaOptions&, SimplePcaResults&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix; EigenVector_ = Eigen::Matrix]’ 359 | internal::run_sparse(mat, options, output.components, output.rotation, output.variance_explained, output.center, output.scale, output.total_variance); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:391:15: required from ‘scran_pca::SimplePcaResults scran_pca::simple_pca(const tatami::Matrix&, const SimplePcaOptions&) [with EigenMatrix_ = Eigen::Matrix; EigenVector_ = Eigen::Matrix; Value_ = double; Index_ = int]’ 391 | simple_pca(mat, options, output); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ run_pca.cpp:87:41: required from here 87 | auto out = scran_pca::simple_pca(*(mat->ptr), opt); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp:95:29: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | std::pair direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) { | ^~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:341: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c run_tsne.cpp -o run_tsne.o In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/kmeans/InitializeKmeanspp.hpp:9, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/kmeans/kmeans.hpp:9, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/knncolle/Kmknn.hpp:11, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/knncolle/knncolle.hpp:13, from run_tsne.cpp:4: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/aarand/aarand.hpp: In instantiation of ‘std::pair<_FIter, _FIter> aarand::standard_normal(Engine&) [with T = double; Engine = std::mersenne_twister_engine]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/qdtsne/utils.hpp:64:54: required from ‘void qdtsne::initialize_random(Float_*, size_t, int) [with int ndim_ = 2; Float_ = double; size_t = long unsigned int]’ 64 | auto paired = aarand::standard_normal(rng); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ run_tsne.cpp:25:33: required from here 25 | qdtsne::initialize_random<2>(optr, nobs, seed); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/aarand/aarand.hpp:69:17: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 69 | std::pair standard_normal(Engine& eng) { | ^~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c run_umap.cpp -o run_umap.o In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/irlba/irlba.hpp:4, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/spectral_init.hpp:4, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/initialize.hpp:8, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/umappp.hpp:11, from run_umap.cpp:4: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/initialize.hpp:6: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/find_ab.hpp: In instantiation of ‘std::pair<_FIter, _FIter> umappp::internal::find_ab(Float_, Float_, Float_, Float_, int, Float_) [with Float_ = double]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/initialize.hpp:87:39: required from ‘umappp::Status umappp::initialize(NeighborList, int, Float_*, Options) [with Index_ = int; Float_ = float; NeighborList = std::vector, std::allocator > >, std::allocator, std::allocator > > > >]’ 87 | auto found = internal::find_ab(options.spread, options.min_dist); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ run_umap.cpp:21:37: required from here 21 | auto status = umappp::initialize(std::move(neighbors), ndim, embedding.data(), opt); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/umappp/find_ab.hpp:48:27: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 48 | std::pair find_ab(Float_ spread, Float_ min_dist, Float_ grid = 300, Float_ limit = 0.5, int iter = 50, Float_ tol = 1e-6) { | ^~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:341: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c sanitize_size_factors.cpp -o sanitize_size_factors.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c scale_by_neighbors.cpp -o scale_by_neighbors.o In file included from scale_by_neighbors.cpp:3: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/mumosa/mumosa.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> mumosa::compute_distance(Index_, Float_*) [with Index_ = int; Float_ = double]’: scale_by_neighbors.cpp:14:63: required from here 14 | values.push_back(mumosa::compute_distance(dist.size(), dist.begin())); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/mumosa/mumosa.hpp:54:27: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 54 | std::pair compute_distance(Index_ num_cells, Float_* distances) { | ^~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/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/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/irlba/irlba.hpp:4, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/gsdecon/compute.hpp:8, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/gsdecon/gsdecon.hpp:4, from score_gene_set.cpp:7: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:5, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/scran_pca.hpp:4, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/gsdecon/compute.hpp:9: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:200:63: required from ‘void scran_pca::internal::run_sparse(const tatami::Matrix&, const scran_pca::SimplePcaOptions&, EigenMatrix_&, EigenMatrix_&, EigenVector_&, EigenVector_&, EigenVector_&, typename EigenVector_::Scalar&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix; EigenVector_ = Eigen::Matrix; typename EigenVector_::Scalar = double]’ 200 | auto results = tatami_stats::variances::direct(values.data() + offset, num_nonzero, ncells, /* skip_nan = */ false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:359:29: required from ‘void scran_pca::simple_pca(const tatami::Matrix&, const SimplePcaOptions&, SimplePcaResults&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix; EigenVector_ = Eigen::Matrix]’ 359 | internal::run_sparse(mat, options, output.components, output.rotation, output.variance_explained, output.center, output.scale, output.total_variance); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_pca/simple_pca.hpp:391:15: required from ‘scran_pca::SimplePcaResults scran_pca::simple_pca(const tatami::Matrix&, const SimplePcaOptions&) [with EigenMatrix_ = Eigen::Matrix; EigenVector_ = Eigen::Matrix; Value_ = double; Index_ = int]’ 391 | simple_pca(mat, options, output); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/gsdecon/compute.hpp:55:37: required from ‘void gsdecon::compute(const tatami::Matrix&, const Options&, const Buffers&) [with Value_ = double; Index_ = int; Float_ = double]’ 55 | auto res = scran_pca::simple_pca(matrix, sopt); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ score_gene_set.cpp:56:25: required from here 56 | gsdecon::compute(matrix, opt, output); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp:95:29: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | std::pair direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) { | ^~~~~~ In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/Core:341: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c score_markers.cpp -o score_markers.o In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_markers/score_markers_pairwise.hpp:4, from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_markers/scran_markers.hpp:4, from score_markers.cpp:10: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_markers/cohens_d.hpp: In instantiation of ‘std::pair<_FIter, _FIter> scran_markers::internal::compute_pairwise_cohens_d_two_sided(size_t, size_t, const Stat_*, const Stat_*, size_t, size_t, const PrecomputedPairwiseWeights&, Stat_) [with Stat_ = double; Weight_ = double; size_t = long unsigned int]’: /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:466:75: required from ‘void scran_markers::internal::process_simple_summary_effects(size_t, size_t, size_t, size_t, const std::vector&, const std::vector&, const std::vector&, const scran_markers::ScoreMarkersSummaryBuffers&, const std::vector&, double, size_t, int) [with Stat_ = double; Rank_ = int; size_t = long unsigned int]’ 466 | auto tmp = compute_pairwise_cohens_d_two_sided(group, other, my_means, my_variances, ngroups, nblocks, preweights, threshold); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:813:45: required from ‘void scran_markers::score_markers_summary_blocked(const tatami::Matrix&, const Group_*, const Block_*, const ScoreMarkersSummaryOptions&, const ScoreMarkersSummaryBuffers&) [with Value_ = double; Index_ = int; Group_ = int; Block_ = int; Stat_ = double; Rank_ = int]’ 813 | internal::process_simple_summary_effects( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 814 | matrix.nrow(), | ~~~~~~~~~~~~~~ 815 | ngroups, | ~~~~~~~~ 816 | nblocks, | ~~~~~~~~ 817 | ncombos, | ~~~~~~~~ 818 | combo_means, | ~~~~~~~~~~~~ 819 | combo_vars, | ~~~~~~~~~~~ 820 | combo_detected, | ~~~~~~~~~~~~~~~ 821 | output, | ~~~~~~~ 822 | combo_weights, | ~~~~~~~~~~~~~~ 823 | options.threshold, | ~~~~~~~~~~~~~~~~~~ 824 | options.cache_size, | ~~~~~~~~~~~~~~~~~~~ 825 | options.num_threads | ~~~~~~~~~~~~~~~~~~~ 826 | ); | ~ score_markers.cpp:100:53: required from here 100 | scran_markers::score_markers_summary_blocked(*mat, static_cast(groups.begin()), ptr, opt, buffers); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/scran_markers/cohens_d.hpp:135:25: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 135 | std::pair compute_pairwise_cohens_d_two_sided( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c summarize_effects.cpp -o summarize_effects.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.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_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 subsample_by_neighbors.o summarize_effects.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.4.2/site-library/00LOCK-scrapper/00new/scrapper/libs ** R ** 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)