############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scrapper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘scrapper’ ... ** this is package ‘scrapper’ version ‘1.1.12’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c adt_quality_control.cpp -o adt_quality_control.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c aggregate_across_cells.cpp -o aggregate_across_cells.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c aggregate_across_genes.cpp -o aggregate_across_genes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c build_snn_graph.cpp -o build_snn_graph.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c center_size_factors.cpp -o center_size_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c choose_pseudo_count.cpp -o choose_pseudo_count.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster_graph.cpp -o cluster_graph.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster_kmeans.cpp -o cluster_kmeans.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c combine_factors.cpp -o combine_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c correct_mnn.cpp -o correct_mnn.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c crispr_quality_control.cpp -o crispr_quality_control.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fit_variance_trend.cpp -o fit_variance_trend.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c model_gene_variances.cpp -o model_gene_variances.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c normalize_counts.cpp -o normalize_counts.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rna_quality_control.cpp -o rna_quality_control.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c run_pca.cpp -o run_pca.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c run_tsne.cpp -o run_tsne.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c run_umap.cpp -o run_umap.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sanitize_size_factors.cpp -o sanitize_size_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c scale_by_neighbors.cpp -o scale_by_neighbors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c score_gene_set.cpp -o score_gene_set.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c score_markers.cpp -o score_markers.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c summarize_effects.cpp -o summarize_effects.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c test_enrichment.cpp -o test_enrichment.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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_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 test_enrichment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)