Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scPipe_2.10.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scPipe.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘scPipe/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘scPipe’ version ‘2.10.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 40 non-default packages.Importing from so many packages makes the package vulnerable to any ofthem becoming unavailable.  Move as many as possible to Suggests anduse conditionally.* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘scPipe’ can be installed ... OK* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* used SDK: ‘MacOSX11.3.1.sdk’* checking C++ specification ... NOTE  Specified C++11: please drop specification unless essential* checking installed package size ... INFO  installed size is 15.6Mb  sub-directories of 1Mb or more:    extdata  12.1Mb    libs      2.2Mb* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking whether startup messages can be suppressed ... OK* checking dependencies in R code ... NOTENamespaces in Imports field not imported from:  ‘flexmix’ ‘vctrs’  All declared Imports should be used.* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEsc_atac_feature_counting: warning in sc_atac_create_sce(input_folder =  output_folder, organism = organism, sample = sample_name,  feature_type = feature_type, pheno_data = pheno_data, report =  create_report): partial argument match of 'sample' to 'sample_name'sc_aligning: no visible binding for global variable ‘Var1’sc_aligning: no visible binding for global variable ‘Freq’sc_atac_bam_tagging: no visible binding for global variable ‘.N’sc_atac_bam_tagging: no visible binding for global variable ‘count’sc_atac_bam_tagging: no visible binding for global variable ‘.SD’sc_atac_create_cell_qc_metrics: no visible binding for global variable  ‘seqnames’sc_atac_create_cell_qc_metrics: no visible binding for global variable  ‘start’sc_atac_create_cell_qc_metrics: no visible binding for global variable  ‘end’sc_atac_create_cell_qc_metrics: no visible binding for global variable  ‘barcode’sc_atac_create_cell_qc_metrics: no visible binding for global variable  ‘count’sc_atac_feature_counting: no visible binding for global variable  ‘start’sc_atac_feature_counting: no visible binding for global variable ‘end’sc_atac_feature_counting: no visible global function definition for  ‘write.csv’sc_atac_plot_cells_per_feature: no visible binding for global variable  ‘log_cells_per_feature’sc_atac_plot_cells_per_feature: no visible binding for global variable  ‘..count..’sc_atac_plot_features_per_cell: no visible binding for global variable  ‘log_features_per_cell’sc_atac_plot_features_per_cell: no visible binding for global variable  ‘..count..’sc_atac_plot_fragments_cells_per_feature: no visible binding for global  variable ‘log_counts_per_feature’sc_atac_plot_fragments_cells_per_feature: no visible binding for global  variable ‘log_cells_per_feature’sc_atac_plot_fragments_features_per_cell: no visible binding for global  variable ‘log_counts_per_cell’sc_atac_plot_fragments_features_per_cell: no visible binding for global  variable ‘log_features_per_cell’sc_atac_plot_fragments_per_cell: no visible binding for global variable  ‘log_counts_per_cell’sc_atac_plot_fragments_per_cell: no visible binding for global variable  ‘..count..’sc_atac_plot_fragments_per_feature: no visible binding for global  variable ‘log_counts_per_feature’sc_atac_plot_fragments_per_feature: no visible binding for global  variable ‘..count..’sc_get_umap_data: no visible global function definition for ‘irlba’sc_get_umap_data: no visible binding for global variable ‘value’sc_get_umap_data: no visible binding for global variable ‘cluster’sc_interactive_umap_plot : server: no visible binding for global  variable ‘UMAP1’sc_interactive_umap_plot : server: no visible binding for global  variable ‘UMAP2’sc_interactive_umap_plot : server: no visible binding for global  variable ‘barcode’sc_mae_plot_umap : <anonymous>: no visible global function definition  for ‘irlba’sc_mae_plot_umap : <anonymous>: no visible binding for global variable  ‘value’sc_mae_plot_umap : <anonymous>: no visible binding for global variable  ‘cluster’sc_mae_plot_umap : <anonymous>: no visible global function definition  for ‘experiments’sc_mae_plot_umap: no visible binding for global variable ‘UMAP1’sc_mae_plot_umap: no visible binding for global variable ‘UMAP2’Undefined global functions or variables:  ..count.. .N .SD Freq UMAP1 UMAP2 Var1 barcode cluster count end  experiments irlba log_cells_per_feature log_counts_per_cell  log_counts_per_feature log_features_per_cell seqnames start value  write.csvConsider adding  importFrom("stats", "end", "start")  importFrom("utils", "write.csv")to your NAMESPACE file.* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  QC_metrics.Rd: SingleCellExperiment  UMI_dup_info.Rd: SingleCellExperiment  create_sce_by_dir.Rd: SingleCellExperiment  demultiplex_info.Rd: SingleCellExperiment  feature_info.Rd: SingleCellExperiment  feature_type.Rd: SingleCellExperiment  gene_id_type.Rd: SingleCellExperiment  organism.Rd: SingleCellExperimentPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking contents of ‘data’ directory ... OK* checking data for non-ASCII characters ... OK* checking data for ASCII and uncompressed saves ... OK* checking line endings in C/C++/Fortran sources/headers ... OK* checking line endings in Makefiles ... OK* checking compilation flags in Makevars ... OK* checking for GNU extensions in Makefiles ... INFOGNU make is a SystemRequirements.* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK* checking use of PKG_*FLAGS in Makefiles ... OK* checking compiled code ... NOTENote: information on .o files is not availableFile ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/scPipe/libs/scPipe.so’:  Found ‘___assert_rtn’, possibly from ‘assert’ (C)  Found ‘___stderrp’, possibly from ‘stderr’ (C)  Found ‘___stdoutp’, possibly from ‘stdout’ (C)  Found ‘_abort’, possibly from ‘abort’ (C)  Found ‘_exit’, possibly from ‘exit’ (C)Compiled code should not call entry points which might terminate R norwrite to stdout/stderr instead of to the console, nor use Fortran I/Onor system RNGs nor [v]sprintf. The detected symbols are linked intothe code but might come from libraries and not actually be called.See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                       user  system elapsedsc_atac_bam_tagging 159.973 242.387 572.693plot_QC_pairs        10.798   0.119  14.975sc_sample_data        9.464   0.086  13.316* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘testthat.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 5 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/scPipe.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scPipe###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘scPipe’ ...** this is package ‘scPipe’ version ‘2.10.0’** using staged installation** libsusing C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using C++11using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FragmentThread.cpp -o FragmentThread.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FragmentUtils.cpp -o FragmentUtils.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Gene.cpp -o Gene.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Interval.cpp -o Interval.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ResizeArray.cpp -o ResizeArray.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ThreadOutputFile.cpp -o ThreadOutputFile.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Trie.cpp -o Trie.oclang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam.c -o bam.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cellbarcode.cpp -o cellbarcode.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c check_barcode_reads.cpp -o check_barcode_reads.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c detect_barcode.cpp -o detect_barcode.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c parsebam.cpp -o parsebam.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c parsecount.cpp -o parsecount.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-cpp.cpp -o test-cpp.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-example.cpp -o test-example.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-fragmentThread.cpp -o test-fragmentThread.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-resizearray.cpp -o test-resizearray.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-str_utils.cpp -o test-str_utils.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-trie_matching.cpp -o test-trie_matching.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c transcriptmapping.cpp -o transcriptmapping.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c trimbarcode.cpp -o trimbarcode.otrimbarcode.cpp:820:45: warning: variable 'barcodeNo' set but not used [-Wunused-but-set-variable]                int barcodeExact = 0, barcodePartial = 0, barcodeNo = 0;                                                          ^1 warning generated.clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tsscreatebins.cpp -o tsscreatebins.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.oclang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scPipe.so FragmentThread.o FragmentUtils.o Gene.o Interval.o RcppExports.o ResizeArray.o ThreadOutputFile.o Trie.o bam.o cellbarcode.o check_barcode_reads.o detect_barcode.o parsebam.o parsecount.o qc_per_bc_file_helper.o rcpp_scPipe_func.o sc_atac_create_fragments.o test-cpp.o test-example.o test-fragmentThread.o test-resizearray.o test-runner.o test-str_utils.o test-trie_matching.o transcriptmapping.o trimbarcode.o tsscreatebins.o utils.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-scPipe/00new/scPipe/libs** R** data** 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 (scPipe)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(testthat)> library(scPipe)Loading required package: SingleCellExperimentLoading required package: SummarizedExperimentLoading required package: MatrixGenericsLoading required package: matrixStatsAttaching package: 'MatrixGenerics'The following objects are masked from 'package:matrixStats':    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,    colWeightedMeans, colWeightedMedians, colWeightedSds,    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,    rowWeightedSds, rowWeightedVarsLoading required package: GenomicRangesLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minLoading required package: S4VectorsAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: SeqinfoLoading required package: BiobaseWelcome to Bioconductor    Vignettes contain introductory material; view with    'browseVignettes()'. To cite Bioconductor, see    'citation("Biobase")', and for packages 'citation("pkgname")'.Attaching package: 'Biobase'The following object is masked from 'package:MatrixGenerics':    rowMediansThe following objects are masked from 'package:matrixStats':    anyMissing, rowMediansLinux/MacOS detected! Checking if samtools is installed ... samtools was not located. Please specify the path of it when running sc_atac_remove_duplicates()> > test_check("scPipe")Successful; continuing with program.Invalid barcode start index given, with only 0 percent of reads containing a barcode match. However, a better barcode start location is 0 , where 55 percent of barcodes were found.Unsuccessful. No location was found with a high number of barcode matches. Did both smallbarcode1col.csv and /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/scPipe/extdata/simu_R1.fastq.gz come from the same provider?[ FAIL 0 | WARN 0 | SKIP 1 | PASS 121 ]══ Skipped tests (1) ═══════════════════════════════════════════════════════════• empty test (1):[ FAIL 0 | WARN 0 | SKIP 1 | PASS 121 ]> > proc.time()   user  system elapsed  19.377   0.867  28.528