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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scPipe_2.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scPipe.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scPipe’ version ‘2.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 46.7Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
    libs     33.3Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespaces 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 ... NOTE
sc_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.csv
Consider 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 ... OK
* 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 ... NOTE
GNU 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.0/site-library/scPipe/libs/scPipe.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
sc_atac_bam_tagging  34.715 16.393  50.626
sc_sample_data        9.453  0.151   9.622
plot_QC_pairs         9.128  0.227   9.375
calculate_QC_metrics  3.088  0.197  11.223
convert_geneid        1.549  0.084  12.491
* 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
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scPipe.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scPipe
###
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* installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c FragmentThread.cpp -o FragmentThread.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c FragmentUtils.cpp -o FragmentUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ResizeArray.cpp -o ResizeArray.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ThreadOutputFile.cpp -o ThreadOutputFile.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Trie.cpp -o Trie.o
Trie.cpp: In member function ‘void Trie::SeqMismatchAux(std::vector<MismatchResult>&, const string&, trie_node*, int, int, int) const’:
Trie.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<trie_node*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  265 |   for (int i = 0; i < valid_nodes.size(); i++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
Trie.cpp:274:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<trie_node*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  274 |    for (int i = 0; i < valid_nodes.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c bam.c -o bam.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cellbarcode.cpp -o cellbarcode.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c check_barcode_reads.cpp -o check_barcode_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c parsecount.cpp -o parsecount.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-cpp.cpp -o test-cpp.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-example.cpp -o test-example.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-fragmentThread.cpp -o test-fragmentThread.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-resizearray.cpp -o test-resizearray.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-str_utils.cpp -o test-str_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-trie_matching.cpp -o test-trie_matching.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c transcriptmapping.cpp -o transcriptmapping.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function ‘void paired_fastq_to_fastq(char*, char*, char*, read_s, filter_s, bool)’:
trimbarcode.cpp:611:24: warning: ‘o_stream_gz’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  611 |             fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
      |             ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
trimbarcode.cpp: In function ‘std::vector<int> sc_atac_paired_fastq_to_fastq(const char*, std::vector<std::__cxx11::basic_string<char> >, const char*, const char*, const char*, bool, bool, bool, int, int, bool)’:
trimbarcode.cpp:812:31: warning: ‘seq3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  812 |             if((l3 = kseq_read(seq3)) < 0){
      |                      ~~~~~~~~~^~~~~~
trimbarcode.cpp:981:16: warning: ‘fq3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  981 |         gzclose(fq3);
      |         ~~~~~~~^~~~~
trimbarcode.cpp: In function ‘std::vector<int> sc_atac_paired_fastq_to_csv(char*, char*, char*, char*, char*, int, int, char*, bool, bool, bool, int, int, int, int, int, int)’:
trimbarcode.cpp:1347:44: warning: ‘bc1_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1347 |         memmove(seq1->seq.s, seq1->seq.s + bc1_end, seq1->name.l - bc1_end);
      |                                            ^~~~~~~
trimbarcode.cpp:1406:57: warning: ‘seq3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1406 |                 memcpy(subStr3 + id2_len + 1, seq3->seq.s + umi_start, umi_length);
      |                                               ~~~~~~~~~~^
trimbarcode.cpp:1498:16: warning: ‘fq3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1498 |         gzclose(fq3);
      |         ~~~~~~~^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c tsscreatebins.cpp -o tsscreatebins.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.0/lib -L/usr/local/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 /home/biocbuild/R/R-4.4.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.4.0/lib -lR
installing to /home/biocbuild/R/R-4.4.0/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R 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.

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Type 'contributors()' for more information and
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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: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching 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, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The 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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome 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':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians



Linux/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 /home/biocbuild/R/R-4.4.0/site-library/scPipe/extdata/simu_R1.fastq.gz come from the same provider?
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 121 ]
> 
> proc.time()
   user  system elapsed 
 21.258   0.735  22.031