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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scPipe.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings scPipe_2.3.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/scPipe.Rcheck'
* using R Under development (unstable) (2024-03-06 r86056 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scPipe' version '2.3.1'
* 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 whether package 'scPipe' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 24.4Mb
  sub-directories of 1Mb or more:
    extdata  12.0Mb
    libs     11.1Mb
* 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 R 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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/scPipe/libs/x64/scPipe.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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  40.64   8.27   49.92
plot_QC_pairs         7.75   0.20    8.01
sc_sample_data        7.47   0.09    7.56
calculate_QC_metrics  3.02   0.23   39.37
get_genes_by_GO       1.09   0.14   73.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-anno_import.R:18:5'): Common annotation sources can be imported ──
  `anno_import(system.file("extdata", "ens_tiny_anno.gff3.gz", package = "scPipe"))` produced warnings.
  ── Failure ('test-anno_import.R:19:5'): Common annotation sources can be imported ──
  `anno_import(system.file("extdata", "ens_tiny_anno.gtf.gz", package = "scPipe"))` produced warnings.
  ── Failure ('test-anno_import.R:24:5'): Common annotation sources can be imported ──
  `anno_import(system.file("extdata", "gen_tiny_anno.gff3.gz", package = "scPipe"))` produced warnings.
  ── Failure ('test-anno_import.R:25:5'): Common annotation sources can be imported ──
  `anno_import(system.file("extdata", "gen_tiny_anno.gtf.gz", package = "scPipe"))` produced warnings.
  ── Failure ('test-anno_import.R:30:5'): Common annotation sources can be imported ──
  `anno_import(system.file("extdata", "ref_tiny_anno.gff3.gz", package = "scPipe"))` produced warnings.
  
  [ FAIL 5 | WARN 64 | SKIP 0 | PASS 116 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 6 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/scPipe.Rcheck/00check.log'
for details.