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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChromSCape_1.5.22.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.5.22'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ChromSCape' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    www    2.1Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CompareWilcox: no visible binding for global variable 'annot.'
bams_to_matrix_indexes: no visible binding for global variable
  'files_dir_list'
filter_correlated_cell_scExp: no visible binding for global variable
  'run_tsne'
generate_analysis: no visible binding for global variable 'k'
generate_analysis: no visible binding for global variable
  'clusterConsensus'
get_most_variable_cyto: no visible binding for global variable
  'cytoBand'
get_most_variable_cyto: no visible binding for global variable
  'Fri_cyto'
num_cell_after_QC_filt_scExp: no visible binding for global variable
  'sample_id'
num_cell_after_QC_filt_scExp: no visible binding for global variable
  'total_counts'
num_cell_scExp: no visible binding for global variable 'sample_id'
num_cell_scExp: no visible binding for global variable 'total_counts'
plot_coverage_BigWig: no visible binding for global variable 'score'
plot_coverage_BigWig: no visible binding for global variable 'molecule'
plot_coverage_BigWig: no visible binding for global variable
  'orientation'
plot_coverage_BigWig: no visible binding for global variable 'Gene'
plot_gain_or_loss_barplots: no visible binding for global variable
  'Gain_or_Loss'
plot_gain_or_loss_barplots: no visible binding for global variable
  'ncells'
plot_gain_or_loss_barplots: no visible binding for global variable
  'cytoBand'
plot_most_contributing_features: no visible binding for global variable
  'genes'
plot_pie_most_contributing_chr: no visible binding for global variable
  'absolute_value'
plot_reduced_dim_scExp: no visible binding for global variable 'V1'
plot_reduced_dim_scExp: no visible binding for global variable 'V2'
plot_reduced_dim_scExp: no visible binding for global variable
  'cluster'
subset_bam_call_peaks: no visible binding for global variable
  'merged_bam'
Undefined global functions or variables:
  Fri_cyto Gain_or_Loss Gene V1 V2 absolute_value annot. cluster
  clusterConsensus cytoBand files_dir_list genes k merged_bam molecule
  ncells orientation run_tsne sample_id score total_counts
* checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/ChromSCape/libs/x64/ChromSCape.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
   'vignettes/PairedTag_Zhu_H3K4me1.Rmd'
   'vignettes/scChIC_Ku_H3K4me3.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ... ERROR
Running examples in 'ChromSCape-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: differential_analysis_scExp
> ### Title: Runs differential analysis between cell clusters
> ### Aliases: differential_analysis_scExp
> 
> ### ** Examples
> 
> data("scExp")
> scExp_cf = differential_analysis_scExp(scExp)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 15 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 14 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 13 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 12 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 11 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 4 (<-riesling1:11417)
Error in `[.data.frame`(res, , logFC.col) : undefined columns selected
Calls: differential_analysis_scExp -> [ -> [.data.frame
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'D:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.