R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

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(ChromSCape)
> 
> test_check("ChromSCape")
[1] "Running Batch Correction ..."
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test_correlation_clustering.R:99:3): Choosing clusters - Wrong inputs. ──
`choose_cluster_scExp(scExp_cf.)` did not throw an error.
── Error (test_diff_analysis_gene_set_enrichment.R:44:1): (code run outside of `test_that()`) ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'normcounts': invalid or not-yet-implemented 'Matrix' subsetting
Backtrace:
     ▆
  1. ├─ChromSCape::differential_analysis_scExp(...) at test_diff_analysis_gene_set_enrichment.R:44:0
  2. │ ├─SingleCellExperiment::normcounts(...)
  3. │ ├─scExp[SingleCellExperiment::rowData(scExp)$top_feature, ]
  4. │ └─scExp[SingleCellExperiment::rowData(scExp)$top_feature, ]
  5. │   ├─methods::callNextMethod()
  6. │   └─SummarizedExperiment .nextMethod(x = x, i = i, j = )
  7. │     ├─x@assays[ii, ]
  8. │     └─x@assays[ii, ]
  9. │       └─SummarizedExperiment:::.extract_Assays_subset(x, i, j)
 10. │         ├─methods::as(endoapply(assays, extract_assay_subset), class(x))
 11. │         │ └─methods:::.class1(object)
 12. │         └─S4Vectors::endoapply(assays, extract_assay_subset)
 13. │           ├─BiocGenerics::lapply(X, FUN, ...)
 14. │           └─S4Vectors::lapply(X, FUN, ...)
 15. │             ├─BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
 16. │             └─base::lapply(as.list(X), match.fun(FUN), ...)
 17. │               └─SummarizedExperiment FUN(X[[i]], ...)
 18. │                 ├─BiocGenerics::do.call(`[`, args)
 19. │                 ├─base::do.call(`[`, args)
 20. │                 ├─methods `<fn>`(`<dgCMatrx[,115]>`, NULL, , drop = FALSE)
 21. │                 └─Matrix `<fn>`(`<dgCMatrx[,115]>`, NULL, , drop = FALSE)
 22. │                   └─base::stop("invalid or not-yet-implemented 'Matrix' subsetting")
 23. └─base::.handleSimpleError(...)
 24.   └─base h(simpleError(msg, call))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ChromSCape_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.4.0’
* 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 ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChromSCape’ can be installed ... OK
* checking installed package size ... OK
* checking package 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_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 V1 V2 absolute_value annot. cluster
  clusterConsensus cytoBand files_dir_list genes k merged_bam ncells
  run_tsne sample_id 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 ... SKIPPED
* 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 ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   14. │           └─S4Vectors::lapply(X, FUN, ...)
   15. │             ├─BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
   16. │             └─base::lapply(as.list(X), match.fun(FUN), ...)
   17. │               └─SummarizedExperiment FUN(X[[i]], ...)
   18. │                 ├─BiocGenerics::do.call(`[`, args)
   19. │                 ├─base::do.call(`[`, args)
   20. │                 ├─methods `<fn>`(`<dgCMatrx[,115]>`, NULL, , drop = FALSE)
   21. │                 └─Matrix `<fn>`(`<dgCMatrx[,115]>`, NULL, , drop = FALSE)
   22. │                   └─base::stop("invalid or not-yet-implemented 'Matrix' subsetting")
   23. └─base::.handleSimpleError(...)
   24.   └─base h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00check.log’
for details.

* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c as_dist.cpp -o as_dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00LOCK-ChromSCape/00new/ChromSCape/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 (ChromSCape)