Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 362/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.20.0  (landing page)
Pacome Prompsy
Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_22
git_last_commit: a5a7bda
git_last_commit_date: 2025-10-29 11:02:56 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for ChromSCape on lconway

To the developers/maintainers of the ChromSCape package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChromSCape.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChromSCape
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.20.0.tar.gz
StartedAt: 2025-10-30 02:54:52 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 03:09:28 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 875.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 51 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* 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 ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘flexdashboard’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bams_to_matrix_indexes: no visible binding for global variable
  ‘files_dir_list’
enrich_TF_ChEA3_genes: no visible binding for global variable
  ‘CheA3_TF_nTargets’
filter_correlated_cell_scExp: no visible binding for global variable
  ‘run_tsne’
generate_analysis: no visible global function definition for ‘head’
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_correlation_PCA_scExp: no visible binding for global variable
  ‘Component’
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_percent_active_feature_scExp: no visible binding for global
  variable ‘group’
plot_percent_active_feature_scExp: no visible binding for global
  variable ‘percent_active’
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’
plot_top_TF_scExp: no visible binding for global variable ‘TF’
rebin_helper: no visible binding for global variable ‘new_row’
rebin_helper: no visible binding for global variable ‘origin_value’
rebin_matrix: no visible binding for global variable ‘group’
subset_bam_call_peaks: no visible binding for global variable
  ‘merged_bam’
Undefined global functions or variables:
  CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2
  absolute_value cluster clusterConsensus cytoBand files_dir_list genes
  group head k merged_bam molecule ncells new_row orientation
  origin_value percent_active run_tsne sample_id total_counts
Consider adding
  importFrom("utils", "head")
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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
get_pathway_mat_scExp                 83.436  7.010  90.715
plot_gain_or_loss_barplots            54.513  0.469  55.085
calculate_CNA                         28.753  2.002  30.952
plot_reduced_dim_scExp_CNA            26.634  0.215  26.879
calculate_logRatio_CNA                25.834  0.802  26.677
calculate_gain_or_loss                25.875  0.669  26.592
calculate_cyto_mat                    25.617  0.718  26.372
get_most_variable_cyto                23.627  0.265  23.935
get_cyto_features                     22.222  0.140  22.397
num_cell_after_cor_filt_scExp         12.815  0.129  12.955
filter_correlated_cell_scExp           9.959  0.117  10.100
preprocessing_filtering_and_reduction  9.702  0.162   9.880
import_scExp                           8.311  1.127   9.486
rebin_matrix                           7.895  0.045  24.712
CompareWilcox                          6.972  0.504   6.912
create_scDataset_raw                   6.760  0.577   7.352
differential_activation                5.671  0.068   5.746
CompareedgeRGLM                        5.294  0.367   5.675
enrich_TF_ChEA3_scExp                  1.176  0.096   5.714
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘ChromSCape’ ...
** this is package ‘ChromSCape’ version ‘1.20.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c as_dist.cpp -o as_dist.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/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)

Tests output

ChromSCape.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 40.466   3.795  44.234 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0090.0030.016
CompareWilcox6.9720.5046.912
CompareedgeRGLM5.2940.3675.675
annotToCol21.0910.0571.152
calculate_CNA28.753 2.00230.952
calculate_cyto_mat25.617 0.71826.372
calculate_gain_or_loss25.875 0.66926.592
calculate_logRatio_CNA25.834 0.80226.677
choose_cluster_scExp3.5940.8414.460
colors_scExp0.3030.0070.310
consensus_clustering_scExp3.1340.9094.063
correlation_and_hierarchical_clust_scExp0.3760.0070.383
create_project_folder0.0010.0020.003
create_scDataset_raw6.7600.5777.352
create_scExp0.5050.0080.514
define_feature0.1640.0050.169
detect_samples1.0220.0801.105
differential_activation5.6710.0685.746
differential_analysis_scExp3.0840.0403.129
enrich_TF_ChEA3_genes0.5500.1852.129
enrich_TF_ChEA3_scExp1.1760.0965.714
exclude_features_scExp0.4710.0100.482
feature_annotation_scExp1.4070.0981.507
filter_correlated_cell_scExp 9.959 0.11710.100
filter_scExp0.6380.0060.646
find_clusters_louvain_scExp0.3840.0080.391
find_top_features0.3720.0060.378
gene_set_enrichment_analysis_scExp0.2850.0080.294
generate_analysis000
generate_coverage_tracks0.0000.0000.001
generate_report0.0010.0000.001
getExperimentNames0.2710.0060.279
getMainExperiment0.3200.0090.330
get_cyto_features22.222 0.14022.397
get_genomic_coordinates0.4440.0030.448
get_most_variable_cyto23.627 0.26523.935
get_pathway_mat_scExp83.436 7.01090.715
has_genomic_coordinates0.6230.0130.636
import_scExp8.3111.1279.486
inter_correlation_scExp0.3770.0200.398
intra_correlation_scExp0.3870.0260.414
launchApp0.0000.0010.001
normalize_scExp0.4550.0260.481
num_cell_after_QC_filt_scExp0.4170.0070.424
num_cell_after_cor_filt_scExp12.815 0.12912.955
num_cell_before_cor_filt_scExp0.2710.0190.291
num_cell_in_cluster_scExp0.4600.0080.468
num_cell_scExp0.3400.0030.344
plot_cluster_consensus_scExp1.1560.0201.179
plot_correlation_PCA_scExp1.3040.0731.381
plot_coverage_BigWig0.2710.0100.282
plot_differential_summary_scExp0.3020.0060.309
plot_differential_volcano_scExp0.3830.0140.398
plot_distribution_scExp0.4870.0100.498
plot_gain_or_loss_barplots54.513 0.46955.085
plot_heatmap_scExp0.3730.0120.385
plot_inter_correlation_scExp0.7750.0130.790
plot_intra_correlation_scExp0.7390.0090.750
plot_most_contributing_features0.5490.0150.565
plot_percent_active_feature_scExp0.5890.0070.597
plot_pie_most_contributing_chr0.3390.0100.348
plot_reduced_dim_scExp1.7800.0251.807
plot_reduced_dim_scExp_CNA26.634 0.21526.879
plot_top_TF_scExp0.7150.0170.734
plot_violin_feature_scExp0.7480.0150.765
preprocess_CPM0.3920.0280.420
preprocess_RPKM0.4230.0250.448
preprocess_TFIDF0.4490.0410.492
preprocess_TPM0.4830.0890.574
preprocess_feature_size_only0.4040.0270.431
preprocessing_filtering_and_reduction9.7020.1629.880
read_sparse_matrix000
rebin_matrix 7.895 0.04524.712
reduce_dims_scExp1.8400.0621.905
scExp1.1990.0421.244
subsample_scExp0.6120.0360.649
subset_bam_call_peaks0.0010.0010.000
summary_DA0.3070.0060.313
swapAltExp_sameColData0.3700.0100.381
table_enriched_genes_scExp0.2360.0090.245
wrapper_Signac_FeatureMatrix0.0010.0000.000