Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-08 12:51 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 358/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 Oct 2025)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: devel
git_last_commit: a4985c2
git_last_commit_date: 2025-08-01 10:39:23 -0400 (Fri, 01 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


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: 1.19.1
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_1.19.1.tar.gz
StartedAt: 2025-10-07 20:35:59 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 20:51:50 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 951.1 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_1.19.1.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 ‘1.19.1’
* 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                 91.709  9.456 101.925
plot_gain_or_loss_barplots            60.512  0.513  61.339
calculate_CNA                         29.125  1.807  31.063
plot_reduced_dim_scExp_CNA            29.877  0.306  30.373
calculate_logRatio_CNA                28.317  0.909  29.393
calculate_cyto_mat                    28.122  0.806  29.072
calculate_gain_or_loss                28.061  0.685  28.902
get_most_variable_cyto                26.885  0.254  27.298
get_cyto_features                     24.028  0.199  24.357
num_cell_after_cor_filt_scExp         13.696  0.184  13.935
preprocessing_filtering_and_reduction 10.523  0.233  10.812
filter_correlated_cell_scExp          10.501  0.113  10.674
import_scExp                           8.495  1.293   9.904
rebin_matrix                           8.455  0.073  26.446
create_scDataset_raw                   7.412  0.565   8.031
CompareWilcox                          7.196  0.549   7.188
differential_activation                6.204  0.071   6.305
CompareedgeRGLM                        5.457  0.378   5.869
enrich_TF_ChEA3_scExp                  1.234  0.098   5.222
* 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 ‘1.19.1’
** 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 
 42.080   3.716  45.978 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0070.0020.009
CompareWilcox7.1960.5497.188
CompareedgeRGLM5.4570.3785.869
annotToCol21.1030.0471.159
calculate_CNA29.125 1.80731.063
calculate_cyto_mat28.122 0.80629.072
calculate_gain_or_loss28.061 0.68528.902
calculate_logRatio_CNA28.317 0.90929.393
choose_cluster_scExp3.7360.5604.338
colors_scExp0.3770.0110.391
consensus_clustering_scExp3.4580.5824.081
correlation_and_hierarchical_clust_scExp0.4120.0070.423
create_project_folder0.0010.0020.003
create_scDataset_raw7.4120.5658.031
create_scExp0.5490.0080.563
define_feature0.1600.0030.164
detect_samples1.1080.0601.174
differential_activation6.2040.0716.305
differential_analysis_scExp3.3630.0313.413
enrich_TF_ChEA3_genes0.6030.1721.970
enrich_TF_ChEA3_scExp1.2340.0985.222
exclude_features_scExp0.5300.0060.539
feature_annotation_scExp1.5860.1021.717
filter_correlated_cell_scExp10.501 0.11310.674
filter_scExp0.6250.0080.636
find_clusters_louvain_scExp0.4300.0110.442
find_top_features0.4250.0140.443
gene_set_enrichment_analysis_scExp0.3080.0070.316
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.3430.0080.358
getMainExperiment0.3640.0080.374
get_cyto_features24.028 0.19924.357
get_genomic_coordinates0.4100.0090.420
get_most_variable_cyto26.885 0.25427.298
get_pathway_mat_scExp 91.709 9.456101.925
has_genomic_coordinates0.7630.0170.784
import_scExp8.4951.2939.904
inter_correlation_scExp0.4580.0340.507
intra_correlation_scExp0.4500.0230.475
launchApp0.0000.0000.001
normalize_scExp0.5010.0280.532
num_cell_after_QC_filt_scExp0.5010.0070.510
num_cell_after_cor_filt_scExp13.696 0.18413.935
num_cell_before_cor_filt_scExp0.3080.0110.325
num_cell_in_cluster_scExp0.5290.0140.545
num_cell_scExp0.4280.0060.437
plot_cluster_consensus_scExp1.3350.0231.371
plot_correlation_PCA_scExp1.5440.0671.630
plot_coverage_BigWig0.3100.0110.324
plot_differential_summary_scExp0.3130.0110.328
plot_differential_volcano_scExp0.3920.0180.412
plot_distribution_scExp0.6010.0140.620
plot_gain_or_loss_barplots60.512 0.51361.339
plot_heatmap_scExp0.3950.0240.425
plot_inter_correlation_scExp0.8080.0160.829
plot_intra_correlation_scExp0.7940.0160.814
plot_most_contributing_features0.5800.0150.599
plot_percent_active_feature_scExp0.6210.0130.636
plot_pie_most_contributing_chr0.3480.0220.399
plot_reduced_dim_scExp2.0180.0442.074
plot_reduced_dim_scExp_CNA29.877 0.30630.373
plot_top_TF_scExp0.7750.0140.791
plot_violin_feature_scExp0.8330.0370.880
preprocess_CPM0.4750.0300.509
preprocess_RPKM0.5050.0270.535
preprocess_TFIDF0.4840.0310.517
preprocess_TPM0.5750.1120.704
preprocess_feature_size_only0.4720.0290.504
preprocessing_filtering_and_reduction10.523 0.23310.812
read_sparse_matrix0.0000.0010.000
rebin_matrix 8.455 0.07326.446
reduce_dims_scExp1.9220.0722.001
scExp1.2360.0361.283
subsample_scExp0.6810.0420.728
subset_bam_call_peaks0.0010.0000.000
summary_DA0.2980.0220.320
swapAltExp_sameColData0.3990.0190.420
table_enriched_genes_scExp0.2940.0210.316
wrapper_Signac_FeatureMatrix0.0000.0000.001