Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-25 12:05 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 356/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 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  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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
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: 2025-09-24 20:04:34 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 20:20:19 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 945.4 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                 89.607  8.719  99.072
plot_gain_or_loss_barplots            60.451  0.555  61.317
calculate_CNA                         29.847  1.863  31.848
calculate_logRatio_CNA                28.397  0.897  29.448
plot_reduced_dim_scExp_CNA            28.570  0.291  29.038
calculate_cyto_mat                    27.884  0.869  28.918
calculate_gain_or_loss                27.933  0.695  28.771
get_most_variable_cyto                26.946  0.267  27.379
get_cyto_features                     23.973  0.180  24.288
num_cell_after_cor_filt_scExp         13.697  0.156  13.919
preprocessing_filtering_and_reduction 10.522  0.261  10.832
filter_correlated_cell_scExp          10.526  0.104  10.684
import_scExp                           8.431  1.162   9.660
rebin_matrix                           8.614  0.081  26.255
create_scDataset_raw                   7.459  0.544   8.059
CompareWilcox                          7.171  0.522   7.144
differential_activation                6.595  0.074   6.711
CompareedgeRGLM                        5.469  0.354   5.855
enrich_TF_ChEA3_scExp                  1.206  0.097   5.171
* 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 
 41.203   3.227  44.523 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0080.0030.011
CompareWilcox7.1710.5227.144
CompareedgeRGLM5.4690.3545.855
annotToCol21.0710.0521.128
calculate_CNA29.847 1.86331.848
calculate_cyto_mat27.884 0.86928.918
calculate_gain_or_loss27.933 0.69528.771
calculate_logRatio_CNA28.397 0.89729.448
choose_cluster_scExp3.7130.5874.356
colors_scExp0.3700.0090.384
consensus_clustering_scExp4.1530.5354.741
correlation_and_hierarchical_clust_scExp0.4070.0100.422
create_project_folder0.0010.0020.003
create_scDataset_raw7.4590.5448.059
create_scExp0.5680.0600.637
define_feature0.1610.0050.166
detect_samples1.1540.0621.222
differential_activation6.5950.0746.711
differential_analysis_scExp3.5150.0323.566
enrich_TF_ChEA3_genes0.6200.1702.002
enrich_TF_ChEA3_scExp1.2060.0975.171
exclude_features_scExp0.5550.0090.566
feature_annotation_scExp1.6740.0741.764
filter_correlated_cell_scExp10.526 0.10410.684
filter_scExp0.6240.0080.635
find_clusters_louvain_scExp0.3890.0100.401
find_top_features0.4250.0070.434
gene_set_enrichment_analysis_scExp0.3050.0060.313
generate_analysis000
generate_coverage_tracks0.0000.0000.001
generate_report000
getExperimentNames0.3330.0120.355
getMainExperiment0.3590.0100.371
get_cyto_features23.973 0.18024.288
get_genomic_coordinates0.4870.0060.496
get_most_variable_cyto26.946 0.26727.379
get_pathway_mat_scExp89.607 8.71999.072
has_genomic_coordinates0.8170.0220.847
import_scExp8.4311.1629.660
inter_correlation_scExp0.4490.0270.478
intra_correlation_scExp0.4680.0190.490
launchApp000
normalize_scExp0.5060.0290.537
num_cell_after_QC_filt_scExp0.5080.0070.516
num_cell_after_cor_filt_scExp13.697 0.15613.919
num_cell_before_cor_filt_scExp0.2860.0130.301
num_cell_in_cluster_scExp0.5040.0170.524
num_cell_scExp0.4320.0050.440
plot_cluster_consensus_scExp1.2890.0271.321
plot_correlation_PCA_scExp1.5140.0621.584
plot_coverage_BigWig0.2970.0100.308
plot_differential_summary_scExp0.3040.0060.314
plot_differential_volcano_scExp0.3810.0130.398
plot_distribution_scExp0.5650.0160.586
plot_gain_or_loss_barplots60.451 0.55561.317
plot_heatmap_scExp0.4120.0180.433
plot_inter_correlation_scExp0.7880.0110.803
plot_intra_correlation_scExp0.8160.0160.837
plot_most_contributing_features0.6050.0170.626
plot_percent_active_feature_scExp0.7390.0170.761
plot_pie_most_contributing_chr0.3940.0140.410
plot_reduced_dim_scExp1.9910.0392.045
plot_reduced_dim_scExp_CNA28.570 0.29129.038
plot_top_TF_scExp0.7520.0170.774
plot_violin_feature_scExp0.8270.0220.854
preprocess_CPM0.4660.0270.496
preprocess_RPKM0.4970.0250.525
preprocess_TFIDF0.4750.0230.500
preprocess_TPM0.5660.0810.695
preprocess_feature_size_only0.4400.0300.472
preprocessing_filtering_and_reduction10.522 0.26110.832
read_sparse_matrix0.0010.0010.001
rebin_matrix 8.614 0.08126.255
reduce_dims_scExp1.9660.0452.019
scExp1.1870.0511.245
subsample_scExp0.6690.0190.691
subset_bam_call_peaks000
summary_DA0.2840.0110.296
swapAltExp_sameColData0.4010.0140.417
table_enriched_genes_scExp0.2930.0150.317
wrapper_Signac_FeatureMatrix000