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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 352/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 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 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'scran' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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: 1.19.1
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: 2025-08-07 20:00:49 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 20:16:26 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 936.4 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 (2025-06-13)
* 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.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                 89.825  8.406  98.935
plot_gain_or_loss_barplots            58.610  0.550  59.476
calculate_CNA                         29.465  1.574  31.205
plot_reduced_dim_scExp_CNA            29.064  0.282  29.478
calculate_gain_or_loss                27.559  0.678  28.373
calculate_cyto_mat                    27.049  0.832  28.030
calculate_logRatio_CNA                26.849  0.623  27.629
get_most_variable_cyto                26.599  0.195  26.925
get_cyto_features                     24.507  0.205  24.877
num_cell_after_cor_filt_scExp         13.496  0.156  13.710
preprocessing_filtering_and_reduction 10.425  0.238  10.710
filter_correlated_cell_scExp          10.194  0.144  10.437
create_scDataset_raw                   8.363  0.593   9.009
import_scExp                           8.358  0.203   8.602
rebin_matrix                           8.215  0.087  25.634
CompareedgeRGLM                        6.435  0.542   7.017
CompareWilcox                          6.188  0.557   6.198
differential_activation                6.285  0.056   6.380
enrich_TF_ChEA3_scExp                  1.192  0.092   5.054
enrich_TF_ChEA3_genes                  0.603  0.155   8.172
* 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.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 (2025-06-13) -- "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 
 42.276   3.441  45.818 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0090.0030.012
CompareWilcox6.1880.5576.198
CompareedgeRGLM6.4350.5427.017
annotToCol21.0940.0261.128
calculate_CNA29.465 1.57431.205
calculate_cyto_mat27.049 0.83228.030
calculate_gain_or_loss27.559 0.67828.373
calculate_logRatio_CNA26.849 0.62327.629
choose_cluster_scExp3.6340.5904.262
colors_scExp0.3910.0140.407
consensus_clustering_scExp3.3890.5834.015
correlation_and_hierarchical_clust_scExp0.4310.0090.443
create_project_folder0.0010.0030.005
create_scDataset_raw8.3630.5939.009
create_scExp0.5350.0070.543
define_feature0.1630.0070.171
detect_samples1.0870.0801.176
differential_activation6.2850.0566.380
differential_analysis_scExp3.4140.0413.471
enrich_TF_ChEA3_genes0.6030.1558.172
enrich_TF_ChEA3_scExp1.1920.0925.054
exclude_features_scExp0.5080.0060.515
feature_annotation_scExp1.6450.0821.735
filter_correlated_cell_scExp10.194 0.14410.437
filter_scExp0.6750.0090.689
find_clusters_louvain_scExp0.4210.0160.440
find_top_features0.4430.0100.458
gene_set_enrichment_analysis_scExp0.2830.0080.293
generate_analysis000
generate_coverage_tracks000
generate_report0.0000.0010.001
getExperimentNames0.3200.0080.329
getMainExperiment0.3720.0110.386
get_cyto_features24.507 0.20524.877
get_genomic_coordinates0.4880.0070.498
get_most_variable_cyto26.599 0.19526.925
get_pathway_mat_scExp89.825 8.40698.935
has_genomic_coordinates0.8241.3672.240
import_scExp8.3580.2038.602
inter_correlation_scExp0.4360.0230.473
intra_correlation_scExp0.4490.0150.468
launchApp0.0010.0000.000
normalize_scExp0.4860.0260.515
num_cell_after_QC_filt_scExp0.4640.0130.480
num_cell_after_cor_filt_scExp13.496 0.15613.710
num_cell_before_cor_filt_scExp0.2840.0160.301
num_cell_in_cluster_scExp0.5110.0140.528
num_cell_scExp0.3950.0060.402
plot_cluster_consensus_scExp1.0870.0661.163
plot_correlation_PCA_scExp1.1860.0161.207
plot_coverage_BigWig0.2750.0100.287
plot_differential_summary_scExp0.3080.0110.321
plot_differential_volcano_scExp0.3760.0150.393
plot_distribution_scExp0.5590.0400.603
plot_gain_or_loss_barplots58.610 0.55059.476
plot_heatmap_scExp0.3940.0170.413
plot_inter_correlation_scExp0.6720.0110.686
plot_intra_correlation_scExp0.6960.0290.729
plot_most_contributing_features0.5070.0110.522
plot_percent_active_feature_scExp0.5340.0120.549
plot_pie_most_contributing_chr0.3780.0120.392
plot_reduced_dim_scExp1.4640.0311.504
plot_reduced_dim_scExp_CNA29.064 0.28229.478
plot_top_TF_scExp0.5220.0200.544
plot_violin_feature_scExp0.6150.0240.642
preprocess_CPM0.4380.0210.461
preprocess_RPKM0.4640.0240.489
preprocess_TFIDF0.5220.0920.616
preprocess_TPM0.4770.0270.507
preprocess_feature_size_only0.4620.0240.486
preprocessing_filtering_and_reduction10.425 0.23810.710
read_sparse_matrix0.0000.0010.001
rebin_matrix 8.215 0.08725.634
reduce_dims_scExp1.9920.0352.036
scExp1.1240.0321.163
subsample_scExp0.5760.0060.583
subset_bam_call_peaks0.0000.0000.001
summary_DA0.3060.0110.318
swapAltExp_sameColData0.3830.0100.394
table_enriched_genes_scExp0.3010.0110.314
wrapper_Signac_FeatureMatrix0.0000.0000.001