Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-03 12:03 -0400 (Wed, 03 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4616
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 353/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChromSCape_1.19.1.tar.gz
StartedAt: 2025-09-02 22:06:57 -0400 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 22:20:50 -0400 (Tue, 02 Sep 2025)
EllapsedTime: 833.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChromSCape_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    www    2.1Mb
* 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 loading without being on the library search path ... 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
num_cell_after_cor_filt_scExp            323.042  0.906  19.662
filter_correlated_cell_scExp             270.582  0.310  14.607
preprocessing_filtering_and_reduction    150.057  0.202  11.710
detect_samples                           145.211  0.204   4.154
get_pathway_mat_scExp                     72.926  2.435  75.405
choose_cluster_scExp                      60.238  0.390   4.786
CompareWilcox                             59.698  0.481   7.129
consensus_clustering_scExp                59.239  0.196   4.265
CompareedgeRGLM                           58.934  0.498   7.017
num_cell_in_cluster_scExp                 53.902  0.036   1.495
correlation_and_hierarchical_clust_scExp  52.849  0.025   1.364
plot_gain_or_loss_barplots                48.854  1.237  50.135
plot_reduced_dim_scExp_CNA                23.756  0.247  24.017
calculate_CNA                             22.853  0.725  23.578
get_most_variable_cyto                    22.402  0.476  22.878
calculate_cyto_mat                        21.904  0.659  22.564
calculate_gain_or_loss                    21.938  0.510  22.449
calculate_logRatio_CNA                    20.966  0.361  21.328
get_cyto_features                         19.208  0.683  19.892
import_scExp                               7.776  0.102   7.879
rebin_matrix                               7.370  0.286  21.543
create_scDataset_raw                       5.737  0.655   6.392
differential_activation                    5.174  0.045   5.218
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ChromSCape’ ...
** this is package ‘ChromSCape’ version ‘1.19.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c as_dist.cpp -o as_dist.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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-pc-linux-gnu

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 
855.391   3.537  58.604 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0430.0000.044
CompareWilcox59.698 0.481 7.129
CompareedgeRGLM58.934 0.498 7.017
annotToCol20.8230.0160.840
calculate_CNA22.853 0.72523.578
calculate_cyto_mat21.904 0.65922.564
calculate_gain_or_loss21.938 0.51022.449
calculate_logRatio_CNA20.966 0.36121.328
choose_cluster_scExp60.238 0.390 4.786
colors_scExp0.2710.0020.273
consensus_clustering_scExp59.239 0.196 4.265
correlation_and_hierarchical_clust_scExp52.849 0.025 1.364
create_project_folder0.0010.0010.001
create_scDataset_raw5.7370.6556.392
create_scExp0.4600.0390.499
define_feature0.1330.0150.148
detect_samples145.211 0.204 4.154
differential_activation5.1740.0455.218
differential_analysis_scExp2.6670.2162.882
enrich_TF_ChEA3_genes0.4310.0321.653
enrich_TF_ChEA3_scExp1.0450.0874.996
exclude_features_scExp0.4200.0650.485
feature_annotation_scExp1.3560.1861.543
filter_correlated_cell_scExp270.582 0.310 14.607
filter_scExp0.5200.0110.532
find_clusters_louvain_scExp0.2980.0070.304
find_top_features0.3280.0020.330
gene_set_enrichment_analysis_scExp0.2120.0010.213
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.2480.0020.251
getMainExperiment0.2730.0070.280
get_cyto_features19.208 0.68319.892
get_genomic_coordinates0.3950.0230.418
get_most_variable_cyto22.402 0.47622.878
get_pathway_mat_scExp72.926 2.43575.405
has_genomic_coordinates0.6060.0010.607
import_scExp7.7760.1027.879
inter_correlation_scExp0.3210.0020.325
intra_correlation_scExp0.3330.0020.335
launchApp000
normalize_scExp0.3940.0020.396
num_cell_after_QC_filt_scExp0.4110.0000.412
num_cell_after_cor_filt_scExp323.042 0.906 19.662
num_cell_before_cor_filt_scExp0.2070.0020.210
num_cell_in_cluster_scExp53.902 0.036 1.495
num_cell_scExp0.3440.0280.372
plot_cluster_consensus_scExp0.8280.0920.920
plot_correlation_PCA_scExp1.0290.0671.096
plot_coverage_BigWig0.2020.0070.209
plot_differential_summary_scExp0.2280.0070.236
plot_differential_volcano_scExp0.3170.0030.319
plot_distribution_scExp0.4160.0280.444
plot_gain_or_loss_barplots48.854 1.23750.135
plot_heatmap_scExp0.2950.0030.298
plot_inter_correlation_scExp0.5110.0030.513
plot_intra_correlation_scExp0.5200.0020.522
plot_most_contributing_features0.3990.0010.400
plot_percent_active_feature_scExp0.4120.0040.416
plot_pie_most_contributing_chr0.2850.0020.287
plot_reduced_dim_scExp1.2260.0021.228
plot_reduced_dim_scExp_CNA23.756 0.24724.017
plot_top_TF_scExp0.4350.0020.437
plot_violin_feature_scExp0.4980.0030.500
preprocess_CPM0.3700.0050.375
preprocess_RPKM0.3890.0150.404
preprocess_TFIDF0.4300.0110.441
preprocess_TPM0.3980.0130.411
preprocess_feature_size_only0.3820.0250.408
preprocessing_filtering_and_reduction150.057 0.202 11.710
read_sparse_matrix000
rebin_matrix 7.370 0.28621.543
reduce_dims_scExp1.5470.0861.633
scExp0.8910.0450.936
subsample_scExp0.5460.0570.604
subset_bam_call_peaks000
summary_DA0.2160.0070.223
swapAltExp_sameColData0.2760.0050.282
table_enriched_genes_scExp0.1940.0030.197
wrapper_Signac_FeatureMatrix000