Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
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 353/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 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 24.04.3 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: 2025-08-31 21:13:26 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 21:26:29 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 782.8 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
get_pathway_mat_scExp                 73.066  2.374  75.442
plot_gain_or_loss_barplots            47.356  0.368  47.724
plot_reduced_dim_scExp_CNA            23.387  0.204  23.590
calculate_CNA                         22.580  0.823  23.403
get_most_variable_cyto                22.642  0.285  22.928
calculate_cyto_mat                    21.680  0.468  22.149
calculate_gain_or_loss                21.337  0.382  21.718
calculate_logRatio_CNA                20.804  0.336  21.140
get_cyto_features                     18.675  0.076  18.753
num_cell_after_cor_filt_scExp         12.299  0.122  12.400
preprocessing_filtering_and_reduction  9.531  0.119   9.644
filter_correlated_cell_scExp           9.282  0.003   9.271
import_scExp                           7.275  0.150   7.425
rebin_matrix                           7.344  0.053  21.780
CompareedgeRGLM                        5.685  0.397   5.745
create_scDataset_raw                   5.553  0.227   5.782
CompareWilcox                          5.454  0.321   5.509
differential_activation                5.123  0.011   5.135
* 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 
 39.874   3.632  43.310 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0380.0010.039
CompareWilcox5.4540.3215.509
CompareedgeRGLM5.6850.3975.745
annotToCol20.8400.0080.848
calculate_CNA22.580 0.82323.403
calculate_cyto_mat21.680 0.46822.149
calculate_gain_or_loss21.337 0.38221.718
calculate_logRatio_CNA20.804 0.33621.140
choose_cluster_scExp3.0540.1073.154
colors_scExp0.2640.0010.264
consensus_clustering_scExp2.8240.0642.882
correlation_and_hierarchical_clust_scExp0.3010.0000.295
create_project_folder0.0000.0000.001
create_scDataset_raw5.5530.2275.782
create_scExp0.4570.0000.457
define_feature0.1340.0020.137
detect_samples1.0920.0301.021
differential_activation5.1230.0115.135
differential_analysis_scExp2.8480.0082.856
enrich_TF_ChEA3_genes0.4310.0111.667
enrich_TF_ChEA3_scExp1.0560.0224.923
exclude_features_scExp0.4230.0130.437
feature_annotation_scExp1.3110.0441.355
filter_correlated_cell_scExp9.2820.0039.271
filter_scExp0.5010.0010.502
find_clusters_louvain_scExp0.2840.0020.286
find_top_features0.2960.0000.296
gene_set_enrichment_analysis_scExp0.1960.0060.202
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.2300.0040.234
getMainExperiment0.2600.0010.261
get_cyto_features18.675 0.07618.753
get_genomic_coordinates0.3800.0240.404
get_most_variable_cyto22.642 0.28522.928
get_pathway_mat_scExp73.066 2.37475.442
has_genomic_coordinates0.6250.0030.628
import_scExp7.2750.1507.425
inter_correlation_scExp0.3280.0020.330
intra_correlation_scExp0.3450.0010.346
launchApp000
normalize_scExp0.4090.0030.412
num_cell_after_QC_filt_scExp0.4060.0000.406
num_cell_after_cor_filt_scExp12.299 0.12212.400
num_cell_before_cor_filt_scExp0.2030.0030.207
num_cell_in_cluster_scExp0.3810.0000.375
num_cell_scExp0.3460.0010.348
plot_cluster_consensus_scExp0.8310.0030.835
plot_correlation_PCA_scExp1.0330.0021.034
plot_coverage_BigWig0.2080.0010.210
plot_differential_summary_scExp0.2320.0010.234
plot_differential_volcano_scExp0.3190.0010.321
plot_distribution_scExp0.3940.0020.396
plot_gain_or_loss_barplots47.356 0.36847.724
plot_heatmap_scExp0.2950.0030.297
plot_inter_correlation_scExp0.5070.0020.509
plot_intra_correlation_scExp0.5010.0010.501
plot_most_contributing_features0.3900.0030.393
plot_percent_active_feature_scExp0.3970.0010.399
plot_pie_most_contributing_chr0.2780.0010.280
plot_reduced_dim_scExp1.2260.0141.240
plot_reduced_dim_scExp_CNA23.387 0.20423.590
plot_top_TF_scExp0.4410.0020.443
plot_violin_feature_scExp0.5050.0020.507
preprocess_CPM0.3810.0040.385
preprocess_RPKM0.4200.0070.427
preprocess_TFIDF0.4520.0130.465
preprocess_TPM0.4130.0030.416
preprocess_feature_size_only0.3850.0080.393
preprocessing_filtering_and_reduction9.5310.1199.644
read_sparse_matrix000
rebin_matrix 7.344 0.05321.780
reduce_dims_scExp1.5650.0331.598
scExp0.9000.0070.907
subsample_scExp0.5470.0050.552
subset_bam_call_peaks000
summary_DA0.2160.0020.218
swapAltExp_sameColData0.2930.0020.295
table_enriched_genes_scExp0.2140.0030.217
wrapper_Signac_FeatureMatrix000