Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-02 12:04 -0400 (Sat, 02 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 352/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-08-01 13:25 -0400 (Fri, 01 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  YES
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  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


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: 2025-08-01 21:00:11 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 21:13:15 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 783.9 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 24.04.2 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                 72.679  2.143  74.824
plot_gain_or_loss_barplots            46.286  0.339  46.627
plot_reduced_dim_scExp_CNA            24.812  0.160  24.973
calculate_CNA                         22.260  1.156  23.418
calculate_gain_or_loss                21.527  0.397  21.924
get_most_variable_cyto                21.173  0.230  21.405
calculate_cyto_mat                    20.691  0.508  21.200
calculate_logRatio_CNA                20.778  0.323  21.102
get_cyto_features                     18.772  0.332  19.105
num_cell_after_cor_filt_scExp         12.600  0.063  12.642
filter_correlated_cell_scExp           9.935  0.726  10.647
preprocessing_filtering_and_reduction  9.678  0.075   9.743
import_scExp                           7.743  0.078   7.822
rebin_matrix                           7.304  0.060  21.379
CompareedgeRGLM                        5.541  0.484   5.804
create_scDataset_raw                   5.557  0.252   5.809
CompareWilcox                          5.164  0.306   5.417
differential_activation                5.193  0.006   5.199
* 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 
 40.265   1.572  41.646 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0340.0000.033
CompareWilcox5.1640.3065.417
CompareedgeRGLM5.5410.4845.804
annotToCol20.8520.0060.858
calculate_CNA22.260 1.15623.418
calculate_cyto_mat20.691 0.50821.200
calculate_gain_or_loss21.527 0.39721.924
calculate_logRatio_CNA20.778 0.32321.102
choose_cluster_scExp3.1310.1213.247
colors_scExp0.2770.0010.278
consensus_clustering_scExp3.0220.0663.079
correlation_and_hierarchical_clust_scExp0.2980.0000.293
create_project_folder0.0010.0000.001
create_scDataset_raw5.5570.2525.809
create_scExp0.4700.0010.471
define_feature0.1420.0010.143
detect_samples1.0470.0120.998
differential_activation5.1930.0065.199
differential_analysis_scExp2.6870.0032.689
enrich_TF_ChEA3_genes0.4640.0241.679
enrich_TF_ChEA3_scExp1.1020.0394.961
exclude_features_scExp0.4260.0170.443
feature_annotation_scExp1.3350.0891.424
filter_correlated_cell_scExp 9.935 0.72610.647
filter_scExp0.5070.0160.524
find_clusters_louvain_scExp0.2960.0020.297
find_top_features0.3150.0070.322
gene_set_enrichment_analysis_scExp0.2070.0100.217
generate_analysis000
generate_coverage_tracks000
generate_report0.0010.0000.001
getExperimentNames0.2350.0020.237
getMainExperiment0.2600.0090.269
get_cyto_features18.772 0.33219.105
get_genomic_coordinates0.3710.0160.386
get_most_variable_cyto21.173 0.23021.405
get_pathway_mat_scExp72.679 2.14374.824
has_genomic_coordinates0.6300.0020.633
import_scExp7.7430.0787.822
inter_correlation_scExp0.3330.0000.332
intra_correlation_scExp0.3520.0010.353
launchApp000
normalize_scExp0.4030.0020.405
num_cell_after_QC_filt_scExp0.4230.0000.423
num_cell_after_cor_filt_scExp12.600 0.06312.642
num_cell_before_cor_filt_scExp0.1950.0010.196
num_cell_in_cluster_scExp0.3690.0010.363
num_cell_scExp0.3390.0000.339
plot_cluster_consensus_scExp0.7980.0030.801
plot_correlation_PCA_scExp1.0090.0131.021
plot_coverage_BigWig0.2000.0010.201
plot_differential_summary_scExp0.2260.0010.227
plot_differential_volcano_scExp0.3170.0000.317
plot_distribution_scExp0.3950.0000.395
plot_gain_or_loss_barplots46.286 0.33946.627
plot_heatmap_scExp0.2950.0020.298
plot_inter_correlation_scExp0.5230.0030.526
plot_intra_correlation_scExp0.5110.0020.513
plot_most_contributing_features0.4050.0090.413
plot_percent_active_feature_scExp0.4070.0030.409
plot_pie_most_contributing_chr0.2830.0060.289
plot_reduced_dim_scExp1.2420.0061.249
plot_reduced_dim_scExp_CNA24.812 0.16024.973
plot_top_TF_scExp0.4710.0010.472
plot_violin_feature_scExp0.5490.0000.550
preprocess_CPM0.3830.0070.391
preprocess_RPKM0.4040.0160.420
preprocess_TFIDF0.4450.0080.453
preprocess_TPM0.4060.0010.407
preprocess_feature_size_only0.3790.0040.383
preprocessing_filtering_and_reduction9.6780.0759.743
read_sparse_matrix000
rebin_matrix 7.304 0.06021.379
reduce_dims_scExp1.5330.0011.534
scExp0.9060.0120.919
subsample_scExp0.5300.0100.539
subset_bam_call_peaks000
summary_DA0.2220.0020.225
swapAltExp_sameColData0.2910.0080.299
table_enriched_genes_scExp0.2000.0010.200
wrapper_Signac_FeatureMatrix000