Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-11 12:06 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 352/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 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
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: 2025-08-10 20:56:39 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 21:09:33 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 773.9 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                 71.508  2.406  73.916
plot_gain_or_loss_barplots            44.179  0.328  44.507
calculate_CNA                         22.980  1.018  23.999
plot_reduced_dim_scExp_CNA            23.226  0.155  23.381
get_most_variable_cyto                22.749  0.054  22.803
calculate_gain_or_loss                21.919  0.489  22.409
calculate_cyto_mat                    21.791  0.458  22.250
calculate_logRatio_CNA                21.461  0.350  21.811
get_cyto_features                     18.277  0.120  18.398
num_cell_after_cor_filt_scExp         10.913  0.177  11.071
filter_correlated_cell_scExp           9.855  0.134   9.975
preprocessing_filtering_and_reduction  9.399  0.110   9.504
rebin_matrix                           7.554  0.093  22.006
import_scExp                           6.878  0.186   7.065
create_scDataset_raw                   5.939  0.232   6.171
CompareedgeRGLM                        5.267  0.434   5.697
CompareWilcox                          5.300  0.289   5.335
differential_activation                5.146  0.007   5.155
* 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 
 35.666   1.595  37.059 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0310.0000.031
CompareWilcox5.3000.2895.335
CompareedgeRGLM5.2670.4345.697
annotToCol20.8530.0210.874
calculate_CNA22.980 1.01823.999
calculate_cyto_mat21.791 0.45822.250
calculate_gain_or_loss21.919 0.48922.409
calculate_logRatio_CNA21.461 0.35021.811
choose_cluster_scExp3.1960.0683.257
colors_scExp0.2860.0030.288
consensus_clustering_scExp3.1840.0743.252
correlation_and_hierarchical_clust_scExp0.3370.0010.331
create_project_folder0.0020.0000.002
create_scDataset_raw5.9390.2326.171
create_scExp0.4520.0000.452
define_feature0.1360.0010.137
detect_samples1.1090.0261.058
differential_activation5.1460.0075.155
differential_analysis_scExp2.7670.0022.769
enrich_TF_ChEA3_genes0.4470.0141.649
enrich_TF_ChEA3_scExp0.9720.0284.754
exclude_features_scExp0.4390.0040.443
feature_annotation_scExp1.3230.0461.369
filter_correlated_cell_scExp9.8550.1349.975
filter_scExp0.5190.0010.520
find_clusters_louvain_scExp0.2850.0000.284
find_top_features0.3010.0000.301
gene_set_enrichment_analysis_scExp0.2000.0080.208
generate_analysis000
generate_coverage_tracks000
generate_report0.0000.0000.001
getExperimentNames0.2230.0020.224
getMainExperiment0.2630.0000.263
get_cyto_features18.277 0.12018.398
get_genomic_coordinates0.3800.0070.387
get_most_variable_cyto22.749 0.05422.803
get_pathway_mat_scExp71.508 2.40673.916
has_genomic_coordinates0.5990.0020.601
import_scExp6.8780.1867.065
inter_correlation_scExp0.3140.0030.317
intra_correlation_scExp0.3290.0000.329
launchApp000
normalize_scExp0.3810.0030.384
num_cell_after_QC_filt_scExp0.40.00.4
num_cell_after_cor_filt_scExp10.913 0.17711.071
num_cell_before_cor_filt_scExp0.1960.0010.198
num_cell_in_cluster_scExp0.3720.0010.364
num_cell_scExp0.3220.0010.322
plot_cluster_consensus_scExp0.7770.0170.795
plot_correlation_PCA_scExp0.9540.0090.964
plot_coverage_BigWig0.1920.0010.194
plot_differential_summary_scExp0.2100.0010.212
plot_differential_volcano_scExp0.2970.0020.300
plot_distribution_scExp0.3830.0010.383
plot_gain_or_loss_barplots44.179 0.32844.507
plot_heatmap_scExp0.2860.0020.288
plot_inter_correlation_scExp0.4880.0030.491
plot_intra_correlation_scExp0.4830.0020.485
plot_most_contributing_features0.3750.0020.377
plot_percent_active_feature_scExp0.3940.0000.395
plot_pie_most_contributing_chr0.2770.0010.278
plot_reduced_dim_scExp1.1720.0091.181
plot_reduced_dim_scExp_CNA23.226 0.15523.381
plot_top_TF_scExp0.4610.0030.465
plot_violin_feature_scExp0.5220.0140.536
preprocess_CPM0.3830.0090.391
preprocess_RPKM0.4140.0090.423
preprocess_TFIDF0.4260.0140.439
preprocess_TPM0.4060.0020.408
preprocess_feature_size_only0.3920.0050.397
preprocessing_filtering_and_reduction9.3990.1109.504
read_sparse_matrix000
rebin_matrix 7.554 0.09322.006
reduce_dims_scExp1.5430.0371.580
scExp0.8990.0050.904
subsample_scExp0.5290.0010.531
subset_bam_call_peaks0.0010.0000.000
summary_DA0.2150.0020.217
swapAltExp_sameColData0.2850.0020.287
table_enriched_genes_scExp0.2010.0000.202
wrapper_Signac_FeatureMatrix000