Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-18 12:06 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4808
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4554
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 356/2330HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-09-17 13:45 -0400 (Wed, 17 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ChromSCape
Version: 1.19.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChromSCape_1.19.1.tar.gz
StartedAt: 2025-09-16 05:39:03 -0000 (Tue, 16 Sep 2025)
EndedAt: 2025-09-16 05:55:58 -0000 (Tue, 16 Sep 2025)
EllapsedTime: 1015.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChromSCape_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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                 92.141  1.804  94.121
plot_gain_or_loss_barplots            71.116  0.455  71.782
plot_reduced_dim_scExp_CNA            34.699  0.275  35.078
calculate_gain_or_loss                32.012  0.993  33.119
calculate_logRatio_CNA                32.256  0.486  32.835
calculate_CNA                         31.382  1.081  32.562
get_most_variable_cyto                31.060  0.511  31.638
calculate_cyto_mat                    30.601  0.686  31.394
get_cyto_features                     28.960  1.145  30.183
num_cell_after_cor_filt_scExp         12.598  0.164  12.788
preprocessing_filtering_and_reduction 10.490  0.004  10.521
filter_correlated_cell_scExp           9.477  0.072   9.571
import_scExp                           8.138  0.152   8.310
rebin_matrix                           7.625  0.427  27.950
differential_activation                7.520  0.056   7.597
create_scDataset_raw                   7.383  0.111   7.514
CompareWilcox                          6.207  0.356   6.283
CompareedgeRGLM                        5.945  0.208   6.167
enrich_TF_ChEA3_scExp                  1.072  0.039  19.936
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘ChromSCape’ ...
** this is package ‘ChromSCape’ version ‘1.19.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c as_dist.cpp -o as_dist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 43.461   2.808  46.168 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0070.0000.007
CompareWilcox6.2070.3566.283
CompareedgeRGLM5.9450.2086.167
annotToCol21.0290.0401.071
calculate_CNA31.382 1.08132.562
calculate_cyto_mat30.601 0.68631.394
calculate_gain_or_loss32.012 0.99333.119
calculate_logRatio_CNA32.256 0.48632.835
choose_cluster_scExp4.110.144.26
colors_scExp0.3180.0040.323
consensus_clustering_scExp3.8580.0803.947
correlation_and_hierarchical_clust_scExp0.4110.0080.420
create_project_folder0.0020.0000.002
create_scDataset_raw7.3830.1117.514
create_scExp0.6340.0000.635
define_feature0.1650.0000.165
detect_samples1.8360.0161.745
differential_activation7.5200.0567.597
differential_analysis_scExp3.8340.0803.924
enrich_TF_ChEA3_genes0.4730.0433.711
enrich_TF_ChEA3_scExp 1.072 0.03919.936
exclude_features_scExp0.6420.0080.653
feature_annotation_scExp1.8620.0481.917
filter_correlated_cell_scExp9.4770.0729.571
filter_scExp0.8110.0040.818
find_clusters_louvain_scExp0.3990.0000.399
find_top_features0.3660.0000.366
gene_set_enrichment_analysis_scExp0.2290.0000.230
generate_analysis0.0000.0000.001
generate_coverage_tracks000
generate_report000
getExperimentNames0.2710.0080.280
getMainExperiment0.330.000.33
get_cyto_features28.960 1.14530.183
get_genomic_coordinates0.5630.0200.583
get_most_variable_cyto31.060 0.51131.638
get_pathway_mat_scExp92.141 1.80494.121
has_genomic_coordinates0.8740.0120.887
import_scExp8.1380.1528.310
inter_correlation_scExp0.4380.0040.443
intra_correlation_scExp0.4550.0040.460
launchApp000
normalize_scExp0.5950.0110.607
num_cell_after_QC_filt_scExp0.5700.0040.576
num_cell_after_cor_filt_scExp12.598 0.16412.788
num_cell_before_cor_filt_scExp0.2600.0000.261
num_cell_in_cluster_scExp0.5620.0000.563
num_cell_scExp0.5190.0000.521
plot_cluster_consensus_scExp1.4790.0111.495
plot_correlation_PCA_scExp1.7930.0321.830
plot_coverage_BigWig0.2480.0030.253
plot_differential_summary_scExp0.2720.0080.281
plot_differential_volcano_scExp0.3650.0040.370
plot_distribution_scExp0.5590.0120.573
plot_gain_or_loss_barplots71.116 0.45571.782
plot_heatmap_scExp0.3630.0040.368
plot_inter_correlation_scExp0.8720.0000.875
plot_intra_correlation_scExp0.8660.0000.870
plot_most_contributing_features0.6130.0000.615
plot_percent_active_feature_scExp0.6830.0080.692
plot_pie_most_contributing_chr0.3590.0000.360
plot_reduced_dim_scExp2.3370.0002.344
plot_reduced_dim_scExp_CNA34.699 0.27535.078
plot_top_TF_scExp0.8610.0080.872
plot_violin_feature_scExp0.9190.0040.926
preprocess_CPM0.5590.0070.569
preprocess_RPKM0.6330.0080.643
preprocess_TFIDF0.5840.0080.594
preprocess_TPM0.6660.0040.672
preprocess_feature_size_only0.6060.0000.608
preprocessing_filtering_and_reduction10.490 0.00410.521
read_sparse_matrix000
rebin_matrix 7.625 0.42727.950
reduce_dims_scExp2.1050.0682.179
scExp1.4290.0871.522
subsample_scExp0.8070.0640.874
subset_bam_call_peaks000
summary_DA0.2600.0040.265
swapAltExp_sameColData0.3970.0200.419
table_enriched_genes_scExp0.2240.0120.237
wrapper_Signac_FeatureMatrix000