Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-05 12:08 -0400 (Fri, 05 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 353/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.19.1  (landing page)
Pacome Prompsy
Snapshot Date: 2025-09-04 13:45 -0400 (Thu, 04 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: 2025-09-05 05:57:50 -0000 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 06:14:10 -0000 (Fri, 05 Sep 2025)
EllapsedTime: 979.9 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                 94.244  2.160  96.744
plot_gain_or_loss_barplots            67.683  0.497  68.435
plot_reduced_dim_scExp_CNA            33.121  0.257  33.523
calculate_CNA                         30.785  0.813  31.699
get_most_variable_cyto                30.870  0.506  31.495
calculate_gain_or_loss                30.488  0.399  30.976
calculate_logRatio_CNA                30.334  0.267  30.705
calculate_cyto_mat                    29.896  0.387  30.377
get_cyto_features                     28.102  0.577  28.794
num_cell_after_cor_filt_scExp         12.697  0.088  12.836
preprocessing_filtering_and_reduction 10.154  0.016  10.197
filter_correlated_cell_scExp           9.457  0.554  10.042
import_scExp                           7.972  0.231   8.235
rebin_matrix                           7.737  0.062  25.660
CompareedgeRGLM                        6.914  0.547   7.479
differential_activation                7.275  0.019   7.319
create_scDataset_raw                   6.540  0.071   6.629
CompareWilcox                          5.372  0.337   5.445
enrich_TF_ChEA3_scExp                  1.164  0.028   7.243
enrich_TF_ChEA3_genes                  0.530  0.027   5.198
* 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 
 43.961   1.650  45.534 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0430.0000.044
CompareWilcox5.3720.3375.445
CompareedgeRGLM6.9140.5477.479
annotToCol21.0580.0121.073
calculate_CNA30.785 0.81331.699
calculate_cyto_mat29.896 0.38730.377
calculate_gain_or_loss30.488 0.39930.976
calculate_logRatio_CNA30.334 0.26730.705
choose_cluster_scExp4.1480.0884.247
colors_scExp0.3360.0000.336
consensus_clustering_scExp3.7890.0763.875
correlation_and_hierarchical_clust_scExp0.4020.0000.402
create_project_folder0.0010.0000.002
create_scDataset_raw6.5400.0716.629
create_scExp0.6360.0040.642
define_feature0.1740.0000.174
detect_samples1.8730.0121.779
differential_activation7.2750.0197.319
differential_analysis_scExp3.7670.0763.855
enrich_TF_ChEA3_genes0.5300.0275.198
enrich_TF_ChEA3_scExp1.1640.0287.243
exclude_features_scExp0.6160.0480.665
feature_annotation_scExp1.9070.1912.108
filter_correlated_cell_scExp 9.457 0.55410.042
filter_scExp0.7510.0120.765
find_clusters_louvain_scExp0.3660.0280.396
find_top_features0.3850.0040.389
gene_set_enrichment_analysis_scExp0.2300.0160.246
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.2770.0000.278
getMainExperiment0.3260.0120.339
get_cyto_features28.102 0.57728.794
get_genomic_coordinates0.5840.0070.593
get_most_variable_cyto30.870 0.50631.495
get_pathway_mat_scExp94.244 2.16096.744
has_genomic_coordinates0.9090.0160.930
import_scExp7.9720.2318.235
inter_correlation_scExp0.4150.0000.417
intra_correlation_scExp0.4270.0040.433
launchApp0.0010.0000.001
normalize_scExp0.5600.0000.562
num_cell_after_QC_filt_scExp0.5680.0000.570
num_cell_after_cor_filt_scExp12.697 0.08812.836
num_cell_before_cor_filt_scExp0.2420.0040.246
num_cell_in_cluster_scExp0.4900.0000.493
num_cell_scExp0.5080.0000.509
plot_cluster_consensus_scExp1.1590.0001.164
plot_correlation_PCA_scExp1.4230.0001.428
plot_coverage_BigWig0.2260.0000.227
plot_differential_summary_scExp0.2560.0080.264
plot_differential_volcano_scExp0.3450.0000.346
plot_distribution_scExp0.5110.0040.516
plot_gain_or_loss_barplots67.683 0.49768.435
plot_heatmap_scExp0.3640.0040.370
plot_inter_correlation_scExp0.7110.0000.714
plot_intra_correlation_scExp0.7040.0000.707
plot_most_contributing_features0.5050.0000.507
plot_percent_active_feature_scExp0.5440.0000.546
plot_pie_most_contributing_chr0.3480.0040.353
plot_reduced_dim_scExp1.7060.0081.722
plot_reduced_dim_scExp_CNA33.121 0.25733.523
plot_top_TF_scExp0.5840.0150.601
plot_violin_feature_scExp0.6960.0270.726
preprocess_CPM0.5600.0160.578
preprocess_RPKM0.5640.0120.578
preprocess_TFIDF0.6240.0240.650
preprocess_TPM0.5730.0000.575
preprocess_feature_size_only0.5380.0040.543
preprocessing_filtering_and_reduction10.154 0.01610.197
read_sparse_matrix000
rebin_matrix 7.737 0.06225.660
reduce_dims_scExp2.1100.0002.115
scExp1.2180.0111.233
subsample_scExp0.7970.0000.799
subset_bam_call_peaks000
summary_DA0.2870.0040.291
swapAltExp_sameColData0.4190.0000.419
table_enriched_genes_scExp0.2390.0080.248
wrapper_Signac_FeatureMatrix0.0000.0000.001