Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-12 12:07 -0400 (Tue, 12 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" 4535
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: 2025-08-11 13:45 -0400 (Mon, 11 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 palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings ChromSCape_1.19.1.tar.gz
StartedAt: 2025-08-12 00:36:38 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 00:55:16 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 1118.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings ChromSCape_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'ChromSCape' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking installed package size ... INFO
  installed size is  5.7Mb
  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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/ChromSCape/libs/x64/ChromSCape.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
get_pathway_mat_scExp                 98.34   4.47  102.91
plot_gain_or_loss_barplots            60.88   0.88   61.78
calculate_CNA                         31.92   1.33   33.25
calculate_logRatio_CNA                30.45   0.69   31.19
calculate_gain_or_loss                29.52   0.53   30.06
calculate_cyto_mat                    29.11   0.66   29.77
plot_reduced_dim_scExp_CNA            29.16   0.35   29.55
get_most_variable_cyto                28.78   0.40   29.20
get_cyto_features                     25.57   0.34   25.94
num_cell_after_cor_filt_scExp         15.53   0.17   15.75
CompareedgeRGLM                       12.11   0.47   12.65
preprocessing_filtering_and_reduction 11.91   0.05   12.02
filter_correlated_cell_scExp          11.82   0.13   11.95
import_scExp                          10.45   0.12   10.56
create_scDataset_raw                   8.44   0.83    9.26
rebin_matrix                           9.16   0.00   32.41
differential_activation                6.56   0.19    6.75
CompareWilcox                          5.41   0.22   59.23
choose_cluster_scExp                   4.56   0.70    5.26
enrich_TF_ChEA3_scExp                  2.56   0.29    6.00
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'ChromSCape' ...
** this is package 'ChromSCape' version '1.19.1'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c as_dist.cpp -o as_dist.o
g++ -std=gnu++17 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-ChromSCape/00new/ChromSCape/libs/x64
** 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
** 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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  42.76    2.68   80.03 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.010.020.04
CompareWilcox 5.41 0.2259.23
CompareedgeRGLM12.11 0.4712.65
annotToCol21.200.151.36
calculate_CNA31.92 1.3333.25
calculate_cyto_mat29.11 0.6629.77
calculate_gain_or_loss29.52 0.5330.06
calculate_logRatio_CNA30.45 0.6931.19
choose_cluster_scExp4.560.705.26
colors_scExp0.450.140.60
consensus_clustering_scExp4.240.734.97
correlation_and_hierarchical_clust_scExp0.440.130.58
create_project_folder0.000.000.16
create_scDataset_raw8.440.839.26
create_scExp0.620.030.66
define_feature0.220.000.22
detect_samples1.220.041.26
differential_activation6.560.196.75
differential_analysis_scExp3.460.173.63
enrich_TF_ChEA3_genes1.020.252.11
enrich_TF_ChEA3_scExp2.560.296.00
exclude_features_scExp0.580.030.61
feature_annotation_scExp1.660.071.74
filter_correlated_cell_scExp11.82 0.1311.95
filter_scExp0.720.020.73
find_clusters_louvain_scExp0.420.210.64
find_top_features0.460.110.57
gene_set_enrichment_analysis_scExp0.330.140.47
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.320.160.48
getMainExperiment0.430.140.56
get_cyto_features25.57 0.3425.94
get_genomic_coordinates0.570.040.61
get_most_variable_cyto28.78 0.4029.20
get_pathway_mat_scExp 98.34 4.47102.91
has_genomic_coordinates0.880.050.94
import_scExp10.45 0.1210.56
inter_correlation_scExp0.560.130.69
intra_correlation_scExp0.550.150.70
launchApp000
normalize_scExp0.580.050.62
num_cell_after_QC_filt_scExp0.670.020.69
num_cell_after_cor_filt_scExp15.53 0.1715.75
num_cell_before_cor_filt_scExp0.280.140.42
num_cell_in_cluster_scExp0.590.160.75
num_cell_scExp0.520.010.54
plot_cluster_consensus_scExp1.200.141.34
plot_correlation_PCA_scExp1.380.111.48
plot_coverage_BigWig0.310.160.47
plot_differential_summary_scExp0.360.140.50
plot_differential_volcano_scExp0.420.090.52
plot_distribution_scExp0.530.140.67
plot_gain_or_loss_barplots60.88 0.8861.78
plot_heatmap_scExp0.450.170.86
plot_inter_correlation_scExp0.660.170.83
plot_intra_correlation_scExp0.700.110.81
plot_most_contributing_features0.590.110.70
plot_percent_active_feature_scExp0.680.140.82
plot_pie_most_contributing_chr0.310.110.42
plot_reduced_dim_scExp1.510.171.72
plot_reduced_dim_scExp_CNA29.16 0.3529.55
plot_top_TF_scExp0.670.120.80
plot_violin_feature_scExp0.720.110.84
preprocess_CPM0.580.030.61
preprocess_RPKM0.460.050.52
preprocess_TFIDF0.520.000.51
preprocess_TPM0.550.010.56
preprocess_feature_size_only0.570.030.61
preprocessing_filtering_and_reduction11.91 0.0512.02
read_sparse_matrix000
rebin_matrix 9.16 0.0032.41
reduce_dims_scExp1.940.031.96
scExp1.200.171.38
subsample_scExp0.520.030.55
subset_bam_call_peaks000
summary_DA0.300.080.37
swapAltExp_sameColData0.570.080.66
table_enriched_genes_scExp0.320.150.47
wrapper_Signac_FeatureMatrix000