Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 348/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.16.0  (landing page)
Pacome Prompsy
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_20
git_last_commit: 243f2f8
git_last_commit_date: 2024-10-29 10:51:14 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 1.16.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ChromSCape_1.16.0.tar.gz
StartedAt: 2024-12-20 00:00:25 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:18:07 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1062.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ChromSCape_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.16.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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) 13.3.0'
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    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
'library' or 'require' call not declared from: 'dplyr'
'library' or 'require' call to 'dplyr' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'generate_analysis.Rd':
generate_analysis
  Code: function(input_data_folder, analysis_name = "Analysis_1",
                 output_directory = "./", input_data_type = c("scBED",
                 "DenseMatrix", "SparseMatrix", "scBAM")[1],
                 feature_count_on = c("bins", "genebody", "peaks")[1],
                 feature_count_parameter = 50000, rebin_sparse_matrix =
                 FALSE, ref_genome = c("hg38", "mm10")[1], run =
                 c("filter", "CNA", "cluster", "consensus", "coverage",
                 "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)],
                 min_reads_per_cell = 1000, max_quantile_read_per_cell
                 = 99, n_top_features = 40000, norm_type = "CPM",
                 subsample_n = NULL, exclude_regions = NULL, n_clust =
                 NULL, corr_threshold = 99, percent_correlation = 1,
                 maxK = 10, qval.th = 0.1, logFC.th = 1,
                 enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels
                 = NULL, control_samples_CNA = NULL, genes_to_plot =
                 c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b",
                 "Cdkn2a", "chr7:15000000-20000000"))
  Docs: function(input_data_folder, analysis_name = "Analysis_1",
                 output_directory = "./", input_data_type = c("scBED",
                 "DenseMatrix", "SparseMatrix", "scBAM")[1],
                 rebin_sparse_matrix = FALSE, feature_count_on =
                 c("bins", "genebody", "peaks")[1],
                 feature_count_parameter = 50000, ref_genome =
                 c("hg38", "mm10")[1], run = c("filter", "CNA",
                 "cluster", "consensus", "peak_call", "coverage", "DA",
                 "GSA", "report")[c(1, 3, 6, 7, 8, 9)],
                 min_reads_per_cell = 1000, max_quantile_read_per_cell
                 = 99, n_top_features = 40000, norm_type = "CPM",
                 subsample_n = NULL, exclude_regions = NULL, n_clust =
                 NULL, corr_threshold = 99, percent_correlation = 1,
                 maxK = 10, qval.th = 0.1, logFC.th = 1,
                 enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels
                 = NULL, control_samples_CNA = NULL, genes_to_plot =
                 c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b",
                 "Cdkn2a", "chr7:15000000-20000000"))
  Mismatches in argument names:
    Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix
    Position: 6 Code: feature_count_parameter Docs: feature_count_on
    Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter
  Mismatches in argument default values:
    Name: 'run'
    Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", 
          "GSA", "report")[c(1, 3, 5, 6, 7, 8)]
    Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", 
          "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)]

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'rebin_matrix.Rd'
  'rebin_function'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.20-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
plot_gain_or_loss_barplots            62.08   0.92   63.05
get_pathway_mat_scExp                 49.33   4.31   53.69
calculate_CNA                         30.49   1.26   31.77
plot_reduced_dim_scExp_CNA            30.75   0.43   31.20
calculate_cyto_mat                    29.64   0.55   30.20
calculate_gain_or_loss                28.76   0.73   29.53
calculate_logRatio_CNA                28.75   0.68   29.43
get_most_variable_cyto                28.08   0.55   28.75
get_cyto_features                     26.72   0.31   27.03
num_cell_after_cor_filt_scExp         12.56   0.20   12.80
filter_correlated_cell_scExp          11.34   0.09   11.45
CompareedgeRGLM                       10.84   0.41   11.25
preprocessing_filtering_and_reduction 10.11   0.09   10.22
create_scDataset_raw                   8.55   0.97    9.51
import_scExp                           8.11   0.16    8.25
rebin_matrix                           7.23   0.05   25.22
differential_activation                6.97   0.15    7.12
CompareWilcox                          5.03   0.22   57.60
choose_cluster_scExp                   4.58   0.47    5.04
enrich_TF_ChEA3_scExp                  2.83   0.28    6.31
* 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: 3 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ChromSCape' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 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 
  44.28    2.28   92.03 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.000.010.02
CompareWilcox 5.03 0.2257.60
CompareedgeRGLM10.84 0.4111.25
annotToCol22.020.252.27
calculate_CNA30.49 1.2631.77
calculate_cyto_mat29.64 0.5530.20
calculate_gain_or_loss28.76 0.7329.53
calculate_logRatio_CNA28.75 0.6829.43
choose_cluster_scExp4.580.475.04
colors_scExp0.390.140.53
consensus_clustering_scExp4.310.514.80
correlation_and_hierarchical_clust_scExp0.460.170.62
create_project_folder000
create_scDataset_raw8.550.979.51
create_scExp0.470.000.47
define_feature0.150.030.19
detect_samples1.240.011.20
differential_activation6.970.157.12
differential_analysis_scExp3.800.093.91
enrich_TF_ChEA3_genes1.060.282.22
enrich_TF_ChEA3_scExp2.830.286.31
exclude_features_scExp0.610.000.61
feature_annotation_scExp2.000.102.11
filter_correlated_cell_scExp11.34 0.0911.45
filter_scExp0.770.030.80
find_clusters_louvain_scExp0.440.130.56
find_top_features0.310.100.42
gene_set_enrichment_analysis_scExp0.190.160.35
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.180.190.37
getMainExperiment0.350.140.49
get_cyto_features26.72 0.3127.03
get_genomic_coordinates0.510.050.56
get_most_variable_cyto28.08 0.5528.75
get_pathway_mat_scExp49.33 4.3153.69
has_genomic_coordinates0.870.040.92
import_scExp8.110.168.25
inter_correlation_scExp0.520.160.67
intra_correlation_scExp0.410.180.59
launchApp000
normalize_scExp0.540.040.58
num_cell_after_QC_filt_scExp0.720.000.72
num_cell_after_cor_filt_scExp12.56 0.2012.80
num_cell_before_cor_filt_scExp0.320.140.45
num_cell_in_cluster_scExp0.540.090.64
num_cell_scExp0.530.000.53
plot_cluster_consensus_scExp1.300.161.46
plot_correlation_PCA_scExp1.390.231.62
plot_coverage_BigWig0.280.190.47
plot_differential_summary_scExp0.380.140.52
plot_differential_volcano_scExp0.470.170.64
plot_distribution_scExp0.450.240.68
plot_gain_or_loss_barplots62.08 0.9263.05
plot_heatmap_scExp0.400.090.50
plot_inter_correlation_scExp0.690.240.92
plot_intra_correlation_scExp0.60.20.8
plot_most_contributing_features0.440.110.54
plot_percent_active_feature_scExp2.270.142.40
plot_pie_most_contributing_chr0.450.160.61
plot_reduced_dim_scExp3.910.224.13
plot_reduced_dim_scExp_CNA30.75 0.4331.20
plot_top_TF_scExp0.590.140.74
plot_violin_feature_scExp2.280.152.40
preprocess_CPM0.710.010.72
preprocess_RPKM0.750.060.81
preprocess_TFIDF0.580.030.61
preprocess_TPM0.550.020.56
preprocess_feature_size_only0.580.020.59
preprocessing_filtering_and_reduction10.11 0.0910.22
read_sparse_matrix000
rebin_matrix 7.23 0.0525.22
reduce_dims_scExp2.230.072.31
scExp1.360.191.55
subsample_scExp0.780.050.83
subset_bam_call_peaks000
summary_DA0.360.140.50
swapAltExp_sameColData0.430.140.56
table_enriched_genes_scExp0.320.130.46
wrapper_Signac_FeatureMatrix000