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 12:06 -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 merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.16.0.tar.gz
StartedAt: 2024-12-20 01:06:05 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:33:58 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1672.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChromSCape’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 is not available
* 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            115.366  0.697 138.158
get_pathway_mat_scExp                  63.520  7.213  87.491
calculate_CNA                          56.517  4.436  64.042
plot_reduced_dim_scExp_CNA             56.580  0.330  63.690
calculate_cyto_mat                     54.701  1.845  60.010
calculate_gain_or_loss                 54.386  1.708  60.399
calculate_logRatio_CNA                 53.006  1.930  59.784
get_most_variable_cyto                 52.675  0.281  65.154
get_cyto_features                      49.659  0.256  60.240
differential_activation                12.668  0.071  13.648
preprocessing_filtering_and_reduction  12.294  0.236  13.674
num_cell_after_cor_filt_scExp          12.109  0.120  15.433
filter_correlated_cell_scExp           11.460  0.090  14.222
create_scDataset_raw                    9.864  0.709  11.631
CompareedgeRGLM                         9.293  0.473  10.230
CompareWilcox                           7.690  0.769   7.673
import_scExp                            7.901  0.556  10.679
rebin_matrix                            7.962  0.066  43.417
plot_reduced_dim_scExp                  7.235  0.058   7.990
choose_cluster_scExp                    6.434  0.449   7.540
differential_analysis_scExp             6.682  0.045   7.423
consensus_clustering_scExp              5.926  0.426   7.051
plot_violin_feature_scExp               5.197  0.054   5.946
plot_percent_active_feature_scExp       4.992  0.053   5.674
enrich_TF_ChEA3_scExp                   1.980  0.113   5.957
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c as_dist.cpp -o as_dist.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 65.991   4.438  80.742 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0140.0040.019
CompareWilcox7.6900.7697.673
CompareedgeRGLM 9.293 0.47310.230
annotToCol23.2510.3133.761
calculate_CNA56.517 4.43664.042
calculate_cyto_mat54.701 1.84560.010
calculate_gain_or_loss54.386 1.70860.399
calculate_logRatio_CNA53.006 1.93059.784
choose_cluster_scExp6.4340.4497.540
colors_scExp0.5940.0100.628
consensus_clustering_scExp5.9260.4267.051
correlation_and_hierarchical_clust_scExp0.7190.0120.887
create_project_folder0.0030.0050.010
create_scDataset_raw 9.864 0.70911.631
create_scExp1.0620.0451.126
define_feature0.2960.0070.304
detect_samples1.2210.0671.343
differential_activation12.668 0.07113.648
differential_analysis_scExp6.6820.0457.423
enrich_TF_ChEA3_genes0.9950.4262.757
enrich_TF_ChEA3_scExp1.9800.1135.957
exclude_features_scExp1.0710.0111.327
feature_annotation_scExp3.1720.0963.941
filter_correlated_cell_scExp11.460 0.09014.222
filter_scExp1.2860.0101.595
find_clusters_louvain_scExp0.6490.0110.797
find_top_features0.6510.0110.780
gene_set_enrichment_analysis_scExp0.4110.0080.484
generate_analysis000
generate_coverage_tracks0.0000.0010.001
generate_report000
getExperimentNames0.4880.0090.594
getMainExperiment0.5940.0100.713
get_cyto_features49.659 0.25660.240
get_genomic_coordinates0.9010.0081.078
get_most_variable_cyto52.675 0.28165.154
get_pathway_mat_scExp63.520 7.21387.491
has_genomic_coordinates1.4530.0181.886
import_scExp 7.901 0.55610.679
inter_correlation_scExp0.7100.0430.971
intra_correlation_scExp0.7350.0310.940
launchApp0.0000.0000.001
normalize_scExp0.9950.0691.544
num_cell_after_QC_filt_scExp0.9730.0111.195
num_cell_after_cor_filt_scExp12.109 0.12015.433
num_cell_before_cor_filt_scExp0.4410.0110.564
num_cell_in_cluster_scExp0.8250.0181.071
num_cell_scExp0.8100.0061.019
plot_cluster_consensus_scExp2.0240.0232.643
plot_correlation_PCA_scExp2.4870.0603.194
plot_coverage_BigWig0.4140.0120.542
plot_differential_summary_scExp0.4620.0130.586
plot_differential_volcano_scExp0.5870.0190.743
plot_distribution_scExp0.8790.0141.127
plot_gain_or_loss_barplots115.366 0.697138.158
plot_heatmap_scExp0.6530.0250.783
plot_inter_correlation_scExp1.2020.0171.339
plot_intra_correlation_scExp1.0650.0161.184
plot_most_contributing_features0.9410.0301.059
plot_percent_active_feature_scExp4.9920.0535.674
plot_pie_most_contributing_chr0.5870.0150.648
plot_reduced_dim_scExp7.2350.0587.990
plot_reduced_dim_scExp_CNA56.58 0.3363.69
plot_top_TF_scExp1.0530.0221.203
plot_violin_feature_scExp5.1970.0545.946
preprocess_CPM0.9810.0581.168
preprocess_RPKM1.1010.0891.302
preprocess_TFIDF0.9980.0621.170
preprocess_TPM1.0260.0621.190
preprocess_feature_size_only0.9580.0661.123
preprocessing_filtering_and_reduction12.294 0.23613.674
read_sparse_matrix0.0000.0010.001
rebin_matrix 7.962 0.06643.417
reduce_dims_scExp3.5760.0494.049
scExp2.1680.0612.503
subsample_scExp1.2940.0231.458
subset_bam_call_peaks0.0000.0010.001
summary_DA0.4740.0110.539
swapAltExp_sameColData0.6480.0180.762
table_enriched_genes_scExp0.4470.0140.519
wrapper_Signac_FeatureMatrix0.0010.0010.000