Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-19 17:37 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 348/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.14.0  (landing page)
Pacome Prompsy
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_19
git_last_commit: ecb3c51
git_last_commit_date: 2024-04-30 11:27:45 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
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 nebbiolo1

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: 1.14.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChromSCape_1.14.0.tar.gz
StartedAt: 2024-07-17 22:02:35 -0400 (Wed, 17 Jul 2024)
EndedAt: 2024-07-17 22:14:58 -0400 (Wed, 17 Jul 2024)
EllapsedTime: 743.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChromSCape_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ChromSCape.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.14.0’
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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            44.257  0.288  44.549
get_pathway_mat_scExp                 30.115  1.491  31.679
calculate_CNA                         22.511  2.732  25.265
plot_reduced_dim_scExp_CNA            21.430  0.008  21.443
calculate_logRatio_CNA                20.305  0.543  20.910
calculate_cyto_mat                    19.937  0.748  20.684
calculate_gain_or_loss                19.796  0.592  20.388
get_most_variable_cyto                19.878  0.189  20.068
get_cyto_features                     18.022  0.096  18.119
num_cell_after_cor_filt_scExp         10.577  0.004  10.562
filter_correlated_cell_scExp           9.736  0.053   9.775
preprocessing_filtering_and_reduction  7.995  0.016   8.006
create_scDataset_raw                   6.221  0.373   6.596
import_scExp                           6.407  0.044   6.592
CompareWilcox                          5.403  0.674   5.609
rebin_matrix                           5.779  0.072  20.653
CompareedgeRGLM                        4.879  0.396   5.269
differential_activation                5.068  0.012   5.081
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.


Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c as_dist.cpp -o as_dist.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 41.283   3.073  44.272 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0060.0040.009
CompareWilcox5.4030.6745.609
CompareedgeRGLM4.8790.3965.269
annotToCol20.8860.0600.946
calculate_CNA22.511 2.73225.265
calculate_cyto_mat19.937 0.74820.684
calculate_gain_or_loss19.796 0.59220.388
calculate_logRatio_CNA20.305 0.54320.910
choose_cluster_scExp3.1310.1003.225
colors_scExp0.2920.0000.293
consensus_clustering_scExp2.8640.0922.950
correlation_and_hierarchical_clust_scExp0.3020.0080.303
create_project_folder0.0000.0020.002
create_scDataset_raw6.2210.3736.596
create_scExp0.6210.0000.621
define_feature0.1350.0080.143
detect_samples1.0300.0441.014
differential_activation5.0680.0125.081
differential_analysis_scExp2.6820.0002.683
enrich_TF_ChEA3_genes0.4510.1121.770
enrich_TF_ChEA3_scExp1.0340.0364.911
exclude_features_scExp0.7200.0230.826
feature_annotation_scExp1.7070.0151.737
filter_correlated_cell_scExp9.7360.0539.775
filter_scExp0.6960.0030.701
find_clusters_louvain_scExp0.3870.2980.476
find_top_features0.3260.0000.326
gene_set_enrichment_analysis_scExp0.2030.0030.206
generate_analysis000
generate_coverage_tracks0.0000.0000.001
generate_report0.0000.0010.000
getExperimentNames0.2210.0140.235
getMainExperiment0.2660.0000.266
get_cyto_features18.022 0.09618.119
get_genomic_coordinates0.4890.0030.494
get_most_variable_cyto19.878 0.18920.068
get_pathway_mat_scExp30.115 1.49131.679
has_genomic_coordinates0.8640.0440.908
import_scExp6.4070.0446.592
inter_correlation_scExp0.3280.0040.333
intra_correlation_scExp0.3210.0080.329
launchApp000
normalize_scExp0.4970.0230.519
num_cell_after_QC_filt_scExp0.5420.0160.559
num_cell_after_cor_filt_scExp10.577 0.00410.562
num_cell_before_cor_filt_scExp0.2070.0000.207
num_cell_in_cluster_scExp0.4280.0000.422
num_cell_scExp0.4500.0000.451
plot_cluster_consensus_scExp0.8410.0160.857
plot_correlation_PCA_scExp0.9480.0040.952
plot_coverage_BigWig0.2140.0000.214
plot_differential_summary_scExp0.2280.0000.229
plot_differential_volcano_scExp0.3170.0040.322
plot_distribution_scExp0.420.000.42
plot_gain_or_loss_barplots44.257 0.28844.549
plot_heatmap_scExp0.3050.0040.309
plot_inter_correlation_scExp0.5010.0040.505
plot_intra_correlation_scExp0.4570.0040.462
plot_most_contributing_features0.3960.0000.396
plot_percent_active_feature_scExp1.8410.0441.885
plot_pie_most_contributing_chr0.2760.0000.276
plot_reduced_dim_scExp2.5870.0042.592
plot_reduced_dim_scExp_CNA21.430 0.00821.443
plot_top_TF_scExp0.4350.0000.434
plot_violin_feature_scExp1.8180.0041.822
preprocess_CPM0.4870.0200.507
preprocess_RPKM0.5280.0320.560
preprocess_TFIDF0.4900.0160.506
preprocess_TPM0.5050.0280.533
preprocess_feature_size_only0.5080.0240.532
preprocessing_filtering_and_reduction7.9950.0168.006
read_sparse_matrix0.0010.0000.000
rebin_matrix 5.779 0.07220.653
reduce_dims_scExp1.7170.0001.717
scExp0.9500.0160.966
subsample_scExp0.7160.0040.720
subset_bam_call_peaks0.0000.0010.001
summary_DA0.2230.0030.226
swapAltExp_sameColData0.290.000.29
table_enriched_genes_scExp0.2070.0000.206
wrapper_Signac_FeatureMatrix000