Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-03-29 11:06:02 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4482
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
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

CHECK results for ChromSCape on lconway


To the developers/maintainers of the ChromSCape package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 324/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.8.0  (landing page)
Pacome Prompsy
Snapshot Date: 2023-03-27 14:00:04 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_16
git_last_commit: d32bd33
git_last_commit_date: 2022-11-01 11:23:01 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChromSCape
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-03-27 19:27:54 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 19:39:25 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 690.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ChromSCape.Rcheck
Warnings: 0

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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ChromSCape.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.8.0’
* 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
* 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 R 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 dependencies in R code ... OK
* 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 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_matrix: no visible binding for global variable ‘new_row’
rebin_matrix: no visible binding for global variable ‘origin_value’
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 k merged_bam molecule ncells new_row orientation origin_value
  percent_active run_tsne sample_id total_counts
* 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 ... 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
plot_gain_or_loss_barplots            44.816  0.500  45.660
get_pathway_mat_scExp                 34.078  4.892  39.367
calculate_gain_or_loss                23.910  1.263  28.632
calculate_CNA                         22.229  1.391  23.846
calculate_logRatio_CNA                22.608  0.734  23.616
get_most_variable_cyto                22.698  0.321  23.254
plot_reduced_dim_scExp_CNA            22.442  0.226  22.868
calculate_cyto_mat                    21.937  0.576  22.718
get_cyto_features                     20.578  0.300  21.111
num_cell_after_cor_filt_scExp          9.947  0.514  10.552
filter_correlated_cell_scExp           9.773  0.510  10.329
preprocessing_filtering_and_reduction  8.300  0.215   8.608
create_scDataset_raw                   6.422  0.513   6.990
import_scExp                           6.260  0.120   6.698
differential_activation                5.323  0.089   5.466
CompareWilcox                          4.350  0.740   3.917
enrich_TF_ChEA3_scExp                  0.979  0.079   5.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c as_dist.cpp -o as_dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
 33.846   3.708  37.692 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0070.0020.009
CompareWilcox4.3500.7403.917
CompareedgeRGLM4.6060.3264.975
annotToCol21.0630.0811.148
calculate_CNA22.229 1.39123.846
calculate_cyto_mat21.937 0.57622.718
calculate_gain_or_loss23.910 1.26328.632
calculate_logRatio_CNA22.608 0.73423.616
choose_cluster_scExp3.5380.7314.324
colors_scExp0.3920.0110.405
consensus_clustering_scExp3.0180.6673.715
correlation_and_hierarchical_clust_scExp0.3710.0100.390
create_project_folder0.0010.0020.004
create_scDataset_raw6.4220.5136.990
create_scExp0.7430.0190.803
define_feature0.1430.0030.147
detect_samples0.9780.1001.084
differential_activation5.3230.0895.466
differential_analysis_scExp2.8660.0422.924
enrich_TF_ChEA3_genes0.5600.1762.021
enrich_TF_ChEA3_scExp0.9790.0795.035
exclude_features_scExp0.6640.0080.677
feature_annotation_scExp1.7240.0851.833
filter_correlated_cell_scExp 9.773 0.51010.329
filter_scExp0.8800.0420.930
find_clusters_louvain_scExp0.6860.5290.757
find_top_features0.4220.0540.479
gene_set_enrichment_analysis_scExp0.2560.0100.268
generate_analysis0.0000.0000.001
generate_coverage_tracks000
generate_report000
getExperimentNames0.2830.0140.299
getMainExperiment0.3300.0190.350
get_cyto_features20.578 0.30021.111
get_genomic_coordinates0.5730.0150.592
get_most_variable_cyto22.698 0.32123.254
get_pathway_mat_scExp34.078 4.89239.367
has_genomic_coordinates0.9100.3871.311
import_scExp6.2600.1206.698
inter_correlation_scExp0.4150.0160.434
intra_correlation_scExp0.4120.0120.429
launchApp0.0000.0000.001
normalize_scExp0.5570.0220.587
num_cell_after_QC_filt_scExp0.6550.0630.727
num_cell_after_cor_filt_scExp 9.947 0.51410.552
num_cell_before_cor_filt_scExp0.2860.0230.312
num_cell_in_cluster_scExp0.5340.0180.558
num_cell_scExp0.5080.0320.548
plot_cluster_consensus_scExp1.0060.0861.101
plot_correlation_PCA_scExp0.8390.0160.858
plot_coverage_BigWig0.2310.0120.245
plot_differential_summary_scExp0.2590.0120.272
plot_differential_volcano_scExp0.3130.0160.331
plot_distribution_scExp0.4590.0140.482
plot_gain_or_loss_barplots44.816 0.50045.660
plot_heatmap_scExp0.3460.0120.365
plot_inter_correlation_scExp0.5470.0100.569
plot_intra_correlation_scExp0.5340.0150.556
plot_most_contributing_features0.4400.0180.463
plot_percent_active_feature_scExp1.6150.0281.648
plot_pie_most_contributing_chr0.3110.0090.321
plot_reduced_dim_scExp2.6760.0462.746
plot_reduced_dim_scExp_CNA22.442 0.22622.868
plot_top_TF_scExp0.4540.0100.466
plot_violin_feature_scExp1.7610.0221.794
preprocess_CPM0.5520.0260.581
preprocess_RPKM0.6060.0550.670
preprocess_TFIDF0.5300.0280.560
preprocess_TPM0.5980.0700.670
preprocess_feature_size_only0.5830.0280.615
preprocessing_filtering_and_reduction8.3000.2158.608
read_sparse_matrix000
rebin_matrix3.2840.0533.367
reduce_dims_scExp1.8190.0451.876
scExp0.9960.0291.043
subsample_scExp0.8320.0500.893
subset_bam_call_peaks0.0010.0000.001
summary_DA0.2490.0110.260
swapAltExp_sameColData0.3140.0070.323
table_enriched_genes_scExp0.2380.0060.245
wrapper_Signac_FeatureMatrix0.0000.0010.001