Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:07:25 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 machv2


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? here 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 313/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.4.0  (landing page)
Pacome Prompsy
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_14
git_last_commit: df9f2c5
git_last_commit_date: 2021-10-26 13:03:23 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChromSCape
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2022-01-23 11:17:46 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 11:35:47 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 1080.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChromSCape.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.4.0’
* 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
CompareWilcox: no visible binding for global variable ‘annot.’
bams_to_matrix_indexes: no visible binding for global variable
  ‘files_dir_list’
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_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_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’
subset_bam_call_peaks: no visible binding for global variable
  ‘merged_bam’
Undefined global functions or variables:
  Fri_cyto Gain_or_Loss V1 V2 absolute_value annot. cluster
  clusterConsensus cytoBand files_dir_list genes k merged_bam ncells
  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’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/PairedTag_Zhu_H3K4me1.Rmd’
   ‘vignettes/scChIC_Ku_H3K4me3.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
plot_gain_or_loss_barplots    95.971  0.427  96.519
calculate_CNA                 46.106  2.949  49.169
plot_reduced_dim_scExp_CNA    47.600  0.162  48.026
calculate_gain_or_loss        42.579  1.046  43.694
calculate_cyto_mat            42.201  1.194  43.450
calculate_logRatio_CNA        40.349  1.285  41.699
get_most_variable_cyto        40.204  0.120  40.349
get_cyto_features             36.875  0.160  37.073
num_cell_after_cor_filt_scExp 11.563  0.496  12.066
filter_correlated_cell_scExp  10.943  0.603  11.544
peaks_to_bins                  9.835  0.926   5.225
create_scDataset_raw           9.287  0.692   9.992
differential_analysis_scExp    7.307  2.491   5.213
CompareWilcox                  7.876  1.176   6.687
CompareedgeRGLM                8.536  0.496   9.044
import_scExp                   6.838  0.201   7.042
choose_cluster_scExp           6.026  0.882   6.921
reduce_dims_scExp              6.178  0.071   6.261
consensus_clustering_scExp     4.950  0.793   5.754
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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/4.1/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/4.1/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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 61.560   5.454  67.348 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CompareWilcox7.8761.1766.687
CompareedgeRGLM8.5360.4969.044
annotToCol22.2840.1212.409
calculate_CNA46.106 2.94949.169
calculate_cyto_mat42.201 1.19443.450
calculate_gain_or_loss42.579 1.04643.694
calculate_logRatio_CNA40.349 1.28541.699
choose_cluster_scExp6.0260.8826.921
colors_scExp0.3910.0030.395
consensus_clustering_scExp4.9500.7935.754
correlation_and_hierarchical_clust_scExp0.6150.0040.621
create_project_folder0.0020.0030.005
create_scDataset_raw9.2870.6929.992
create_scExp2.0370.0092.051
define_feature0.3760.0090.386
detect_samples1.1660.0801.246
differential_analysis_scExp7.3072.4915.213
exclude_features_scExp1.9440.1902.138
feature_annotation_scExp4.5020.2414.759
filter_correlated_cell_scExp10.943 0.60311.544
filter_scExp2.6090.0982.710
find_top_features0.5390.0260.565
gene_set_enrichment_analysis_scExp0.2060.0030.210
generate_analysis0.0000.0000.001
generate_coverage_tracks0.0000.0010.000
getExperimentNames0.2870.0080.295
getMainExperiment0.4270.0210.449
get_cyto_features36.875 0.16037.073
get_genomic_coordinates1.6360.0371.673
get_most_variable_cyto40.204 0.12040.349
has_genomic_coordinates2.6480.0382.687
import_scExp6.8380.2017.042
inter_correlation_scExp0.8920.0170.909
intra_correlation_scExp1.1400.0151.156
launchApp0.0000.0010.000
normalize_scExp2.9050.0672.977
num_cell_after_QC_filt_scExp1.9620.0141.982
num_cell_after_cor_filt_scExp11.563 0.49612.066
num_cell_before_cor_filt_scExp0.2200.0080.228
num_cell_in_cluster_scExp1.1400.0081.150
num_cell_scExp1.7390.0851.833
peaks_to_bins9.8350.9265.225
plot_cluster_consensus_scExp1.2780.0231.303
plot_coverage_BigWig1.1230.0441.172
plot_differential_H1_scExp0.2300.0050.236
plot_differential_summary_scExp0.2220.0040.226
plot_differential_volcano_scExp0.2490.0100.260
plot_distribution_scExp0.8610.0390.905
plot_gain_or_loss_barplots95.971 0.42796.519
plot_heatmap_scExp0.4910.0090.503
plot_inter_correlation_scExp0.9210.0070.929
plot_intra_correlation_scExp1.0780.0091.119
plot_most_contributing_features0.6700.0100.702
plot_pie_most_contributing_chr0.4320.0070.441
plot_reduced_dim_scExp4.7370.0424.813
plot_reduced_dim_scExp_CNA47.600 0.16248.026
preprocess_CPM1.7400.0751.817
preprocess_RPKM1.8270.0551.883
preprocess_TFIDF1.7980.1311.959
preprocess_TPM1.8580.0451.913
preprocess_feature_size_only1.7800.0891.871
read_sparse_matrix0.0010.0010.001
reduce_dims_scExp6.1780.0716.261
scExp1.8640.0301.901
subsample_scExp2.7110.0262.745
subset_bam_call_peaks0.0000.0010.001
swapAltExp_sameColData0.5600.0050.569
table_enriched_genes_scExp0.2390.0040.245
wrapper_Signac_FeatureMatrix0.0000.0010.001