Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-18 12:04:28 -0400 (Mon, 18 Oct 2021).

CHECK results for ChromSCape on merida1

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 307/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.3.22  (landing page)
Pacome Prompsy
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: master
git_last_commit: 8f4b09e
git_last_commit_date: 2021-09-28 04:52:10 -0400 (Tue, 28 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChromSCape
Version: 1.3.22
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_1.3.22.tar.gz
StartedAt: 2021-10-18 02:06:19 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 02:23:17 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 1017.8 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_1.3.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.3.22’
* 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    89.238  0.416  89.749
calculate_CNA                 43.594  1.323  44.965
plot_reduced_dim_scExp_CNA    43.630  0.170  43.864
calculate_gain_or_loss        39.912  0.473  40.436
calculate_cyto_mat            39.601  0.438  40.081
calculate_logRatio_CNA        38.907  0.400  39.358
get_most_variable_cyto        36.576  0.172  36.799
get_cyto_features             34.318  0.124  34.479
peaks_to_bins                 15.277  7.749   7.997
num_cell_after_cor_filt_scExp 10.940  0.432  11.367
filter_correlated_cell_scExp  10.695  0.617  11.317
CompareedgeRGLM               10.109  0.981  10.082
differential_analysis_scExp    6.277  2.281   4.423
create_scDataset_raw           8.032  0.402   8.450
CompareWilcox                  6.225  1.008   5.802
import_scExp                   6.693  0.103   6.806
choose_cluster_scExp           5.623  0.534   6.177
reduce_dims_scExp              5.926  0.092   6.025
consensus_clustering_scExp     4.494  0.576   5.083
* 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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 
 55.941   4.270  59.927 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CompareWilcox6.2251.0085.802
CompareedgeRGLM10.109 0.98110.082
annotToCol22.4780.1372.618
calculate_CNA43.594 1.32344.965
calculate_cyto_mat39.601 0.43840.081
calculate_gain_or_loss39.912 0.47340.436
calculate_logRatio_CNA38.907 0.40039.358
choose_cluster_scExp5.6230.5346.177
colors_scExp0.4060.0030.410
consensus_clustering_scExp4.4940.5765.083
correlation_and_hierarchical_clust_scExp0.4410.0040.448
create_project_folder0.0020.0010.003
create_scDataset_raw8.0320.4028.450
create_scExp1.3910.0581.454
define_feature0.2660.0050.273
detect_samples1.0050.0581.068
differential_analysis_scExp6.2772.2814.423
exclude_features_scExp1.6570.1521.812
feature_annotation_scExp3.5990.1523.759
filter_correlated_cell_scExp10.695 0.61711.317
filter_scExp2.3310.0902.426
find_top_features0.4640.0230.488
gene_set_enrichment_analysis_scExp0.1990.0030.202
generate_analysis000
generate_coverage_tracks000
getExperimentNames0.2810.0080.289
getMainExperiment0.4120.0230.434
get_cyto_features34.318 0.12434.479
get_genomic_coordinates1.2670.0141.285
get_most_variable_cyto36.576 0.17236.799
has_genomic_coordinates2.4350.0492.486
import_scExp6.6930.1036.806
inter_correlation_scExp0.7630.0090.773
intra_correlation_scExp0.9970.0091.009
launchApp000
normalize_scExp1.5300.0541.585
num_cell_after_QC_filt_scExp1.7170.0081.729
num_cell_after_cor_filt_scExp10.940 0.43211.367
num_cell_before_cor_filt_scExp0.1980.0070.205
num_cell_in_cluster_scExp0.9830.0080.992
num_cell_scExp1.4640.0681.534
peaks_to_bins15.277 7.749 7.997
plot_cluster_consensus_scExp1.2870.0201.309
plot_coverage_BigWig1.0870.0421.131
plot_differential_H1_scExp0.2160.0050.220
plot_differential_summary_scExp0.2230.0050.228
plot_differential_volcano_scExp0.2790.0100.289
plot_distribution_scExp0.8000.0340.836
plot_gain_or_loss_barplots89.238 0.41689.749
plot_heatmap_scExp0.4960.0090.506
plot_inter_correlation_scExp1.0100.0071.017
plot_intra_correlation_scExp0.9710.0070.978
plot_most_contributing_features0.5800.0060.587
plot_pie_most_contributing_chr1.4050.0101.416
plot_reduced_dim_scExp4.1820.0464.242
plot_reduced_dim_scExp_CNA43.630 0.17043.864
preprocess_CPM1.7200.0371.761
preprocess_RPKM1.7520.0241.779
preprocess_TFIDF1.6200.0451.667
preprocess_TPM1.7290.0221.753
preprocess_feature_size_only1.6740.0551.731
read_sparse_matrix0.0000.0000.001
reduce_dims_scExp5.9260.0926.025
scExp1.7760.0271.808
subsample_scExp2.3850.0312.417
subset_bam_call_peaks000
swapAltExp_sameColData0.5030.0040.508
table_enriched_genes_scExp0.2300.0030.233
wrapper_Signac_FeatureMatrix000