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This page was generated on 2021-10-18 12:03:38 -0400 (Mon, 18 Oct 2021).

CHECK results for ChromSCape on nebbiolo2

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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChromSCape_1.3.22.tar.gz
StartedAt: 2021-10-17 19:27:23 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 19:38:15 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 651.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChromSCape.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChromSCape_1.3.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   1.0Mb
    www    2.1Mb
* 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    44.925  0.196  45.122
calculate_CNA                 25.400  0.492  25.892
calculate_cyto_mat            25.197  0.192  25.389
plot_reduced_dim_scExp_CNA    24.492  0.164  24.655
calculate_gain_or_loss        23.316  0.100  23.416
calculate_logRatio_CNA        22.709  0.176  22.884
get_most_variable_cyto        21.084  0.000  21.085
get_cyto_features             19.823  0.120  19.944
filter_correlated_cell_scExp  11.608  0.417  11.970
num_cell_after_cor_filt_scExp 10.667  0.310  10.917
create_scDataset_raw           6.969  0.272   7.241
import_scExp                   6.830  0.068   6.898
CompareWilcox                  6.132  0.554   5.880
peaks_to_bins                  5.846  0.506   3.506
differential_analysis_scExp    4.295  1.428   3.940
* 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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.



Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c as_dist.cpp -o as_dist.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 42.300   2.033  44.102 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CompareWilcox6.1320.5545.880
CompareedgeRGLM4.7150.1994.909
annotToCol21.2770.0121.289
calculate_CNA25.400 0.49225.892
calculate_cyto_mat25.197 0.19225.389
calculate_gain_or_loss23.316 0.10023.416
calculate_logRatio_CNA22.709 0.17622.884
choose_cluster_scExp3.6290.0643.688
colors_scExp0.2680.0040.272
consensus_clustering_scExp3.2970.1043.394
correlation_and_hierarchical_clust_scExp0.3000.0040.299
create_project_folder0.0010.0000.002
create_scDataset_raw6.9690.2727.241
create_scExp0.9150.0000.914
define_feature0.1960.0000.195
detect_samples1.3430.0041.274
differential_analysis_scExp4.2951.4283.940
exclude_features_scExp1.7640.3091.082
feature_annotation_scExp2.1770.0602.237
filter_correlated_cell_scExp11.608 0.41711.970
filter_scExp1.2700.0241.293
find_top_features0.2970.0160.313
gene_set_enrichment_analysis_scExp0.1320.0000.133
generate_analysis000
generate_coverage_tracks000
getExperimentNames0.1810.0000.182
getMainExperiment0.2280.0000.229
get_cyto_features19.823 0.12019.944
get_genomic_coordinates0.7820.0120.794
get_most_variable_cyto21.084 0.00021.085
has_genomic_coordinates1.2330.0121.245
import_scExp6.8300.0686.898
inter_correlation_scExp0.4590.0000.458
intra_correlation_scExp0.5770.0040.581
launchApp000
normalize_scExp1.8820.0041.886
num_cell_after_QC_filt_scExp0.8710.0000.871
num_cell_after_cor_filt_scExp10.667 0.31010.917
num_cell_before_cor_filt_scExp0.1250.0000.124
num_cell_in_cluster_scExp0.5330.0040.530
num_cell_scExp0.760.040.80
peaks_to_bins5.8460.5063.506
plot_cluster_consensus_scExp0.5980.0080.607
plot_coverage_BigWig0.4970.0280.524
plot_differential_H1_scExp0.1210.0040.126
plot_differential_summary_scExp0.1150.0000.115
plot_differential_volcano_scExp0.1920.0040.196
plot_distribution_scExp0.3840.0280.413
plot_gain_or_loss_barplots44.925 0.19645.122
plot_heatmap_scExp0.270.000.27
plot_inter_correlation_scExp0.4990.0000.498
plot_intra_correlation_scExp0.4940.0000.493
plot_most_contributing_features0.3100.0000.311
plot_pie_most_contributing_chr0.2150.0040.219
plot_reduced_dim_scExp1.9150.0001.914
plot_reduced_dim_scExp_CNA24.492 0.16424.655
preprocess_CPM0.8850.0200.905
preprocess_RPKM0.9040.0160.920
preprocess_TFIDF0.9420.0120.954
preprocess_TPM0.9670.0080.976
preprocess_feature_size_only0.9660.0040.971
read_sparse_matrix000
reduce_dims_scExp3.5330.0683.601
scExp1.0810.0121.092
subsample_scExp1.3660.0001.367
subset_bam_call_peaks000
swapAltExp_sameColData0.3280.0040.331
table_enriched_genes_scExp0.140.000.14
wrapper_Signac_FeatureMatrix000