Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:04:45 -0500 (Fri, 03 Dec 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 313/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.4.0  (landing page)
Pacome Prompsy
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
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 20.04.3 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: /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_1.4.0.tar.gz
StartedAt: 2021-12-02 06:35:30 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:46:55 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 685.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.4.0’
* 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 ... 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    50.713  1.776  52.490
calculate_CNA                 28.725  1.040  29.765
plot_reduced_dim_scExp_CNA    25.831  0.400  26.231
calculate_cyto_mat            24.766  0.420  25.186
calculate_gain_or_loss        24.524  0.384  24.908
calculate_logRatio_CNA        23.760  0.268  24.030
get_most_variable_cyto        22.616  0.079  22.696
get_cyto_features             20.449  0.115  20.566
peaks_to_bins                 13.621  4.501   6.794
num_cell_after_cor_filt_scExp 12.605  0.362  12.849
filter_correlated_cell_scExp  11.844  0.419  12.193
CompareWilcox                  7.469  1.609   7.821
create_scDataset_raw           7.997  0.384   8.382
import_scExp                   6.812  0.055   6.868
differential_analysis_scExp    5.083  1.629   4.216
CompareedgeRGLM                4.965  0.163   5.123
* 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

##############################################################################
##############################################################################
###
### 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
 42.074   1.332  43.186 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CompareWilcox7.4691.6097.821
CompareedgeRGLM4.9650.1635.123
annotToCol21.4190.0671.487
calculate_CNA28.725 1.04029.765
calculate_cyto_mat24.766 0.42025.186
calculate_gain_or_loss24.524 0.38424.908
calculate_logRatio_CNA23.760 0.26824.030
choose_cluster_scExp3.9780.0644.037
colors_scExp0.2680.0040.273
consensus_clustering_scExp3.4250.1163.535
correlation_and_hierarchical_clust_scExp0.3070.0030.306
create_project_folder0.0010.0000.002
create_scDataset_raw7.9970.3848.382
create_scExp0.9870.0201.007
define_feature0.2100.0070.218
detect_samples1.3030.0011.227
differential_analysis_scExp5.0831.6294.216
exclude_features_scExp1.3900.2201.152
feature_annotation_scExp2.4130.0602.472
filter_correlated_cell_scExp11.844 0.41912.193
filter_scExp1.3820.0241.405
find_top_features0.3180.0080.325
gene_set_enrichment_analysis_scExp0.1330.0000.132
generate_analysis000
generate_coverage_tracks0.0000.0000.001
getExperimentNames0.1760.0040.181
getMainExperiment0.2510.0080.259
get_cyto_features20.449 0.11520.566
get_genomic_coordinates0.7900.0040.795
get_most_variable_cyto22.616 0.07922.696
has_genomic_coordinates1.4550.0251.478
import_scExp6.8120.0556.868
inter_correlation_scExp0.5320.0040.536
intra_correlation_scExp0.6340.0010.634
launchApp000
normalize_scExp0.9960.0041.000
num_cell_after_QC_filt_scExp1.0070.0001.007
num_cell_after_cor_filt_scExp12.605 0.36212.849
num_cell_before_cor_filt_scExp0.130.000.13
num_cell_in_cluster_scExp0.5710.0000.565
num_cell_scExp0.7810.0400.821
peaks_to_bins13.621 4.501 6.794
plot_cluster_consensus_scExp0.6730.0280.701
plot_coverage_BigWig0.5450.0400.585
plot_differential_H1_scExp0.1270.0040.131
plot_differential_summary_scExp0.1300.0000.131
plot_differential_volcano_scExp0.1960.0080.204
plot_distribution_scExp0.4170.0200.438
plot_gain_or_loss_barplots50.713 1.77652.490
plot_heatmap_scExp0.2910.0040.295
plot_inter_correlation_scExp0.5630.0080.571
plot_intra_correlation_scExp0.5230.0040.527
plot_most_contributing_features0.3360.0000.336
plot_pie_most_contributing_chr0.2420.0080.251
plot_reduced_dim_scExp2.0590.0322.092
plot_reduced_dim_scExp_CNA25.831 0.40026.231
preprocess_CPM0.9520.0120.964
preprocess_RPKM0.9410.0160.958
preprocess_TFIDF0.9610.0160.977
preprocess_TPM0.9780.0241.002
preprocess_feature_size_only0.9250.0320.957
read_sparse_matrix000
reduce_dims_scExp3.5680.0163.584
scExp1.0710.0201.091
subsample_scExp1.2730.0311.304
subset_bam_call_peaks0.0000.0000.001
swapAltExp_sameColData0.2910.0000.291
table_enriched_genes_scExp0.1290.0040.133
wrapper_Signac_FeatureMatrix000