Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:04:48 -0400 (Wed, 22 Sep 2021).

CHECK results for ChromSCape on nebbiolo1

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 306/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.2.62  (landing page)
Pacome Prompsy
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_13
git_last_commit: 752d173
git_last_commit_date: 2021-09-14 04:58:21 -0400 (Tue, 14 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.2.62
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChromSCape_1.2.62.tar.gz
StartedAt: 2021-09-21 09:17:07 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:29:13 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 726.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ChromSCape.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChromSCape_1.2.62.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.2.62’
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
plot_gain_or_loss_barplots    56.267  0.252  56.522
calculate_CNA                 31.747  2.944  34.692
calculate_gain_or_loss        28.756  0.928  29.685
plot_reduced_dim_scExp_CNA    29.163  0.100  29.262
calculate_cyto_mat            27.945  1.088  29.034
calculate_logRatio_CNA        25.763  0.876  26.640
get_most_variable_cyto        26.120  0.216  26.337
get_cyto_features             22.864  0.068  22.934
peaks_to_bins                 11.503  4.578   6.202
num_cell_after_cor_filt_scExp 12.613  0.104  12.696
filter_correlated_cell_scExp  11.865  0.132  11.976
create_scDataset_raw           8.424  0.420   8.845
CompareWilcox                  6.666  1.006   6.868
import_scExp                   7.554  0.080   7.635
differential_analysis_scExp    4.975  1.600   4.287
CompareedgeRGLM                5.848  0.493   5.713
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.



Installation output

ChromSCape.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 
 41.887   2.036  43.710 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CompareWilcox6.6661.0066.868
CompareedgeRGLM5.8480.4935.713
annotToCol21.3830.2161.600
calculate_CNA31.747 2.94434.692
calculate_cyto_mat27.945 1.08829.034
calculate_gain_or_loss28.756 0.92829.685
calculate_logRatio_CNA25.763 0.87626.640
choose_cluster_scExp4.0640.1004.159
colors_scExp0.2800.0040.284
consensus_clustering_scExp3.6730.0603.727
correlation_and_hierarchical_clust_scExp0.3280.0040.325
create_project_folder0.0020.0000.001
create_scDataset_raw8.4240.4208.845
create_scExp1.1190.0161.135
define_feature0.2140.0000.214
detect_samples1.1660.0081.112
differential_analysis_scExp4.9751.6004.287
exclude_features_scExp1.6980.2811.408
feature_annotation_scExp2.8210.0842.906
filter_correlated_cell_scExp11.865 0.13211.976
filter_scExp1.4160.0441.459
find_top_features0.3140.0080.322
gene_set_enrichment_analysis_scExp0.1340.0080.142
generate_analysis000
generate_coverage_tracks0.0000.0010.000
getExperimentNames0.1980.0070.205
getMainExperiment0.3010.0120.313
get_cyto_features22.864 0.06822.934
get_genomic_coordinates1.0300.0081.040
get_most_variable_cyto26.120 0.21626.337
has_genomic_coordinates1.6560.0351.692
import_scExp7.5540.0807.635
inter_correlation_scExp0.5050.0080.513
intra_correlation_scExp0.6070.0040.611
launchApp000
normalize_scExp1.0600.0281.087
num_cell_after_QC_filt_scExp1.0940.0041.097
num_cell_after_cor_filt_scExp12.613 0.10412.696
num_cell_before_cor_filt_scExp0.1360.0000.136
num_cell_in_cluster_scExp0.5850.0080.579
num_cell_scExp0.9470.0080.955
peaks_to_bins11.503 4.578 6.202
plot_cluster_consensus_scExp0.6170.0120.628
plot_coverage_BigWig0.5390.0040.543
plot_differential_H1_scExp0.1240.0080.132
plot_differential_summary_scExp0.1310.0000.131
plot_differential_volcano_scExp0.2080.0040.212
plot_distribution_scExp0.4360.0000.436
plot_gain_or_loss_barplots56.267 0.25256.522
plot_heatmap_scExp0.3140.0000.314
plot_inter_correlation_scExp0.5720.0040.576
plot_intra_correlation_scExp0.6020.0000.601
plot_most_contributing_features0.3980.0000.398
plot_pie_most_contributing_chr0.310.000.31
plot_reduced_dim_scExp2.3100.0122.323
plot_reduced_dim_scExp_CNA29.163 0.10029.262
preprocess_CPM0.9700.0521.022
preprocess_RPKM1.0400.0321.072
preprocess_TFIDF0.9450.0400.986
preprocess_TPM1.0170.0361.053
preprocess_feature_size_only0.9380.0200.959
read_sparse_matrix000
reduce_dims_scExp3.5620.0243.585
scExp1.0460.0161.062
subsample_scExp1.3190.0081.327
subset_bam_call_peaks000
swapAltExp_sameColData0.3040.0070.311
table_enriched_genes_scExp0.1490.0040.153
wrapper_Signac_FeatureMatrix000