Package: scFeatureFilter

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scFeatureFilter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scFeatureFilter_1.6.0.tar.gz

StartedAt: 2020-04-15 05:29:11 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:31:20 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 129.1 seconds

RetCode: 0

Status:  OK

CheckDir: scFeatureFilter.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scFeatureFilter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scFeatureFilter_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/scFeatureFilter.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scFeatureFilter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scFeatureFilter’ version ‘1.6.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scFeatureFilter’ 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 ... OK
* checking Rd files ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
plot_correlations_distributions 19.865  2.691  22.805
plot_metric                     11.365  2.404  13.920
sc_feature_filter                9.839  2.364  12.360
bin_scdata                       7.127  0.336   7.507
plot_mean_variance               6.921  0.420   7.404
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scFeatureFilter
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scFeatureFilter’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scFeatureFilter)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(dplyr)

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(scFeatureFilter)
> 
> test_check("scFeatureFilter")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 34 | SKIPPED: 0 | WARNINGS: 30 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.331   0.551  10.920 

name	user	system	elapsed
bin_scdata	7.127	0.336	7.507
calculate_cvs	0.074	0.000	0.075
correlate_windows	0.129	0.002	0.131
correlations_to_densities	0.166	0.012	0.180
define_top_genes	0.157	0.019	0.182
determine_bin_cutoff	0.041	0.005	0.047
filter_expression_table	0.067	0.008	0.075
get_mean_median	0.113	0.010	0.124
plot_correlations_distributions	19.865	2.691	22.805
plot_mean_variance	6.921	0.420	7.404
plot_metric	11.365	2.404	13.920
plot_top_window_autocor	1.947	0.338	2.300
sc_feature_filter	9.839	2.364	12.360