Package: scFeatureFilter

Version: 1.2.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scFeatureFilter.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scFeatureFilter_1.2.1.tar.gz

StartedAt: 2019-04-16 02:54:00 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:55:36 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 96.4 seconds

RetCode: 0

Status:  OK

CheckDir: scFeatureFilter.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scFeatureFilter.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scFeatureFilter_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/scFeatureFilter.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.1’
* 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 17.292  0.212  17.522
plot_metric                     10.264  0.100  10.379
sc_feature_filter                9.652  0.124   9.801
plot_mean_variance               6.616  0.032   6.652
bin_scdata                       5.724  0.216   5.959
* 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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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL scFeatureFilter
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘scFeatureFilter’ ...
** 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
* DONE (scFeatureFilter)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  7.536   0.288   7.827 

name	user	system	elapsed
bin_scdata	5.724	0.216	5.959
calculate_cvs	0.156	0.008	0.161
correlate_windows	0.100	0.000	0.099
correlations_to_densities	0.136	0.000	0.136
define_top_genes	0.236	0.000	0.235
determine_bin_cutoff	0.016	0.000	0.016
filter_expression_table	0.052	0.000	0.050
get_mean_median	0.060	0.008	0.066
plot_correlations_distributions	17.292	0.212	17.522
plot_mean_variance	6.616	0.032	6.652
plot_metric	10.264	0.100	10.379
plot_top_window_autocor	2.224	0.000	2.229
sc_feature_filter	9.652	0.124	9.801