Package: DEP

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEP_1.6.1.tar.gz

StartedAt: 2019-10-16 02:06:36 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:14:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 467.8 seconds

RetCode: 0

Status:  OK

CheckDir: DEP.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:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEP_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DEP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.6.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DEP’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_volcano 8.655  0.216   8.876
plot_dist    7.427  0.121   7.549
plot_heatmap 5.825  0.205   6.033
* 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 DEP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DEP’ ...
** 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 (DEP)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(DEP)
> 
> test_check("DEP")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 333 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 78.635   4.627  83.578 

name	user	system	elapsed
LFQ	2.849	0.187	3.035
TMT	0.000	0.001	0.000
add_rejections	1.784	0.085	1.868
analyze_dep	4.121	0.351	4.473
filter_missval	1.02	0.08	1.10
filter_proteins	0.639	0.049	0.689
get_df_long	1.667	0.103	1.772
get_df_wide	1.372	0.098	1.469
get_prefix	0.004	0.001	0.004
get_results	2.244	0.095	2.339
get_suffix	0.003	0.000	0.003
import_IsobarQuant	0.000	0.000	0.001
import_MaxQuant	0.048	0.003	0.051
impute	2.291	0.135	2.426
make_se	0.080	0.017	0.099
make_se_parse	0.170	0.044	0.215
make_unique	0.041	0.009	0.050
manual_impute	1.415	0.161	1.577
meanSdPlot	1.085	0.076	1.163
normalize_vsn	0.772	0.082	0.854
plot_all	2.800	0.181	2.982
plot_cond	2.275	0.113	2.389
plot_cond_freq	1.864	0.077	1.942
plot_cond_overlap	1.766	0.070	1.837
plot_cor	2.444	0.087	2.532
plot_coverage	1.050	0.034	1.087
plot_detect	1.516	0.062	1.578
plot_dist	7.427	0.121	7.549
plot_frequency	0.902	0.043	0.947
plot_gsea	1.256	0.070	1.326
plot_heatmap	5.825	0.205	6.033
plot_imputation	2.219	0.140	2.361
plot_missval	2.856	0.152	3.010
plot_normalization	2.396	0.169	2.565
plot_numbers	0.881	0.043	0.926
plot_p_hist	3.217	0.082	3.299
plot_pca	2.835	0.082	2.919
plot_single	3.110	0.090	3.201
plot_volcano	8.655	0.216	8.876
process	3.428	0.127	3.556
report	0.001	0.000	0.001
run_app	0	0	0
se2msn	0.141	0.003	0.143
test_diff	1.957	0.119	2.076
test_gsea	1.728	0.089	1.817
theme_DEP1	0.896	0.045	0.943
theme_DEP2	1.112	0.051	1.164