Package: DEP

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2020-04-15 01:44:43 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:50:57 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 374.4 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DEP.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 ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.8.0’
* 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 ... 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 7.033  0.061   7.149
plot_dist    5.405  0.054   5.516
* 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 3.6.3 (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(DEP)
> 
> test_check("DEP")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 333 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 67.022   2.361  70.225 

name	user	system	elapsed
LFQ	2.183	0.102	2.305
TMT	0.001	0.000	0.000
add_rejections	1.245	0.045	1.297
analyze_dep	2.617	0.107	2.742
filter_missval	0.635	0.032	0.672
filter_proteins	0.405	0.018	0.425
get_df_long	1.203	0.039	1.257
get_df_wide	1.204	0.039	1.258
get_prefix	0.003	0.000	0.004
get_results	1.982	0.038	2.041
get_suffix	0.001	0.000	0.001
import_IsobarQuant	0.000	0.000	0.001
import_MaxQuant	0.060	0.001	0.063
impute	1.845	0.060	1.920
make_se	0.072	0.009	0.081
make_se_parse	0.104	0.007	0.114
make_unique	0.027	0.000	0.027
manual_impute	0.898	0.028	0.930
meanSdPlot	0.879	0.026	0.919
normalize_vsn	1.081	0.028	1.118
plot_all	2.150	0.099	2.259
plot_cond	1.776	0.056	1.859
plot_cond_freq	1.322	0.039	1.377
plot_cond_overlap	1.443	0.047	1.499
plot_cor	1.795	0.045	1.859
plot_coverage	0.867	0.026	0.899
plot_detect	1.092	0.032	1.141
plot_dist	5.405	0.054	5.516
plot_frequency	0.609	0.020	0.635
plot_gsea	1.175	0.040	1.226
plot_heatmap	4.008	0.057	4.119
plot_imputation	1.858	0.068	1.949
plot_missval	2.013	0.055	2.091
plot_normalization	1.856	0.080	1.951
plot_numbers	0.699	0.018	0.727
plot_p_hist	2.234	0.041	2.298
plot_pca	2.086	0.085	2.192
plot_single	2.432	0.079	2.527
plot_volcano	7.033	0.061	7.149
process	1.828	0.058	1.904
report	0	0	0
run_app	0	0	0
se2msn	0.104	0.001	0.104
test_diff	1.347	0.050	1.409
test_gsea	1.020	0.030	1.057
theme_DEP1	0.555	0.016	0.577
theme_DEP2	0.708	0.018	0.733