Package: DEP

Version: 1.5.3

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_1.5.3.tar.gz

StartedAt: 2019-04-09 01:17:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:24:53 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 461.4 seconds

RetCode: 0

Status:  OK

CheckDir: DEP.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DEP.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.3’
* 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 9.486  0.155   9.643
plot_dist    6.785  0.173   6.959
plot_heatmap 6.061  0.251   6.313
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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: 334 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 75.221   4.400  79.961 

name	user	system	elapsed
LFQ	3.214	0.203	3.417
TMT	0.000	0.000	0.001
add_rejections	1.763	0.138	1.901
analyze_dep	3.734	0.321	4.054
filter_missval	1.528	0.131	1.659
filter_proteins	0.781	0.062	0.844
get_df_long	2.130	0.108	2.239
get_df_wide	1.910	0.154	2.064
get_prefix	0.006	0.000	0.007
get_results	1.963	0.113	2.077
get_suffix	0.003	0.000	0.003
import_IsobarQuant	0.000	0.000	0.001
import_MaxQuant	0.090	0.003	0.094
impute	3.554	0.138	3.693
make_se	0.069	0.002	0.072
make_se_parse	0.078	0.007	0.085
make_unique	0.037	0.001	0.039
manual_impute	1.320	0.137	1.457
meanSdPlot	1.241	0.090	1.332
normalize_vsn	0.980	0.077	1.056
plot_all	2.782	0.217	2.998
plot_cond	2.306	0.121	2.433
plot_cond_freq	2.090	0.091	2.181
plot_cond_overlap	2.277	0.120	2.398
plot_cor	2.228	0.163	2.391
plot_coverage	1.009	0.072	1.081
plot_detect	1.671	0.126	1.797
plot_dist	6.785	0.173	6.959
plot_frequency	0.915	0.075	0.991
plot_gsea	2.778	0.162	2.941
plot_heatmap	6.061	0.251	6.313
plot_imputation	2.513	0.199	2.712
plot_missval	2.570	0.165	2.736
plot_normalization	2.825	0.207	3.039
plot_numbers	1.241	0.066	1.308
plot_p_hist	2.809	0.139	2.949
plot_pca	2.940	0.105	3.045
plot_single	3.574	0.114	3.689
plot_volcano	9.486	0.155	9.643
process	2.765	0.137	2.903
report	0.000	0.000	0.001
run_app	0.000	0.000	0.001
se2msn	0.146	0.001	0.147
test_diff	2.073	0.123	2.196
test_gsea	1.804	0.092	1.897
theme_DEP1	1.169	0.125	1.295
theme_DEP2	1.210	0.075	1.286