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 00:24:27 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:30:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 348.7 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) (2018-11-27 r75683)
* 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 7.196  0.053   7.335
plot_dist    5.149  0.071   5.282
* 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’ ...
** 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 (DEP)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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 
 60.876   2.196  63.948 

name	user	system	elapsed
LFQ	2.352	0.080	2.453
TMT	0.001	0.000	0.000
add_rejections	1.438	0.076	1.538
analyze_dep	2.736	0.133	2.889
filter_missval	0.881	0.035	0.926
filter_proteins	0.460	0.019	0.486
get_df_long	1.798	0.045	1.856
get_df_wide	1.097	0.043	1.143
get_prefix	0.003	0.000	0.003
get_results	1.249	0.037	1.292
get_suffix	0.002	0.000	0.001
import_IsobarQuant	0	0	0
import_MaxQuant	0.053	0.002	0.055
impute	1.651	0.044	1.710
make_se	0.047	0.001	0.048
make_se_parse	0.102	0.003	0.106
make_unique	0.022	0.000	0.023
manual_impute	0.955	0.030	0.992
meanSdPlot	0.881	0.032	0.920
normalize_vsn	0.545	0.029	0.583
plot_all	2.124	0.080	2.220
plot_cond	1.893	0.058	1.962
plot_cond_freq	1.452	0.041	1.507
plot_cond_overlap	1.434	0.040	1.484
plot_cor	1.700	0.044	1.762
plot_coverage	0.886	0.016	0.920
plot_detect	1.026	0.019	1.057
plot_dist	5.149	0.071	5.282
plot_frequency	0.677	0.024	0.716
plot_gsea	1.337	0.035	1.383
plot_heatmap	4.302	0.070	4.409
plot_imputation	2.397	0.087	2.498
plot_missval	1.998	0.071	2.089
plot_normalization	1.995	0.083	2.093
plot_numbers	0.785	0.023	0.814
plot_p_hist	2.086	0.070	2.173
plot_pca	2.302	0.049	2.370
plot_single	2.630	0.050	2.704
plot_volcano	7.196	0.053	7.335
process	1.989	0.054	2.063
report	0.000	0.001	0.000
run_app	0.001	0.000	0.000
se2msn	0.161	0.001	0.164
test_diff	1.480	0.052	1.551
test_gsea	1.877	0.044	1.934
theme_DEP1	0.675	0.021	0.701
theme_DEP2	0.766	0.016	0.790