Package: DEP

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2020-01-16 03:38:56 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:47:49 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 533.2 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DEP.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.0’
* 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 (user + system) or elapsed time > 5s
              user system elapsed
plot_volcano 9.115  0.140   9.258
plot_dist    7.733  0.163   7.899
plot_heatmap 5.292  0.140   5.436
* 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/4.0/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) (2019-12-14 r77572) -- "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: 333 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 86.530   4.957  92.492 

name	user	system	elapsed
LFQ	3.163	0.163	3.326
TMT	0.000	0.000	0.001
add_rejections	1.836	0.097	1.933
analyze_dep	3.715	0.230	3.949
filter_missval	1.071	0.075	1.145
filter_proteins	1.498	0.049	1.548
get_df_long	1.737	0.147	1.884
get_df_wide	1.754	0.093	1.847
get_prefix	0.006	0.000	0.006
get_results	2.143	0.114	2.257
get_suffix	0.003	0.001	0.002
import_IsobarQuant	0.000	0.000	0.001
import_MaxQuant	0.111	0.013	0.124
impute	2.819	0.151	2.971
make_se	0.097	0.014	0.111
make_se_parse	0.138	0.014	0.152
make_unique	0.038	0.001	0.040
manual_impute	1.310	0.062	1.372
meanSdPlot	1.193	0.065	1.258
normalize_vsn	0.761	0.047	0.808
plot_all	2.718	0.184	2.906
plot_cond	2.436	0.179	2.686
plot_cond_freq	2.094	0.095	2.191
plot_cond_overlap	2.068	0.091	2.160
plot_cor	2.458	0.066	2.524
plot_coverage	1.867	0.051	1.918
plot_detect	1.530	0.193	1.724
plot_dist	7.733	0.163	7.899
plot_frequency	0.886	0.043	0.929
plot_gsea	1.455	0.071	1.525
plot_heatmap	5.292	0.140	5.436
plot_imputation	2.486	0.193	2.679
plot_missval	2.693	0.141	2.835
plot_normalization	2.581	0.192	2.777
plot_numbers	0.837	0.033	0.870
plot_p_hist	3.159	0.092	3.251
plot_pca	2.952	0.075	3.027
plot_single	3.575	0.184	3.760
plot_volcano	9.115	0.140	9.258
process	2.242	0.117	2.359
report	0.000	0.000	0.001
run_app	0.000	0.001	0.001
se2msn	0.203	0.002	0.205
test_diff	2.161	0.114	2.276
test_gsea	1.573	0.088	1.662
theme_DEP1	0.607	0.034	0.641
theme_DEP2	1.054	0.047	1.107