Package: DEP

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2018-10-16 20:52:48 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:59:04 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 376.9 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DEP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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 7.641  0.105   7.817
plot_heatmap 6.128  0.044   6.237
* 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/3.5/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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: 327 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 70.947   2.287  74.647 

name	user	system	elapsed
LFQ	2.651	0.088	2.774
TMT	0.002	0.001	0.002
add_rejections	1.796	0.141	1.961
analyze_dep	3.260	0.139	3.438
filter_missval	1.438	0.026	1.473
filter_proteins	0.790	0.005	0.804
get_df_long	1.634	0.052	1.710
get_df_wide	2.162	0.028	2.215
get_prefix	0.004	0.000	0.004
get_results	1.706	0.041	1.764
get_suffix	0.002	0.000	0.002
import_IsobarQuant	0.002	0.000	0.003
import_MaxQuant	0.066	0.002	0.069
impute	2.226	0.040	2.288
make_se	0.089	0.006	0.095
make_se_parse	0.091	0.004	0.098
make_unique	0.032	0.001	0.032
manual_impute	1.188	0.020	1.218
meanSdPlot	1.233	0.016	1.262
normalize_vsn	0.846	0.013	0.871
plot_all	2.841	0.069	2.941
plot_cond	2.215	0.083	2.324
plot_cond_freq	1.825	0.042	1.885
plot_cond_overlap	1.695	0.027	1.742
plot_cor	2.220	0.030	2.267
plot_coverage	1.263	0.007	1.287
plot_detect	1.586	0.034	1.641
plot_dist	3.772	0.031	3.837
plot_frequency	0.950	0.008	0.967
plot_gsea	1.646	0.025	1.687
plot_heatmap	6.128	0.044	6.237
plot_imputation	3.042	0.091	3.159
plot_missval	2.560	0.035	2.628
plot_normalization	2.510	0.083	2.621
plot_numbers	1.068	0.005	1.096
plot_p_hist	2.465	0.034	2.537
plot_pca	2.808	0.029	2.867
plot_single	2.871	0.027	2.931
plot_volcano	7.641	0.105	7.817
process	2.525	0.058	2.603
report	0.001	0.000	0.001
run_app	0.001	0.000	0.001
se2msn	0.139	0.005	0.143
test_diff	1.797	0.035	1.843
test_gsea	1.721	0.028	1.769
theme_DEP1	0.960	0.009	0.971
theme_DEP2	0.982	0.006	0.993