Package: DEP

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEP_1.0.1.tar.gz

StartedAt: 2018-04-12 02:42:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:47:39 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 310.7 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 --no-vignettes --timings DEP_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DEP.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.1’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_heatmap 8.478  0.049   8.696
plot_volcano 5.839  0.038   5.977
LFQ          5.514  0.136   6.471
* 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

* installing *source* package ‘DEP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEP)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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")
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 290 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 61.921   1.448  64.935 

name	user	system	elapsed
LFQ	5.514	0.136	6.471
TMT	0.000	0.000	0.001
add_rejections	3.188	0.055	3.280
analyze_dep	4.174	0.102	4.340
filter_missval	1.571	0.016	1.620
get_df_long	1.316	0.030	1.365
get_df_wide	1.316	0.032	1.376
get_prefix	0.005	0.000	0.005
get_results	1.565	0.036	1.623
import_IsobarQuant	0.001	0.000	0.001
import_MaxQuant	0.508	0.003	0.533
impute	1.642	0.027	1.696
make_se	0.063	0.001	0.069
make_se_parse	0.126	0.002	0.129
make_unique	0.031	0.000	0.034
manual_impute	0.785	0.012	0.810
meanSdPlot	1.722	0.033	1.779
normalize_vsn	0.715	0.008	0.726
plot_all	2.748	0.064	2.854
plot_cond	1.741	0.021	1.789
plot_cond_freq	1.546	0.019	1.605
plot_cond_overlap	2.108	0.023	2.167
plot_cor	2.734	0.031	2.811
plot_coverage	0.897	0.006	0.912
plot_detect	1.303	0.005	1.322
plot_frequency	0.867	0.004	0.885
plot_gsea	1.256	0.015	1.280
plot_heatmap	8.478	0.049	8.696
plot_imputation	2.242	0.050	2.322
plot_missval	2.238	0.034	2.312
plot_normalization	2.190	0.051	2.275
plot_numbers	0.894	0.007	0.913
plot_p_hist	2.803	0.033	2.892
plot_pca	2.074	0.020	2.140
plot_single	2.370	0.021	2.444
plot_volcano	5.839	0.038	5.977
process	2.270	0.050	2.346
report	0.001	0.000	0.001
run_app	0.001	0.000	0.001
se2msn	0.114	0.001	0.116
test_diff	1.890	0.029	1.946
test_gsea	1.190	0.016	1.219
theme_DEP1	0.845	0.013	0.871
theme_DEP2	0.876	0.004	0.891