Package: MWASTools

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MWASTools_1.2.0.tar.gz

StartedAt: 2018-04-12 06:56:38 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:00:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 207.9 seconds

RetCode: 0

Status:  OK

CheckDir: MWASTools.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 MWASTools_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MWASTools.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 ‘MWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MWASTools’ 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 ‘MWASTools’ 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 ... NOTE
MWAS_heatmap: no visible binding for '<<-' assignment to ‘hr’
MWAS_heatmap: no visible binding for global variable ‘hr’
MWAS_scatterplotMS: no visible binding for global variable ‘logpval’
QC_CV_scatterplot: no visible binding for global variable ‘abs.CV’
Undefined global functions or variables:
  abs.CV hr logpval
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
MWAS_bootstrapping 5.799  0.104   6.032
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/MWASTools.Rcheck/00check.log’
for details.

* installing *source* package ‘MWASTools’ ...
** 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 (MWASTools)

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.

> BiocGenerics:::testPackage("MWASTools")
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
506 samples will be included in the analysis
10 QC samples were detected
CV summary:
   % metabolite features with CV < 0.15 : 92
   % metabolite features with CV < 0.3 : 99

506 samples will be included in the analysis
10 QC samples were detected
CV summary:
   % metabolite features with CV < 0.15 : 92
   % metabolite features with CV < 0.3 : 99



RUNIT TEST PROTOCOL -- Thu Apr 12 07:00:01 2018 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MWASTools RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
There were 16 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 12.517   0.342  13.063 

name	user	system	elapsed
CV_filter	1.976	0.072	2.083
MWAS_KEGG_network	0	0	0
MWAS_KEGG_pathways	0	0	0
MWAS_KEGG_shortestpaths	0	0	0
MWAS_SummarizedExperiment	0.002	0.001	0.002
MWAS_barplot	2.878	0.017	2.951
MWAS_bootstrapping	5.799	0.104	6.032
MWAS_filter	0.211	0.002	0.218
MWAS_heatmap	1.290	0.004	1.319
MWAS_network	0.115	0.002	0.119
MWAS_scatterplotMS	1.210	0.010	1.251
MWAS_skylineNMR	1.827	0.030	1.910
MWAS_stats	0.544	0.017	0.569
QC_CV	0.921	0.005	0.933
QC_CV_scatterplot	0.988	0.011	1.018
QC_CV_specNMR	1.377	0.010	1.421
QC_PCA	0.007	0.001	0.008
QC_PCA_scoreplot	1.400	0.014	1.444
STOCSY_NMR	1.987	0.014	2.031
plot_spectraNMR	0.051	0.002	0.056