Package: MWASTools

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MWASTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MWASTools_1.4.0.tar.gz

StartedAt: 2018-10-16 22:53:03 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:56:42 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 219.3 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 --install=check:MWASTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MWASTools_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MWASTools.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 ‘MWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MWASTools’ version ‘1.4.0’
* 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
JBA_binning: no visible binding for global variable ‘median’
JBA_corDistribution: no visible binding for global variable ‘r.coeff’
JBA_mergeClusters: no visible binding for global variable ‘median’
JBA_plotBins: no visible binding for global variable ‘limits’
JBA_plotBins: no visible binding for global variable ‘value’
JBA_plotBins: no visible binding for global variable ‘intensity’
JBA_plotBins: no visible binding for global variable ‘mean_cor’
JBA_plotBins: no visible binding for global variable ‘clean_mean’
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 clean_mean hr intensity limits logpval mean_cor median r.coeff
  value
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
MWAS_bootstrapping 5.34  0.328   5.716
* 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-3.7-bioc/meat/MWASTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MWASTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MWASTools’ ...
** 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 (MWASTools)

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.

> 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 -- Tue Oct 16 22:56:36 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 
 10.255   0.550  10.879 

name	user	system	elapsed
CV_filter	0.752	0.054	0.814
JBA_binning	0.000	0.000	0.001
JBA_corDistribution	0.001	0.000	0.001
JBA_plotBins	0	0	0
MWAS_KEGG_network	0.000	0.000	0.001
MWAS_KEGG_pathways	0.001	0.000	0.000
MWAS_KEGG_shortestpaths	0.001	0.000	0.001
MWAS_SummarizedExperiment	0.002	0.001	0.003
MWAS_barplot	2.697	0.116	2.832
MWAS_bootstrapping	5.340	0.328	5.716
MWAS_filter	0.078	0.002	0.079
MWAS_heatmap	0.658	0.004	0.670
MWAS_network	0.068	0.003	0.071
MWAS_scatterplotMS	1.316	0.018	1.353
MWAS_skylineNMR	2.698	0.067	2.796
MWAS_stats	0.701	0.039	0.747
QC_CV	0.671	0.014	0.693
QC_CV_scatterplot	1.070	0.017	1.104
QC_CV_specNMR	1.862	0.021	1.897
QC_PCA	0.015	0.002	0.018
QC_PCA_scoreplot	1.202	0.021	1.240
STOCSY_NMR	2.068	0.044	2.128
plot_spectraNMR	0.074	0.008	0.084