BioC 3.6: CHECK report for MWASTools on veracruz1

Package: MWASTools

Version: 1.1.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MWASTools_1.1.11.tar.gz

StartedAt: 2017-08-16 06:06:16 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:10:14 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 237.9 seconds

RetCode: 0

Status:  OK

CheckDir: MWASTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MWASTools_1.1.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MWASTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.1.11’
* 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 5.229  0.111   5.496
* 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)

name	user	system	elapsed
CV_filter	1.707	0.047	1.797
MWAS_KEGG_network	0.000	0.000	0.001
MWAS_KEGG_pathways	0	0	0
MWAS_KEGG_shortestpaths	0	0	0
MWAS_SummarizedExperiment	0.001	0.000	0.002
MWAS_barplot	2.519	0.015	2.626
MWAS_bootstrapping	5.229	0.111	5.496
MWAS_filter	0.190	0.002	0.200
MWAS_heatmap	1.156	0.003	1.184
MWAS_network	0.094	0.001	0.099
MWAS_scatterplotMS	0.899	0.006	0.937
MWAS_skylineNMR	2.342	0.038	2.452
MWAS_stats	0.999	0.030	1.042
QC_CV	0.667	0.006	0.702
QC_CV_scatterplot	1.085	0.021	1.140
QC_CV_specNMR	1.400	0.021	1.453
QC_PCA	0.006	0.001	0.007
QC_PCA_scoreplot	1.515	0.014	1.568
STOCSY_NMR	1.596	0.019	1.672
plot_spectraNMR	0.061	0.006	0.068