Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MWASTools on malbec1

This page was generated on 2021-05-05 12:10:21 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the MWASTools package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1191/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MWASTools 1.14.0  (landing page)
Andrea Rodriguez-Martinez , Rafael Ayala
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/MWASTools
Branch: RELEASE_3_12
Last Commit: 6fba3b0
Last Changed Date: 2020-10-27 11:19:37 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MWASTools
Version: 1.14.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MWASTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MWASTools_1.14.0.tar.gz
StartedAt: 2021-05-05 03:55:35 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 03:59:49 -0400 (Wed, 05 May 2021)
EllapsedTime: 254.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MWASTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MWASTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MWASTools_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MWASTools.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 global function definition for ‘ecdf’
JBA_corDistribution: no visible binding for global variable ‘r.coeff’
JBA_corDistribution: no visible binding for global variable ‘cum’
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 cum ecdf hr intensity limits logpval mean_cor
  median r.coeff value
Consider adding
  importFrom("stats", "ecdf", "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
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MWASTools.Rcheck/00check.log’
for details.



Installation output

MWASTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MWASTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MWASTools’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MWASTools)

Tests output

MWASTools.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Wed May  5 03:59:45 2021 
*********************************************** 
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 
 12.436   0.348  12.841 

Example timings

MWASTools.Rcheck/MWASTools-Ex.timings

nameusersystemelapsed
CV_filter0.9160.0280.945
JBA_binning000
JBA_corDistribution000
JBA_plotBins000
MWAS_KEGG_network000
MWAS_KEGG_pathways000
MWAS_KEGG_shortestpaths000
MWAS_SummarizedExperiment0.0040.0000.001
MWAS_barplot1.1160.0881.208
MWAS_bootstrapping4.4160.0324.455
MWAS_filter0.8600.0040.865
MWAS_heatmap0.5320.0000.530
MWAS_network0.0560.0000.057
MWAS_scatterplotMS0.9720.0080.991
MWAS_skylineNMR1.6640.0201.687
MWAS_stats1.5000.0361.537
QC_CV0.5560.0000.556
QC_CV_scatterplot1.4760.0081.485
QC_CV_specNMR1.6720.0081.686
QC_PCA0.0200.0000.018
QC_PCA_scoreplot1.2720.0201.298
STOCSY_NMR1.0280.0001.031
plot_spectraNMR0.0960.0000.096