Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:05:24 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MWASTools on nebbiolo2


To the developers/maintainers of the MWASTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MWASTools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1258/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MWASTools 1.18.0  (landing page)
Andrea Rodriguez-Martinez , Rafael Ayala
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/MWASTools
git_branch: RELEASE_3_14
git_last_commit: 17465ce
git_last_commit_date: 2021-10-26 12:31:39 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MWASTools
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MWASTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MWASTools_1.18.0.tar.gz
StartedAt: 2022-01-16 08:51:44 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 08:54:59 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 195.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MWASTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MWASTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MWASTools_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MWASTools.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.18.0’
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
MWAS_bootstrapping 5.132  0.059   5.193
* 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-3.14-bioc/meat/MWASTools.Rcheck/00check.log’
for details.



Installation output

MWASTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MWASTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 -- Sun Jan 16 08:54:57 2022 
*********************************************** 
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 
  8.714   0.361   9.057 

Example timings

MWASTools.Rcheck/MWASTools-Ex.timings

nameusersystemelapsed
CV_filter0.3440.0240.368
JBA_binning000
JBA_corDistribution000
JBA_plotBins000
MWAS_KEGG_network000
MWAS_KEGG_pathways000
MWAS_KEGG_shortestpaths000
MWAS_SummarizedExperiment0.0010.0000.001
MWAS_barplot1.0260.0521.078
MWAS_bootstrapping5.1320.0595.193
MWAS_filter0.0620.0040.066
MWAS_heatmap0.4470.0080.454
MWAS_network0.0680.0000.068
MWAS_scatterplotMS0.5370.0000.537
MWAS_skylineNMR1.0270.0401.067
MWAS_stats0.3900.0000.391
QC_CV0.3130.0080.321
QC_CV_scatterplot0.8850.0120.897
QC_CV_specNMR0.9420.0120.954
QC_PCA0.0060.0040.010
QC_PCA_scoreplot0.9760.0080.984
STOCSY_NMR0.7560.0030.760
plot_spectraNMR0.0840.0010.084