Multiple platform build/check report for BioC 3.12 - CHECK report for MWASTools on tokay1

Package: MWASTools

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MWASTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MWASTools_1.14.0.tar.gz

StartedAt: 2021-05-06 04:58:36 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:04:23 -0400 (Thu, 06 May 2021)

EllapsedTime: 346.6 seconds

RetCode: 0

Status: OK

CheckDir: MWASTools.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MWASTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MWASTools_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MWASTools.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
MWAS_bootstrapping 7.03   0.08    7.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
MWAS_bootstrapping 6.96      0    6.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MWASTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MWASTools_1.14.0.tar.gz && rm -rf MWASTools.buildbin-libdir && mkdir MWASTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MWASTools.buildbin-libdir MWASTools_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MWASTools_1.14.0.zip && rm MWASTools_1.14.0.tar.gz MWASTools_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1961k  100 1961k    0     0  49.9M      0 --:--:-- --:--:-- --:--:-- 51.7M

install for i386

* 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
  converting help for package 'MWASTools'
    finding HTML links ... done
    CV_filter                               html  
    JBA_binning                             html  
    JBA_corDistribution                     html  
    JBA_plotBins                            html  
    KEGG_metabolic_paths                    html  
    MS_data                                 html  
    MWAS_KEGG_network                       html  
    MWAS_KEGG_pathways                      html  
    MWAS_KEGG_shortestpaths                 html  
    MWAS_SummarizedExperiment               html  
    MWAS_barplot                            html  
    MWAS_bootstrapping                      html  
    MWAS_filter                             html  
    MWAS_heatmap                            html  
    MWAS_network                            html  
    MWAS_scatterplotMS                      html  
    MWAS_skylineNMR                         html  
    MWAS_stats                              html  
    QC_CV                                   html  
    QC_CV_scatterplot                       html  
    QC_CV_specNMR                           html  
    QC_PCA                                  html  
    QC_PCA_scoreplot                        html  
    STOCSY_NMR                              html  
    metabo_SE                               html  
    plot_spectraNMR                         html  
    targetMetabo_SE                         html  
** 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

install for x64

* installing *source* package 'MWASTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MWASTools' as MWASTools_1.14.0.zip
* DONE (MWASTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MWASTools' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 May 06 05:04:05 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 
   9.87    0.60   10.46


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 May 06 05:04:18 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 
  11.46    0.42   11.87

name	user	system	elapsed
CV_filter	0.63	0.03	0.66
JBA_binning	0	0	0
JBA_corDistribution	0	0	0
JBA_plotBins	0	0	0
MWAS_KEGG_network	0	0	0
MWAS_KEGG_pathways	0	0	0
MWAS_KEGG_shortestpaths	0	0	0
MWAS_SummarizedExperiment	0	0	0
MWAS_barplot	1.73	0.08	1.81
MWAS_bootstrapping	7.03	0.08	7.11
MWAS_filter	0.10	0.00	0.09
MWAS_heatmap	1.59	0.12	1.72
MWAS_network	0.12	0.04	0.16
MWAS_scatterplotMS	0.96	0.43	1.41
MWAS_skylineNMR	1.78	0.00	1.78
MWAS_stats	0.81	0.03	0.84
QC_CV	1.39	0.04	1.42
QC_CV_scatterplot	1.78	0.01	1.80
QC_CV_specNMR	1.77	0.03	1.80
QC_PCA	0.02	0.00	0.02
QC_PCA_scoreplot	1.30	0.03	1.33
STOCSY_NMR	1.48	0.05	1.53
plot_spectraNMR	0.13	0.02	0.14

name	user	system	elapsed
CV_filter	1.44	0.01	1.45
JBA_binning	0	0	0
JBA_corDistribution	0	0	0
JBA_plotBins	0	0	0
MWAS_KEGG_network	0	0	0
MWAS_KEGG_pathways	0	0	0
MWAS_KEGG_shortestpaths	0	0	0
MWAS_SummarizedExperiment	0.00	0.02	0.02
MWAS_barplot	1.86	0.11	1.97
MWAS_bootstrapping	6.96	0.00	6.95
MWAS_filter	0.10	0.01	0.13
MWAS_heatmap	0.94	0.00	0.93
MWAS_network	0.13	0.00	0.13
MWAS_scatterplotMS	1	0	1
MWAS_skylineNMR	1.93	0.06	2.00
MWAS_stats	1.68	0.07	1.73
QC_CV	0.61	0.01	0.63
QC_CV_scatterplot	1.65	0.05	1.70
QC_CV_specNMR	1.36	0.00	1.36
QC_PCA	0.02	0.00	0.02
QC_PCA_scoreplot	1.01	0.00	1.01
STOCSY_NMR	1.58	0.03	1.61
plot_spectraNMR	0.08	0.00	0.08

CHECK report for MWASTools on tokay1

Summary

Command output

Installation output

Tests output

Example timings