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This page was generated on 2021-07-31 12:06:14 -0400 (Sat, 31 Jul 2021).

CHECK results for MWASTools on riesling1

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 1221/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MWASTools 1.17.0  (landing page)
Andrea Rodriguez-Martinez , Rafael Ayala
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/MWASTools
Branch: master
Last Commit: bfeddb1
Last Changed Date: 2021-05-19 12:24:36 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'KEGGgraph' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MWASTools
Version: 1.17.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MWASTools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MWASTools_1.17.0.tar.gz
StartedAt: 2021-07-31 01:23:34 -0400 (Sat, 31 Jul 2021)
EndedAt: 2021-07-31 01:29:03 -0400 (Sat, 31 Jul 2021)
EllapsedTime: 329.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MWASTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MWASTools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MWASTools_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/MWASTools.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.17.0'
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/MWASTools.Rcheck/00check.log'
for details.



Installation output

MWASTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MWASTools_1.17.0.tar.gz && rm -rf MWASTools.buildbin-libdir && mkdir MWASTools.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MWASTools.buildbin-libdir MWASTools_1.17.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MWASTools_1.17.0.zip && rm MWASTools_1.17.0.tar.gz MWASTools_1.17.0.zip
###
##############################################################################
##############################################################################


  % 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 1959k  100 1959k    0     0  6362k      0 --:--:-- --:--:-- --:--:-- 6362k

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_1.17.0.zip
* DONE (MWASTools)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'MWASTools' successfully unpacked and MD5 sums checked

Tests output

MWASTools.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 -- Sat Jul 31 01:26:44 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 
   6.31    0.42    6.71 

MWASTools.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 -- Sat Jul 31 01:26:51 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 
   6.62    0.35    7.00 

Example timings

MWASTools.Rcheck/examples_i386/MWASTools-Ex.timings

nameusersystemelapsed
CV_filter0.280.000.29
JBA_binning000
JBA_corDistribution000
JBA_plotBins000
MWAS_KEGG_network000
MWAS_KEGG_pathways000
MWAS_KEGG_shortestpaths000
MWAS_SummarizedExperiment000
MWAS_barplot0.900.020.92
MWAS_bootstrapping3.860.023.88
MWAS_filter0.080.000.08
MWAS_heatmap0.460.040.50
MWAS_network0.040.000.04
MWAS_scatterplotMS0.360.080.44
MWAS_skylineNMR0.800.030.83
MWAS_stats0.370.000.37
QC_CV0.250.020.27
QC_CV_scatterplot1.250.001.25
QC_CV_specNMR0.710.000.70
QC_PCA0.000.010.02
QC_PCA_scoreplot0.670.000.67
STOCSY_NMR0.550.020.56
plot_spectraNMR0.040.000.05

MWASTools.Rcheck/examples_x64/MWASTools-Ex.timings

nameusersystemelapsed
CV_filter0.670.050.72
JBA_binning000
JBA_corDistribution000
JBA_plotBins000
MWAS_KEGG_network000
MWAS_KEGG_pathways000
MWAS_KEGG_shortestpaths000
MWAS_SummarizedExperiment000
MWAS_barplot0.810.060.87
MWAS_bootstrapping3.370.023.39
MWAS_filter0.050.010.07
MWAS_heatmap0.390.000.39
MWAS_network0.060.000.06
MWAS_scatterplotMS0.420.000.42
MWAS_skylineNMR1.220.021.24
MWAS_stats0.910.020.92
QC_CV0.390.000.39
QC_CV_scatterplot1.060.011.08
QC_CV_specNMR0.800.030.83
QC_PCA0.020.000.01
QC_PCA_scoreplot0.810.000.81
STOCSY_NMR0.560.030.60
plot_spectraNMR0.080.020.09