| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:08 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1264/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MWASTools 1.19.1 (landing page) Andrea Rodriguez-Martinez
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MWASTools |
| Version: 1.19.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MWASTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MWASTools_1.19.1.tar.gz |
| StartedAt: 2022-03-17 19:42:08 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:45:14 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 186.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MWASTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MWASTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MWASTools_1.19.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MWASTools.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.19.1'
* 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
* 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
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/MWASTools.Rcheck/00check.log'
for details.
MWASTools.Rcheck/00install.out
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MWASTools
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* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (MWASTools)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'hypeR' is missing or broken
done
MWASTools.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 Mar 17 19:45:04 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
8.09 0.64 8.70
MWASTools.Rcheck/MWASTools-Ex.timings
| name | user | system | elapsed | |
| CV_filter | 0.31 | 0.10 | 0.40 | |
| 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 | 0.01 | 0.00 | 0.02 | |
| MWAS_barplot | 1.27 | 0.09 | 1.36 | |
| MWAS_bootstrapping | 4.03 | 0.05 | 4.08 | |
| MWAS_filter | 0.06 | 0.00 | 0.06 | |
| MWAS_heatmap | 0.38 | 0.04 | 0.42 | |
| MWAS_network | 0.04 | 0.00 | 0.05 | |
| MWAS_scatterplotMS | 0.74 | 0.05 | 0.78 | |
| MWAS_skylineNMR | 0.86 | 0.05 | 0.90 | |
| MWAS_stats | 0.39 | 0.04 | 0.44 | |
| QC_CV | 0.3 | 0.0 | 0.3 | |
| QC_CV_scatterplot | 0.87 | 0.04 | 0.91 | |
| QC_CV_specNMR | 1.28 | 0.01 | 1.29 | |
| QC_PCA | 0.00 | 0.02 | 0.02 | |
| QC_PCA_scoreplot | 0.75 | 0.04 | 0.79 | |
| STOCSY_NMR | 0.69 | 0.03 | 0.72 | |
| plot_spectraNMR | 0.05 | 0.00 | 0.05 | |