Andrea Rodriguez-Martinez
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MWASTools |
| Branch: RELEASE_3_8 |
| Last Commit: 9f15823 |
| Last Changed Date: 2018-10-30 11:42:03 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:20 -0400 (Sat, 13 Apr 2019).
| Package 1031/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MWASTools 1.6.0 Andrea Rodriguez-Martinez
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MWASTools |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MWASTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MWASTools_1.6.0.tar.gz |
| StartedAt: 2019-04-13 04:06:11 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:11:27 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 316.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MWASTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MWASTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MWASTools_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MWASTools.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 or elapsed time > 5s
user system elapsed
MWAS_bootstrapping 4.98 0.13 5.11
** 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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/MWASTools.Rcheck/00check.log'
for details.
MWASTools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MWASTools_1.6.0.tar.gz && rm -rf MWASTools.buildbin-libdir && mkdir MWASTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MWASTools.buildbin-libdir MWASTools_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MWASTools_1.6.0.zip && rm MWASTools_1.6.0.tar.gz MWASTools_1.6.0.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 23.6M 0 --:--:-- --:--:-- --:--:-- 24.8M
install for i386
* installing *source* package 'MWASTools' ...
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'MWASTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MWASTools' as MWASTools_1.6.0.zip
* DONE (MWASTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MWASTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
MWASTools.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 Apr 13 04:11:14 2019
***********************************************
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
10.21 0.84 11.07
|
MWASTools.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 Apr 13 04:11:22 2019
***********************************************
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
8.01 0.28 8.29
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MWASTools.Rcheck/examples_i386/MWASTools-Ex.timings
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MWASTools.Rcheck/examples_x64/MWASTools-Ex.timings
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