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CHECK report for MetNet on tokay2

This page was generated on 2020-10-17 11:57:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MetNet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1069/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetNet 1.6.0
Thomas Naake
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MetNet
Branch: RELEASE_3_11
Last Commit: 8c187e6
Last Changed Date: 2020-04-27 15:18:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MetNet
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MetNet_1.6.0.tar.gz
StartedAt: 2020-10-17 05:59:29 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:03:18 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 228.9 seconds
RetCode: 0
Status:  OK  
CheckDir: MetNet.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MetNet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MetNet.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetNet' version '1.6.0'
* 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 'MetNet' 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 ... OK
* 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
MetNet-package 67.85   0.05    67.9
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MetNet-package 61.04   0.01   61.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: OK


Installation output

MetNet.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MetNet_1.6.0.tar.gz && rm -rf MetNet.buildbin-libdir && mkdir MetNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetNet.buildbin-libdir MetNet_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MetNet_1.6.0.zip && rm MetNet_1.6.0.tar.gz MetNet_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 3515k  100 3515k    0     0  37.5M      0 --:--:-- --:--:-- --:--:-- 40.3M

install for i386

* installing *source* package 'MetNet' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MetNet'
    finding HTML links ... done
    MetNet-package                          html  
    addToList                               html  
    aracne                                  html  
    bayes                                   html  
    clr                                     html  
    combine                                 html  
    correlation                             html  
    getLinks                                html  
    lasso                                   html  
    mat_test                                html  
    mat_test_z                              html  
    peaklist                                html  
    randomForest                            html  
    rtCorrection                            html  
    statistical                             html  
    structural                              html  
    threeDotsCall                           html  
    threshold                               html  
    topKnet                                 html  
    x_test                                  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 'MetNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetNet' as MetNet_1.6.0.zip
* DONE (MetNet)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MetNet' successfully unpacked and MD5 sums checked

Tests output

MetNet.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library("testthat")
> library("MetNet")
> 
> test_check("MetNet")
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."
[1] "randomForest finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "pearson_partial finished."
[1] "pearson_semipartial finished."
[1] "spearman finished."
[1] "spearman_partial finished."
[1] "spearman_semipartial finished."
[1] "bayes finished."
== testthat results  ===========================================================
[ OK: 281 | SKIPPED: 0 | WARNINGS: 20 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   6.48    0.12   12.37 

MetNet.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library("testthat")
> library("MetNet")
> 
> test_check("MetNet")
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."
[1] "randomForest finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "pearson_partial finished."
[1] "pearson_semipartial finished."
[1] "spearman finished."
[1] "spearman_partial finished."
[1] "spearman_semipartial finished."
[1] "bayes finished."
== testthat results  ===========================================================
[ OK: 281 | SKIPPED: 0 | WARNINGS: 20 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   6.31    0.21   12.60 

Example timings

MetNet.Rcheck/examples_i386/MetNet-Ex.timings

nameusersystemelapsed
MetNet-package67.85 0.0567.90
addToList0.010.000.02
aracne0.250.050.55
bayes2.210.002.20
clr0.470.030.28
combine0.180.030.22
correlation0.020.000.01
getLinks000
lasso000
randomForest2.160.122.29
rtCorrection000
statistical0.010.000.01
structural000
threeDotsCall000
threshold0.030.000.03
topKnet000

MetNet.Rcheck/examples_x64/MetNet-Ex.timings

nameusersystemelapsed
MetNet-package61.04 0.0161.06
addToList000
aracne0.410.020.34
bayes2.450.002.46
clr0.420.030.25
combine0.160.000.15
correlation0.010.000.02
getLinks000
lasso000
randomForest1.860.061.92
rtCorrection000
statistical0.030.000.03
structural000
threeDotsCall000
threshold0.050.000.05
topKnet000