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CHECK report for CeTF on tokay1

This page was generated on 2020-08-06 12:10:50 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CeTF PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 252/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CeTF 1.1.2
Carlos Alberto Oliveira de Biagi Junior
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/CeTF
Branch: master
Last Commit: c01e721
Last Changed Date: 2020-05-31 13:38:17 -0400 (Sun, 31 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CeTF
Version: 1.1.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CeTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CeTF_1.1.2.tar.gz
StartedAt: 2020-08-06 06:10:07 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 06:19:08 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 540.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CeTF.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CeTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CeTF_1.1.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CeTF.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CeTF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CeTF' version '1.1.2'
* 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 'CeTF' 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
netConditionsPlot 5.61   0.10    5.72
runAnalysis       5.49   0.00    5.48
clustCoef         4.89   0.23    5.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
clustCoefPercentage 9.53   0.00    9.53
clustCoef           9.44   0.02    9.45
netConditionsPlot   9.10   0.05    9.15
runAnalysis         7.04   0.01    7.06
* 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

CeTF.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CeTF_1.1.2.tar.gz && rm -rf CeTF.buildbin-libdir && mkdir CeTF.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CeTF.buildbin-libdir CeTF_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CeTF_1.1.2.zip && rm CeTF_1.1.2.tar.gz CeTF_1.1.2.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
  0 1267k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1267k  100 1267k    0     0  26.9M      0 --:--:-- --:--:-- --:--:-- 28.7M

install for i386

* installing *source* package 'CeTF' ...
** 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 'CeTF'
    finding HTML links ... done
    CeTF-class                              html  
    CeTFdemo                                html  
    CircosTargets                           html  
    InputData-methods                       html  
    NetworkData-methods                     html  
    OutputData-methods                      html  
    PCIT                                    html  
    RIF                                     html  
    RIFPlot                                 html  
    RIF_input                               html  
    SmearPlot                               html  
    TFs                                     html  
    bivar.awk                               html  
    clustCoef                               html  
    clustCoefPercentage                     html  
    densityPlot                             html  
    diffusion                               html  
    enrichPlot                              html  
    enrichdemo                              html  
    expDiff                                 html  
    getDE-methods                           html  
    getData-methods                         html  
    getEnrich                               html  
    getGroupGO                              html  
    heatPlot                                html  
    histPlot                                html  
    netConditionsPlot                       html  
    netGOTFPlot                             html  
    normExp                                 html  
    refGenes                                html  
    runAnalysis                             html  
    simCounts                               html  
    simNorm                                 html  
    tolerance                               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 'CeTF' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CeTF' as CeTF_1.1.2.zip
* DONE (CeTF)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CeTF' successfully unpacked and MD5 sums checked

Tests output

CeTF.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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("CeTF")

========================================
CeTF version 1.1.2
Bioconductor page: http://bioconductor.org/packages/CeTF/
Github page: https://github.com/cbiagii/CeTF or https://cbiagii.github.io/CeTF/
Documentation: http://bioconductor.org/packages/CeTF/
If you use it in published research, please cite:

Carlos Alberto Oliveira de Biagi Junior, Ricardo Perecin Nociti, Breno Osvaldo 
Funicheli, Patricia de Cassia Ruy, Joao Paulo Bianchi Ximenez, Wilson A Silva Jr.
CeTF: an R package to Coexpression for Transcription Factors using Regulatory 
Impact Factors (RIF) and Partial Correlation and Information (PCIT) analysis.
bioRxiv. 2020, DOI: 10.1101/2020.03.30.015784
========================================

> test_check("CeTF")
== testthat results  ===========================================================
[ OK: 43 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.85    1.20   14.14 

CeTF.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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("CeTF")

========================================
CeTF version 1.1.2
Bioconductor page: http://bioconductor.org/packages/CeTF/
Github page: https://github.com/cbiagii/CeTF or https://cbiagii.github.io/CeTF/
Documentation: http://bioconductor.org/packages/CeTF/
If you use it in published research, please cite:

Carlos Alberto Oliveira de Biagi Junior, Ricardo Perecin Nociti, Breno Osvaldo 
Funicheli, Patricia de Cassia Ruy, Joao Paulo Bianchi Ximenez, Wilson A Silva Jr.
CeTF: an R package to Coexpression for Transcription Factors using Regulatory 
Impact Factors (RIF) and Partial Correlation and Information (PCIT) analysis.
bioRxiv. 2020, DOI: 10.1101/2020.03.30.015784
========================================

> test_check("CeTF")
== testthat results  ===========================================================
[ OK: 43 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  19.62    0.89   21.62 

Example timings

CeTF.Rcheck/examples_i386/CeTF-Ex.timings

nameusersystemelapsed
CeTFdemo000
CircosTargets000
InputData-methods0.810.000.82
NetworkData-methods0.040.000.03
OutputData-methods0.010.030.04
PCIT0.420.130.55
RIF0.440.170.61
RIFPlot0.800.060.86
RIF_input000
SmearPlot1.610.161.76
TFs000
bivar.awk0.010.000.02
clustCoef4.890.235.13
clustCoefPercentage4.720.004.71
densityPlot1.450.001.46
diffusion000
enrichPlot0.540.020.54
enrichdemo000
expDiff0.260.010.29
getDE-methods0.020.020.03
getData-methods0.040.000.04
getEnrich000
getGroupGO000
heatPlot1.360.021.38
histPlot1.110.001.11
netConditionsPlot5.610.105.72
netGOTFPlot000
normExp0.140.050.18
refGenes000
runAnalysis5.490.005.48
simCounts000
simNorm000
tolerance000

CeTF.Rcheck/examples_x64/CeTF-Ex.timings

nameusersystemelapsed
CeTFdemo000
CircosTargets000
InputData-methods0.050.000.05
NetworkData-methods0.080.000.07
OutputData-methods0.040.000.05
PCIT0.770.130.89
RIF1.030.111.14
RIFPlot1.630.011.64
RIF_input0.000.020.02
SmearPlot2.200.052.25
TFs0.000.010.01
bivar.awk0.010.000.02
clustCoef9.440.029.45
clustCoefPercentage9.530.009.53
densityPlot2.770.002.79
diffusion000
enrichPlot1.090.011.11
enrichdemo0.000.020.01
expDiff0.660.000.66
getDE-methods0.030.000.03
getData-methods0.020.010.03
getEnrich000
getGroupGO000
heatPlot1.840.001.84
histPlot1.420.001.43
netConditionsPlot9.100.059.15
netGOTFPlot000
normExp0.110.020.13
refGenes000
runAnalysis7.040.017.06
simCounts0.000.020.02
simNorm000
tolerance000