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CHECK report for RTNduals on tokay2

This page was generated on 2019-10-16 12:37:44 -0400 (Wed, 16 Oct 2019).

Package 1432/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTNduals 1.8.3
Mauro Castro , Clarice Groeneveld
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RTNduals
Branch: RELEASE_3_9
Last Commit: 540b93c
Last Changed Date: 2019-08-29 11:00:37 -0400 (Thu, 29 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTNduals
Version: 1.8.3
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNduals.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTNduals_1.8.3.tar.gz
StartedAt: 2019-10-16 06:49:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:58:41 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 554.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RTNduals.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNduals.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTNduals_1.8.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTNduals.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTNduals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTNduals' version '1.8.3'
* 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 'RTNduals' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
mbrAssociation-methods        35.32   0.81   37.39
mbrGet-methods                30.25   1.10   31.51
mbrPlotDuals                  29.49   0.68   30.20
tni2mbrPreprocess-methods     28.93   0.90   29.84
mbrPriorEvidenceTable-methods 26.22   0.94   27.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
mbrPriorEvidenceTable-methods 34.94   1.14   36.08
mbrPlotDuals                  29.83   1.12   31.00
mbrAssociation-methods        28.80   1.36   30.16
tni2mbrPreprocess-methods     28.22   1.28   29.50
mbrGet-methods                28.29   1.18   29.49
* 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: OK


Installation output

RTNduals.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RTNduals_1.8.3.tar.gz && rm -rf RTNduals.buildbin-libdir && mkdir RTNduals.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTNduals.buildbin-libdir RTNduals_1.8.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RTNduals_1.8.3.zip && rm RTNduals_1.8.3.tar.gz RTNduals_1.8.3.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  192k  100  192k    0     0  3031k      0 --:--:-- --:--:-- --:--:-- 3440k

install for i386

* installing *source* package 'RTNduals' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTNduals'
    finding HTML links ... done
    MBR-class                               html  
    RTNduals-package                        html  
    mbrAssociation-methods                  html  
    mbrGet-methods                          html  
    mbrPlotDuals                            html  
    mbrPlotInteraction                      html  
    mbrPriorEvidenceTable-methods           html  
    tni2mbrPreprocess-methods               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 'RTNduals' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTNduals' as RTNduals_1.8.3.zip
* DONE (RTNduals)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RTNduals' successfully unpacked and MD5 sums checked

Tests output

RTNduals.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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("RTNduals")
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
--Checking 'regulatoryElements' in 'expData'...
-Preprocessing complete!

-Performing permutation analysis...
--For 2 regulons...

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-Permutation analysis complete! 

-Performing bootstrap analysis...
--For 2 regulons...

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-Bootstrap analysis complete! 

-Applying dpi filter...
-DPI filter complete! 

-Checking regulons and regulatory elements...
-Extrating inferred regulatory associations...
-Mapping network triplets between regulons...
-Assessing overlap between 2 regulons...

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-Assessing correlation between 2 regulons...


RUNIT TEST PROTOCOL -- Wed Oct 16 06:58:17 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RTNduals RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning message:
No 'dual regulon' has been observed for the input parameters. 
> 
> proc.time()
   user  system elapsed 
  21.09    1.01   22.09 

RTNduals.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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("RTNduals")
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
--Checking 'regulatoryElements' in 'expData'...
-Preprocessing complete!

-Performing permutation analysis...
--For 2 regulons...

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-Permutation analysis complete! 

-Performing bootstrap analysis...
--For 2 regulons...

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  |======================================================================| 100%
-Bootstrap analysis complete! 

-Applying dpi filter...
-DPI filter complete! 

-Checking regulons and regulatory elements...
-Extrating inferred regulatory associations...
-Mapping network triplets between regulons...
-Assessing overlap between 2 regulons...

  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
-Assessing correlation between 2 regulons...


RUNIT TEST PROTOCOL -- Wed Oct 16 06:58:36 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RTNduals RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning message:
No 'dual regulon' has been observed for the input parameters. 
> 
> proc.time()
   user  system elapsed 
  17.89    0.73   18.62 

Example timings

RTNduals.Rcheck/examples_i386/RTNduals-Ex.timings

nameusersystemelapsed
mbrAssociation-methods35.32 0.8137.39
mbrGet-methods30.25 1.1031.51
mbrPlotDuals29.49 0.6830.20
mbrPlotInteraction0.030.020.05
mbrPriorEvidenceTable-methods26.22 0.9427.16
tni2mbrPreprocess-methods28.93 0.9029.84

RTNduals.Rcheck/examples_x64/RTNduals-Ex.timings

nameusersystemelapsed
mbrAssociation-methods28.80 1.3630.16
mbrGet-methods28.29 1.1829.49
mbrPlotDuals29.83 1.1231.00
mbrPlotInteraction0.040.000.05
mbrPriorEvidenceTable-methods34.94 1.1436.08
tni2mbrPreprocess-methods28.22 1.2829.50