Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:01 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for RTNduals on tokay2


To the developers/maintainers of the RTNduals package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTNduals.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.

raw results

Package 1671/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTNduals 1.18.0  (landing page)
Mauro Castro , Clarice Groeneveld
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/RTNduals
git_branch: RELEASE_3_14
git_last_commit: 04c447b
git_last_commit_date: 2021-10-26 12:32:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RTNduals
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNduals.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RTNduals_1.18.0.tar.gz
StartedAt: 2022-01-21 02:03:03 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 02:13:01 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 597.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RTNduals.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTNduals.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RTNduals_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RTNduals.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.18.0'
* 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 (user + system) or elapsed time > 5s
                               user system elapsed
mbrAssociation-methods        37.03   0.86   37.91
mbrPriorEvidenceTable-methods 37.19   0.14   37.32
mbrGet-methods                36.33   0.25   36.59
mbrPlotDuals                  33.78   0.09   33.90
tni2mbrPreprocess-methods     32.48   0.19   32.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
mbrAssociation-methods        41.09   0.53   41.64
mbrGet-methods                40.25   0.35   40.60
tni2mbrPreprocess-methods     34.05   0.09   34.14
mbrPlotDuals                  33.80   0.08   33.87
mbrPriorEvidenceTable-methods 33.26   0.09   33.36
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RTNduals_1.18.0.tar.gz && rm -rf RTNduals.buildbin-libdir && mkdir RTNduals.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTNduals.buildbin-libdir RTNduals_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RTNduals_1.18.0.zip && rm RTNduals_1.18.0.tar.gz RTNduals_1.18.0.zip
###
##############################################################################
##############################################################################


  % 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     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  607k  100  607k    0     0  1704k      0 --:--:-- --:--:-- --:--:-- 1702k

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_1.18.0.zip
* DONE (RTNduals)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RTNduals' successfully unpacked and MD5 sums checked

Tests output

RTNduals.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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'...
-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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  |======================================================================| 100%
-Assessing correlation between 2 regulons...


RUNIT TEST PROTOCOL -- Fri Jan 21 02:12:31 2022 
*********************************************** 
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 
  18.56    0.92   19.48 

RTNduals.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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("RTNduals")
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking '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...

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


RUNIT TEST PROTOCOL -- Fri Jan 21 02:12:53 2022 
*********************************************** 
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 
  20.89    0.60   21.48 

Example timings

RTNduals.Rcheck/examples_i386/RTNduals-Ex.timings

nameusersystemelapsed
mbrAssociation-methods37.03 0.8637.91
mbrGet-methods36.33 0.2536.59
mbrPlotDuals33.78 0.0933.90
mbrPlotInteraction0.060.000.07
mbrPriorEvidenceTable-methods37.19 0.1437.32
tni2mbrPreprocess-methods32.48 0.1932.71

RTNduals.Rcheck/examples_x64/RTNduals-Ex.timings

nameusersystemelapsed
mbrAssociation-methods41.09 0.5341.64
mbrGet-methods40.25 0.3540.60
mbrPlotDuals33.80 0.0833.87
mbrPlotInteraction0.050.000.05
mbrPriorEvidenceTable-methods33.26 0.0933.36
tni2mbrPreprocess-methods34.05 0.0934.14