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CHECK report for consensus on tokay2

This page was generated on 2019-04-09 12:41:17 -0400 (Tue, 09 Apr 2019).

Package 329/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensus 1.1.2
Tim Peters
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/consensus
Branch: master
Last Commit: c061e05
Last Changed Date: 2019-01-04 13:26:23 -0400 (Fri, 04 Jan 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: consensus
Version: 1.1.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensus.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings consensus_1.1.2.tar.gz
StartedAt: 2019-04-09 01:58:12 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:58:49 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 37.1 seconds
RetCode: 0
Status:  OK  
CheckDir: consensus.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:consensus.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings consensus_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/consensus.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'consensus/DESCRIPTION' ... OK
* this is package 'consensus' version '1.1.2'
* 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 'consensus' 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
** 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: OK


Installation output

consensus.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/consensus_1.1.2.tar.gz && rm -rf consensus.buildbin-libdir && mkdir consensus.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=consensus.buildbin-libdir consensus_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL consensus_1.1.2.zip && rm consensus_1.1.2.tar.gz consensus_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
100  742k  100  742k    0     0  10.2M      0 --:--:-- --:--:-- --:--:-- 11.3M

install for i386

* installing *source* package 'consensus' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'consensus'
    finding HTML links ... done
    Agilent                                 html  
    ConsensusFit-class                      html  
    Huex                                    html  
    MultiMeasure-class                      html  
    MultiMeasure                            html  
    RNASeq                                  html  
    U133A                                   html  
    consensus-internal                      html  
    consensus-package                       html  
    fitConsensus                            html  
    plotMarginals                           html  
    plotMostDiscordant                      html  
    plotOneFit                              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 'consensus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'consensus' as consensus_1.1.2.zip
* DONE (consensus)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'consensus' successfully unpacked and MD5 sums checked

Tests output

consensus.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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("consensus")


RUNIT TEST PROTOCOL -- Tue Apr 09 01:58:44 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensus RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> 
> 
>   
> 
> proc.time()
   user  system elapsed 
   0.57    0.06    0.60 

consensus.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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("consensus")


RUNIT TEST PROTOCOL -- Tue Apr 09 01:58:44 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensus RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> 
> 
>   
> 
> proc.time()
   user  system elapsed 
   0.53    0.04    0.57 

Example timings

consensus.Rcheck/examples_i386/consensus-Ex.timings

nameusersystemelapsed
Agilent0.040.000.05
Huex0.020.000.02
MultiMeasure0.020.010.03
RNASeq0.010.020.03
U133A0.020.000.02
consensus-package0.610.000.61
fitConsensus0.580.000.58
plotMarginals0.530.000.53
plotMostDiscordant0.670.010.69
plotOneFit0.050.000.04

consensus.Rcheck/examples_x64/consensus-Ex.timings

nameusersystemelapsed
Agilent0.030.010.04
Huex0.020.000.02
MultiMeasure0.030.000.03
RNASeq0.020.000.01
U133A0.020.020.03
consensus-package0.670.000.68
fitConsensus0.610.000.61
plotMarginals0.680.000.68
plotMostDiscordant0.540.000.53
plotOneFit0.040.000.05