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CHECK report for CAnD on tokay1

This page was generated on 2018-04-12 13:26:13 -0400 (Thu, 12 Apr 2018).

Package 179/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAnD 1.10.0
Caitlin McHugh
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CAnD
Branch: RELEASE_3_6
Last Commit: 170c88c
Last Changed Date: 2017-10-30 12:40:51 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAnD
Version: 1.10.0
Command: rm -rf CAnD.buildbin-libdir CAnD.Rcheck && mkdir CAnD.buildbin-libdir CAnD.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAnD.buildbin-libdir CAnD_1.10.0.tar.gz >CAnD.Rcheck\00install.out 2>&1 && cp CAnD.Rcheck\00install.out CAnD-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CAnD.buildbin-libdir --install="check:CAnD-install.out" --force-multiarch --no-vignettes --timings CAnD_1.10.0.tar.gz
StartedAt: 2018-04-11 22:41:19 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:42:02 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 42.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CAnD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CAnD.buildbin-libdir CAnD.Rcheck && mkdir CAnD.buildbin-libdir CAnD.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAnD.buildbin-libdir CAnD_1.10.0.tar.gz >CAnD.Rcheck\00install.out 2>&1 && cp CAnD.Rcheck\00install.out CAnD-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CAnD.buildbin-libdir --install="check:CAnD-install.out" --force-multiarch --no-vignettes --timings CAnD_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CAnD.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAnD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAnD' version '1.10.0'
* 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 'CAnD' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
CAnD : pairedTtest: no visible global function definition for 't.test'
barPlotAncest: no visible binding for global variable 'id'
barPlotAncest: no visible binding for global variable 'value'
barPlotAncest: no visible binding for global variable 'variable'
calc_combP: no visible binding for global variable 'var'
calc_combP: no visible global function definition for 'pchisq'
plotPvals: no visible binding for global variable 'numPs'
plotPvals: no visible binding for global variable 'pval'
Undefined global functions or variables:
  id numPs pchisq pval t.test value var variable
Consider adding
  importFrom("stats", "pchisq", "t.test", "var")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CAnD.Rcheck/00check.log'
for details.



Installation output

CAnD.Rcheck/00install.out


install for i386

* installing *source* package 'CAnD' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CAnD'
    finding HTML links ... done
    BonfCorr-method                         html  
    CAnD                                    html  
    CAnDResult-class                        html  
    ancestries                              html  
    barPlotAncest                           html  
    calc_combP                              html  
    getDiffMatrices                         html  
    overallStatistic-method                 html  
    overallpValue-method                    html  
    pValues-method                          html  
    plotPvals                               html  
    test-method                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CAnD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAnD' as CAnD_1.10.0.zip
* DONE (CAnD)
In R CMD INSTALL
In R CMD INSTALL

Tests output

CAnD.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("CAnD")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:41:56 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CAnD RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.93    0.00    0.92 

CAnD.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("CAnD")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:41:58 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CAnD RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.12    0.03    1.15 

Example timings

CAnD.Rcheck/examples_i386/CAnD-Ex.timings

nameusersystemelapsed
BonfCorr-method0.080.000.08
CAnD0.060.010.08
CAnDResult-class000
barPlotAncest000
calc_combP0.010.000.02
overallStatistic-method0.020.000.01
overallpValue-method000
pValues-method0.020.000.02
plotPvals0.030.000.03
test-method000

CAnD.Rcheck/examples_x64/CAnD-Ex.timings

nameusersystemelapsed
BonfCorr-method0.110.000.11
CAnD0.120.020.14
CAnDResult-class000
barPlotAncest000
calc_combP0.030.000.03
overallStatistic-method0.010.000.02
overallpValue-method0.040.000.03
pValues-method0.010.000.02
plotPvals0.050.010.06
test-method0.010.000.01