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CHECK report for dualKS on tokay2

This page was generated on 2021-01-25 12:35:47 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE dualKS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 512/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dualKS 1.51.0
Eric J. Kort
Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/dualKS
Branch: master
Last Commit: e27f200
Last Changed Date: 2020-10-27 10:55:06 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dualKS
Version: 1.51.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dualKS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dualKS_1.51.0.tar.gz
StartedAt: 2021-01-25 04:05:16 -0500 (Mon, 25 Jan 2021)
EndedAt: 2021-01-25 04:06:32 -0500 (Mon, 25 Jan 2021)
EllapsedTime: 75.9 seconds
RetCode: 0
Status:  OK  
CheckDir: dualKS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dualKS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dualKS_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/dualKS.Rcheck'
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dualKS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dualKS' version '1.51.0'
* 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 'dualKS' 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 ... NOTE
dksPerm : gammaLL: no visible global function definition for 'dgamma'
dksPerm: no visible global function definition for 'var'
dksPerm: no visible global function definition for 'optim'
dksWeights : ag: no visible global function definition for 'aggregate'
plot,DKSPredicted-missing: no visible global function definition for
  'rainbow'
Undefined global functions or variables:
  aggregate dgamma optim rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "aggregate", "dgamma", "optim", "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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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-3.13-bioc/meat/dualKS.Rcheck/00check.log'
for details.



Installation output

dualKS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.13/bioc/src/contrib/dualKS_1.51.0.tar.gz && rm -rf dualKS.buildbin-libdir && mkdir dualKS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dualKS.buildbin-libdir dualKS_1.51.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL dualKS_1.51.0.zip && rm dualKS_1.51.0.tar.gz dualKS_1.51.0.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  161k  100  161k    0     0  3140k      0 --:--:-- --:--:-- --:--:-- 3582k

install for i386

* installing *source* package 'dualKS' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dualKS'
    finding HTML links ... done
    KS                                      html  
REDIRECT:topic	 KS -> KS.html [ SUCCESS ]
    class.DKSClassifier                     html  
REDIRECT:topic	 class:DKSClassifier -> class.DKSClassifier.html [ FAIL ]
REDIRECT:topic	 DKSClassifier -> class.DKSClassifier.html [ SUCCESS ]
REDIRECT:topic	 DKSClassifier-class -> class.DKSClassifier.html [ SUCCESS ]
REDIRECT:file	 class.DKSClassifier.html -> class.DKSClassifier.html [ SUCCESS ]
    class.DKSGeneScores                     html  
REDIRECT:topic	 class:DKSGeneScores -> class.DKSGeneScores.html [ FAIL ]
REDIRECT:topic	 DKSGeneScores -> class.DKSGeneScores.html [ SUCCESS ]
REDIRECT:topic	 DKSGeneScores-class -> class.DKSGeneScores.html [ SUCCESS ]
REDIRECT:file	 class.DKSGeneScores.html -> class.DKSGeneScores.html [ SUCCESS ]
    class.DKSGeneSet                        html  
REDIRECT:topic	 class:DKSGeneSet -> class.DKSGeneSet.html [ FAIL ]
REDIRECT:topic	 DKSGeneSet -> class.DKSGeneSet.html [ SUCCESS ]
REDIRECT:topic	 DKSGeneSet-class -> class.DKSGeneSet.html [ SUCCESS ]
REDIRECT:file	 class.DKSGeneSet.html -> class.DKSGeneSet.html [ SUCCESS ]
    class.DKSPredicted                      html  
REDIRECT:topic	 class:DKSPredicted -> class.DKSPredicted.html [ FAIL ]
REDIRECT:topic	 DKSPredicted -> class.DKSPredicted.html [ SUCCESS ]
REDIRECT:topic	 DKSPredicted-class -> class.DKSPredicted.html [ SUCCESS ]
REDIRECT:topic	 plot,DKSPredicted-method -> class.DKSPredicted.html [ SUCCESS ]
REDIRECT:topic	 plot,DKSPredicted,missing-method -> class.DKSPredicted.html [ SUCCESS ]
REDIRECT:topic	 show,DKSPredicted-method -> class.DKSPredicted.html [ SUCCESS ]
REDIRECT:topic	 summary,DKSPredicted-method -> class.DKSPredicted.html [ SUCCESS ]
REDIRECT:file	 class.DKSPredicted.html -> class.DKSPredicted.html [ SUCCESS ]
    dks                                     html  
REDIRECT:topic	 dks -> dks.html [ SUCCESS ]
REDIRECT:topic	 eset -> dks.html [ SUCCESS ]
REDIRECT:topic	 pv.f -> dks.html [ SUCCESS ]
REDIRECT:topic	 pvr.f -> dks.html [ SUCCESS ]
    dksClassify                             html  
REDIRECT:topic	 dksClassify -> dksClassify.html [ SUCCESS ]
    dksCustomClass                          html  
REDIRECT:topic	 dksCustomClass -> dksCustomClass.html [ SUCCESS ]
    dksPerm                                 html  
REDIRECT:topic	 dksPerm -> dksPerm.html [ SUCCESS ]
    dksSelectGenes                          html  
REDIRECT:topic	 dksSelectGenes -> dksSelectGenes.html [ SUCCESS ]
    dksTrain                                html  
REDIRECT:topic	 dksTrain -> dksTrain.html [ SUCCESS ]
    dksWeights                              html  
REDIRECT:topic	 dksWeights -> dksWeights.html [ SUCCESS ]
    dualKS-package                          html  
REDIRECT:topic	 dualKS-package -> dualKS-package.html [ SUCCESS ]
REDIRECT:topic	 dualKS -> dualKS-package.html [ SUCCESS ]
** 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 'dualKS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dualKS' as dualKS_1.51.0.zip
* DONE (dualKS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'dualKS' successfully unpacked and MD5 sums checked

Tests output


Example timings

dualKS.Rcheck/examples_i386/dualKS-Ex.timings

nameusersystemelapsed
KS1.510.001.52
dksClassify0.750.020.76
dksCustomClass0.010.000.01
dksPerm0.770.000.77
dksSelectGenes0.720.000.72
dksTrain0.70.00.7
dksWeights1.580.001.58

dualKS.Rcheck/examples_x64/dualKS-Ex.timings

nameusersystemelapsed
KS2.530.012.55
dksClassify1.270.001.27
dksCustomClass0.020.000.02
dksPerm1.200.001.21
dksSelectGenes1.090.001.09
dksTrain0.990.001.03
dksWeights2.310.002.31