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CHECK report for dualKS on tokay1

This page was generated on 2021-01-19 11:55:10 -0500 (Tue, 19 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 515/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dualKS 1.50.0
Eric J. Kort
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/dualKS
Branch: RELEASE_3_12
Last Commit: 5eb36a6
Last Changed Date: 2020-10-27 10:55:06 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dualKS
Version: 1.50.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dualKS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings dualKS_1.50.0.tar.gz
StartedAt: 2021-01-19 02:35:47 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 02:36:58 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 70.2 seconds
RetCode: 0
Status:  OK  
CheckDir: dualKS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dualKS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings dualKS_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/dualKS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.50.0'
* 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-3.12-bioc/meat/dualKS.Rcheck/00check.log'
for details.



Installation output

dualKS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/dualKS_1.50.0.tar.gz && rm -rf dualKS.buildbin-libdir && mkdir dualKS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dualKS.buildbin-libdir dualKS_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL dualKS_1.50.0.zip && rm dualKS_1.50.0.tar.gz dualKS_1.50.0.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  161k  100  161k    0     0  4297k      0 --:--:-- --:--:-- --:--:-- 4898k

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  
    class.DKSClassifier                     html  
    class.DKSGeneScores                     html  
    class.DKSGeneSet                        html  
    class.DKSPredicted                      html  
    dks                                     html  
    dksClassify                             html  
    dksCustomClass                          html  
    dksPerm                                 html  
    dksSelectGenes                          html  
    dksTrain                                html  
    dksWeights                              html  
    dualKS-package                          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 'dualKS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dualKS' as dualKS_1.50.0.zip
* DONE (dualKS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'dualKS' successfully unpacked and MD5 sums checked

Tests output


Example timings

dualKS.Rcheck/examples_i386/dualKS-Ex.timings

nameusersystemelapsed
KS1.710.021.72
dksClassify0.870.010.89
dksCustomClass0.010.000.02
dksPerm1.080.001.08
dksSelectGenes0.880.020.89
dksTrain0.780.020.79
dksWeights2.330.002.33

dualKS.Rcheck/examples_x64/dualKS-Ex.timings

nameusersystemelapsed
KS2.390.002.40
dksClassify0.870.000.87
dksCustomClass0.010.000.01
dksPerm0.990.011.00
dksSelectGenes1.400.001.41
dksTrain0.930.000.92
dksWeights2.340.022.36