Package: SVM2CRM

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SVM2CRM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SVM2CRM_1.16.0.tar.gz

StartedAt: 2019-10-16 07:27:32 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:42:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 896.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SVM2CRM.Rcheck

Warnings: 3

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SVM2CRM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SVM2CRM_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SVM2CRM.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SVM2CRM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SVM2CRM' version '1.16.0'
* 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 'SVM2CRM' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'SVM2CRM' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SVM2CRM.Rcheck/00install.out' for details.
* 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
cisREfindbed: no visible global function definition for 'as'
createBed: no visible global function definition for 'write.table'
featSelectionWithKmeans: no visible global function definition for
  'kmeans'
featSelectionWithKmeans: no visible global function definition for
  'dist'
featSelectionWithKmeans: no visible global function definition for
  'hclust'
featSelectionWithKmeans: no visible global function definition for
  'pdf'
featSelectionWithKmeans: no visible global function definition for
  'par'
featSelectionWithKmeans: no visible global function definition for
  'axis'
featSelectionWithKmeans: no visible global function definition for
  'abline'
featSelectionWithKmeans: no visible global function definition for
  'dev.off'
getSignal: no visible global function definition for 'read.table'
getSignal: no visible global function definition for 'as'
plotROC: no visible global function definition for 'predict'
plotROC: no visible global function definition for 'pdf'
plotROC: no visible global function definition for 'dev.off'
predictionGW: no visible global function definition for 'predict'
smoothInputFS: no visible global function definition for 'na.omit'
tuningParametersCombROC: no visible global function definition for
  'combn'
tuningParametersCombROC: no visible global function definition for
  'txtProgressBar'
tuningParametersCombROC: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  abline as axis combn dev.off dist hclust kmeans na.omit par pdf
  predict read.table setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "par")
  importFrom("methods", "as")
  importFrom("stats", "dist", "hclust", "kmeans", "na.omit", "predict")
  importFrom("utils", "combn", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SVM2CRMdata/extdata', resetting
* 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: 3 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SVM2CRM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SVM2CRM_1.16.0.tar.gz && rm -rf SVM2CRM.buildbin-libdir && mkdir SVM2CRM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SVM2CRM.buildbin-libdir SVM2CRM_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SVM2CRM_1.16.0.zip && rm SVM2CRM_1.16.0.tar.gz SVM2CRM_1.16.0.zip
###
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install for i386

* installing *source* package 'SVM2CRM' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SVM2CRM'
    finding HTML links ... done
    cisREfindbed                            html  
    createBed                               html  
    createSVMinput                          html  
    featSelectionWithKmeans                 html  
    findFeatureOverlap                      html  
    frequencyHM                             html  
    getSignal                               html  
    performanceSVM                          html  
    plotFscore                              html  
    plotROC                                 html  
    predictionGW                            html  
    smoothInputFS                           html  
    tuningParametersCombROC                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'SVM2CRM' is deprecated and will be removed from Bioconductor
  version 3.10
** testing if installed package can be loaded from final location
Warning: Package 'SVM2CRM' is deprecated and will be removed from Bioconductor
  version 3.10
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SVM2CRM' ...
** testing if installed package can be loaded
Warning: Package 'SVM2CRM' is deprecated and will be removed from Bioconductor
  version 3.10
* MD5 sums
packaged installation of 'SVM2CRM' as SVM2CRM_1.16.0.zip
* DONE (SVM2CRM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SVM2CRM' successfully unpacked and MD5 sums checked