Package: Rnits

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rnits.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Rnits_1.20.0.tar.gz

StartedAt: 2020-04-15 06:13:56 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:15:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 87.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rnits.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rnits.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Rnits_1.20.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Rnits.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rnits/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rnits' version '1.20.0'
* 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 'Rnits' 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
build.Rnits: no visible global function definition for 'median'
build.Rnits: no visible global function definition for 'sd'
finds0: no visible global function definition for 'rnorm'
finds0: no visible global function definition for 'quantile'
finds0: no visible global function definition for 'mad'
finds0 : <anonymous>: no visible global function definition for 'sd'
modelfit: no visible global function definition for 'hat'
ranknormalization: no visible binding for global variable 'median'
ranknormalization: no visible global function definition for
  'smooth.spline'
ranknormalization: no visible global function definition for 'predict'
ranknormalization: no visible global function definition for 'par'
solvemat: no visible global function definition for 'hat'
tsFit: no visible global function definition for 'txtProgressBar'
tsFit: no visible global function definition for 'setTxtProgressBar'
calculateGCV,Rnits: no visible global function definition for 'glm'
calculateGCV,Rnits: no visible binding for global variable 'gaussian'
fit,Rnits: no visible global function definition for 'kmeans'
fit,Rnits : <anonymous>: no visible global function definition for
  'p.adjust'
fit,Rnits: no visible global function definition for 'par'
fit,Rnits: no visible global function definition for 'hist'
getCID,Rnits: no visible global function definition for 'setNames'
getPval,Rnits: no visible global function definition for 'setNames'
getStat,Rnits: no visible global function definition for 'setNames'
plotResults,Rnits: no visible global function definition for 'aes'
plotResults,Rnits: no visible binding for global variable 'Time'
plotResults,Rnits: no visible binding for global variable 'value'
plotResults,Rnits: no visible global function definition for
  'geom_point'
plotResults,Rnits: no visible binding for global variable 'Sample'
plotResults,Rnits: no visible global function definition for
  'geom_smooth'
plotResults,Rnits: no visible global function definition for 'ylab'
plotResults,Rnits: no visible global function definition for 'theme_bw'
plotResults,Rnits: no visible global function definition for 'theme'
plotResults,Rnits: no visible global function definition for
  'scale_color_brewer'
plotResults,Rnits: no visible global function definition for
  'facet_wrap'
plotResults,Rnits: no visible global function definition for 'dev.off'
summary,Rnits: no visible global function definition for 'hist'
timeAlign,Rnits: no visible global function definition for 'quantile'
timeAlign,Rnits: no visible global function definition for 'mvfft'
timeAlign,Rnits: no visible global function definition for 'abline'
Undefined global functions or variables:
  Sample Time abline aes dev.off facet_wrap gaussian geom_point
  geom_smooth glm hat hist kmeans mad median mvfft p.adjust par predict
  quantile rnorm scale_color_brewer sd setNames setTxtProgressBar
  smooth.spline theme theme_bw txtProgressBar value ylab
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "gaussian", "glm", "hat", "kmeans", "mad",
             "median", "mvfft", "p.adjust", "predict", "quantile",
             "rnorm", "sd", "setNames", "smooth.spline")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 ... WARNING
Documented arguments not in \usage in documentation object 'plotResults':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/Rnits.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Rnits_1.20.0.tar.gz && rm -rf Rnits.buildbin-libdir && mkdir Rnits.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rnits.buildbin-libdir Rnits_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Rnits_1.20.0.zip && rm Rnits_1.20.0.tar.gz Rnits_1.20.0.zip
###
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100  321k  100  321k    0     0  6338k      0 --:--:-- --:--:-- --:--:-- 6836k

install for i386

* installing *source* package 'Rnits' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rnits'
    finding HTML links ... done
    Rnits-class                             html  
    build.Rnits                             html  
    finding level-2 HTML links ... done

    calculateGCV-methods                    html  
    extract-methods                         html  
    fit-methods                             html  
    getCID-methods                          html  
    getFitModel-methods                     html  
    getLR-methods                           html  
    getNormTwoChannel-methods               html  
    getPval-methods                         html  
    getStat-methods                         html  
    plotResults-methods                     html  
    rnits                                   html  
    summarizeProbes-methods                 html  
    summary-methods                         html  
    timeAlign-methods                       html  
    topData-methods                         html  
    yeastchemostat                          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 'Rnits' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rnits' as Rnits_1.20.0.zip
* DONE (Rnits)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Rnits' successfully unpacked and MD5 sums checked