Package: anota

Version: 1.30.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:anota.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings anota_1.30.0.tar.gz

StartedAt: 2019-04-13 00:31:09 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:33:42 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 152.5 seconds

RetCode: 0

Status:  OK

CheckDir: anota.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:anota.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings anota_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/anota.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'anota/DESCRIPTION' ... OK
* this is package 'anota' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'anota' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'qvalue'
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: 'qvalue'
  All declared Imports should be used.
Package in Depends field not imported from: 'qvalue'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
anotaAdjustPvalsQ: no visible global function definition for 'qvalue'
anotaDfbsSummaryFull: no visible global function definition for 'pdf'
anotaDfbsSummaryFull: no visible global function definition for
  'barplot'
anotaDfbsSummaryFull: no visible global function definition for
  'legend'
anotaDfbsSummaryFull: no visible global function definition for 'text'
anotaDfbsSummaryFull: no visible global function definition for
  'dev.off'
anotaDfbsSummaryOnly: no visible global function definition for 'lm'
anotaDfbsSummaryOnly: no visible global function definition for
  'dfbetas'
anotaGetSigGenes: no visible global function definition for
  'contrasts<-'
anotaGetSigGenes: no visible global function definition for
  'txtProgressBar'
anotaGetSigGenes: no visible global function definition for 'lm'
anotaGetSigGenes: no visible global function definition for 'anova'
anotaGetSigGenes: no visible global function definition for
  'setTxtProgressBar'
anotaGetSigGenes: no visible global function definition for 'pf'
anotaGetSigGenes: no visible global function definition for 'jpeg'
anotaGetSigGenes: no visible global function definition for 'par'
anotaGetSigGenes: no visible global function definition for 'dev.off'
anotaGetab : flik: no visible global function definition for 'df'
anotaGetab: no visible global function definition for 'nlm'
anotaPerformQc: no visible global function definition for 'pdf'
anotaPerformQc: no visible global function definition for 'par'
anotaPerformQc: no visible global function definition for
  'txtProgressBar'
anotaPerformQc: no visible global function definition for
  'setTxtProgressBar'
anotaPerformQc: no visible global function definition for 'lm'
anotaPerformQc: no visible global function definition for 'anova'
anotaPerformQc: no visible global function definition for 'dfbetas'
anotaPerformQc: no visible global function definition for 'dev.off'
anotaPerformQc: no visible global function definition for 'jpeg'
anotaPerformRVM: no visible global function definition for 'pf'
anotaPlotIGFit: no visible global function definition for 'pf'
anotaPlotIGFit: no visible global function definition for 'rf'
anotaPlotIGFit: no visible global function definition for 'qqplot'
anotaPlotIGFit: no visible global function definition for 'abline'
anotaPlotIGFit: no visible global function definition for 'ks.test'
anotaPlotIGFit: no visible global function definition for 'lines'
anotaPlotIGFit: no visible global function definition for 'legend'
anotaPlotIntPvals: no visible global function definition for 'pdf'
anotaPlotIntPvals: no visible global function definition for 'par'
anotaPlotIntPvals: no visible global function definition for 'density'
anotaPlotIntPvals: no visible global function definition for 'hist'
anotaPlotIntPvals: no visible global function definition for 'dev.off'
anotaPlotSigGenes: no visible global function definition for 'pdf'
anotaPlotSigGenes: no visible global function definition for 'par'
anotaPlotSigGenes: no visible global function definition for 'text'
anotaPlotSigGenes: no visible global function definition for 'lines'
anotaPlotSigGenes: no visible global function definition for 'dev.off'
anotaPlotSingleRegression: no visible global function definition for
  'text'
anotaPlotSingleRegression: no visible global function definition for
  'lines'
anotaResidOutlierPlot: no visible global function definition for
  'matplot'
anotaResidOutlierPlot: no visible global function definition for 'par'
anotaResidOutlierPlot: no visible global function definition for
  'segments'
anotaResidOutlierPlot: no visible global function definition for 'axis'
anotaResidOutlierPlot: no visible global function definition for 'box'
anotaResidOutlierPlot: no visible global function definition for
  'mtext'
anotaResidOutlierPlotAll: no visible global function definition for
  'points'
anotaResidOutlierPlotAll: no visible global function definition for
  'text'
anotaResidOutlierPlotAll: no visible global function definition for
  'segments'
anotaResidOutlierTest: no visible global function definition for 'pdf'
anotaResidOutlierTest: no visible global function definition for 'par'
anotaResidOutlierTest: no visible global function definition for
  'txtProgressBar'
anotaResidOutlierTest: no visible global function definition for
  'setTxtProgressBar'
anotaResidOutlierTest: no visible global function definition for
  'rnorm'
anotaResidOutlierTest: no visible global function definition for
  'qqnorm'
anotaResidOutlierTest: no visible global function definition for
  'dev.off'
anotaResidOutlierTest: no visible global function definition for 'jpeg'
anotaSimDfbs: no visible global function definition for
  'txtProgressBar'
anotaSimDfbs: no visible global function definition for
  'setTxtProgressBar'
anotaSimDfbs: no visible global function definition for 'rnorm'
anotaSimDfbs: no visible global function definition for 'cor'
anotaSimDfbs: no visible global function definition for 'median'
anotaSlopeTest: no visible global function definition for 'pt'
getSummaryDfb: no visible binding for global variable 'IQR'
Undefined global functions or variables:
  IQR abline anova axis barplot box contrasts<- cor density dev.off df
  dfbetas hist jpeg ks.test legend lines lm matplot median mtext nlm
  par pdf pf points pt qqnorm qqplot qvalue rf rnorm segments
  setTxtProgressBar text txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "box", "hist",
             "legend", "lines", "matplot", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "IQR", "anova", "contrasts<-", "cor", "density",
             "df", "dfbetas", "ks.test", "lm", "median", "nlm", "pf",
             "pt", "qqnorm", "qqplot", "rf", "rnorm")
  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 ... 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
Examples with CPU or elapsed time > 5s
                   user system elapsed
anotaPlotSigGenes 11.09   0.22   11.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
anotaPlotSigGenes 13.38   0.09    13.6
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/anota.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/anota_1.30.0.tar.gz && rm -rf anota.buildbin-libdir && mkdir anota.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=anota.buildbin-libdir anota_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL anota_1.30.0.zip && rm anota_1.30.0.tar.gz anota_1.30.0.zip
###
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install for i386

* installing *source* package 'anota' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'anota'
    finding HTML links ... done
    anotaDataSet                            html  
    anotaGetSigGenes                        html  
    anotaPerformQc                          html  
    anotaPlotSigGenes                       html  
    anotaResidOutlierTest                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'anota' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'anota' as anota_1.30.0.zip
* DONE (anota)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'anota' successfully unpacked and MD5 sums checked
In R CMD INSTALL