Package: qusage

Version: 2.16.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qusage.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings qusage_2.16.1.tar.gz

StartedAt: 2019-04-13 04:49:18 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:52:33 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 195.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: qusage.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qusage.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings qusage_2.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/qusage.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 'qusage/DESCRIPTION' ... OK
* this is package 'qusage' version '2.16.1'
* 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 'qusage' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/calcVIF.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/makeComparison.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/qgen.Rd:21: file link 'corStruct' in package 'nlme' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/qusage.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/qusage.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
absoluteTest : <anonymous>: no visible global function definition for
  'pchisq'
absoluteTest.genePvals: no visible global function definition for 'qt'
absoluteTest.genePvals: no visible global function definition for
  'approx'
absoluteTest.genePvals: no visible global function definition for 'dt'
absoluteTest.genePvals: no visible global function definition for
  'pnorm'
absoluteTest.genePvals: no visible global function definition for 'pt'
absoluteTest.genePvalsFAST : <anonymous>: no visible global function
  definition for 'pt'
aggregateGeneSet: no visible global function definition for 'qt'
aggregateGeneSet : <anonymous>: no visible global function definition
  for 'dt'
calcPCor: no visible global function definition for 'model.matrix'
calcPCor: no visible global function definition for 'formula'
calcPCor : <anonymous>: no visible global function definition for 'cov'
calcVIF: no visible global function definition for 'model.matrix'
calcVIF: no visible global function definition for 'formula'
calcVIF : <anonymous>: no visible global function definition for 'cov'
combinePDFs : <anonymous> : <anonymous>: no visible global function
  definition for 'approx'
combinePDFs : <anonymous>: no visible global function definition for
  'approx'
compareTwoDistsFaster: no visible global function definition for
  'runif'
getExAbs: no visible global function definition for 'approx'
homogeneityScore : <anonymous>: no visible global function definition
  for 'pchisq'
makeComparison: no visible global function definition for
  'model.matrix'
makeComparison: no visible global function definition for 'formula'
multi_conv : <anonymous>: no visible global function definition for
  'fft'
multi_conv: no visible global function definition for 'fft'
plotCIs: no visible global function definition for 'p.adjust'
plotCIs: no visible global function definition for 'par'
plotCIs: no visible global function definition for 'rgb'
plotCIs: no visible global function definition for 'abline'
plotCIs: no visible global function definition for 'gray'
plotCIs: no visible global function definition for 'axis'
plotCIs: no visible global function definition for 'text'
plotCIs: no visible global function definition for 'arrows'
plotCIs: no visible global function definition for 'points'
plotCIs: no visible global function definition for 'strwidth'
plotCIs: no visible global function definition for 'strheight'
plotCIs: no visible global function definition for 'polygon'
plotCIs: no visible global function definition for 'box'
plotCIsGenes : <anonymous>: no visible global function definition for
  'qt'
plotCIsGenes: no visible global function definition for 'dt'
plotCIsGenes: no visible global function definition for 'par'
plotCIsGenes: no visible global function definition for 'abline'
plotCIsGenes: no visible global function definition for 'gray'
plotCIsGenes: no visible global function definition for 'polygon'
plotCIsGenes: no visible global function definition for 'grey'
plotCIsGenes: no visible global function definition for 'points'
plotCIsGenes: no visible global function definition for 'arrows'
plotCIsGenes: no visible global function definition for 'axis'
plotCIsGenes: no visible global function definition for 'text'
plotCIsGenes: no visible global function definition for 'box'
plotCombinedPDF: no visible global function definition for 'par'
plotCombinedPDF: no visible global function definition for 'abline'
plotCombinedPDF: no visible global function definition for 'lines'
plotDensityCurves: no visible global function definition for 'par'
plotDensityCurves: no visible global function definition for 'abline'
plotDensityCurves: no visible global function definition for 'lines'
plotGeneSetDistributions: no visible global function definition for
  'layout'
plotGeneSetDistributions: no visible global function definition for
  'par'
plotGeneSetDistributions: no visible global function definition for
  'frame'
plotGeneSetDistributions: no visible global function definition for
  'text'
plotGeneSetDistributions: no visible global function definition for
  'axis'
plotGeneSetDistributions: no visible global function definition for
  'dt'
plotGeneSetDistributions: no visible global function definition for
  'quantile'
plotGeneSetDistributions: no visible global function definition for
  'rect'
plotGeneSetDistributions: no visible global function definition for
  'col2rgb'
plotGeneSetDistributions: no visible global function definition for
  'rainbow'
plotGeneSetDistributions: no visible global function definition for
  'colorRamp'
plotGeneSetDistributions: no visible global function definition for
  'rgb'
plotGeneSetDistributions: no visible global function definition for
  'approx'
plotGeneSetDistributions: no visible global function definition for
  'lines'
plotGeneSetDistributions: no visible global function definition for
  'abline'
qgen: no visible global function definition for 'median'
qgen: no visible global function definition for 'model.matrix'
qgen: no visible global function definition for 'formula'
qgen: no visible global function definition for 'residuals'
qgen: no visible global function definition for 'lm'
qgen: no visible global function definition for 'setNames'
qsTable: no visible global function definition for 'p.adjust'
twoCurve.pVal : <anonymous>: no visible global function definition for
  'approx'
weighted_conv: no visible global function definition for 'approx'
weighted_conv: no visible global function definition for 'convolve'
Undefined global functions or variables:
  abline approx arrows axis box col2rgb colorRamp convolve cov dt fft
  formula frame gray grey layout lines lm median model.matrix p.adjust
  par pchisq pnorm points polygon pt qt quantile rainbow rect residuals
  rgb runif setNames strheight strwidth text
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "gray", "grey",
             "rainbow", "rgb")
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "layout", "lines", "par", "points", "polygon", "rect",
             "strheight", "strwidth", "text")
  importFrom("stats", "approx", "convolve", "cov", "dt", "fft",
             "formula", "lm", "median", "model.matrix", "p.adjust",
             "pchisq", "pnorm", "pt", "qt", "quantile", "residuals",
             "runif", "setNames")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GeneSets.Rd:20: Dropping empty section \format
* 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
qgen 15.17   0.19   15.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
      user system elapsed
qgen 22.53   0.23   22.77
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/qusage.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/qusage_2.16.1.tar.gz && rm -rf qusage.buildbin-libdir && mkdir qusage.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qusage.buildbin-libdir qusage_2.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL qusage_2.16.1.zip && rm qusage_2.16.1.tar.gz qusage_2.16.1.zip
###
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install for i386

* installing *source* package 'qusage' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qusage'
    finding HTML links ... done
    GeneSets                                html  
    QSarray-class                           html  
    aggregateGeneSet                        html  
    calcBayesCI                             html  
    calcVIF                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/calcVIF.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    combinePDFs                             html  
    eset.full                               html  
    fluVaccine                              html  
    getXcoords                              html  
    makeComparison                          html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/makeComparison.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    newQSarray                              html  
    pVal                                    html  
    plotCIs                                 html  
    plotCIsGenes                            html  
    plotCombinedPDF                         html  
    plotDensityCurves                       html  
    plotGeneSetDistributions                html  
    qgen                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/qgen.Rd:21: file link 'corStruct' in package 'nlme' does not exist and so has been treated as a topic
    qsTable                                 html  
    qusage                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEV3V79/R.INSTALL13344b674998/qusage/man/qusage.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    read.gmt                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'qusage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qusage' as qusage_2.16.1.zip
* DONE (qusage)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'qusage' successfully unpacked and MD5 sums checked
In R CMD INSTALL