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CHECK report for qusage on tokay1

This page was generated on 2020-04-15 12:22:04 -0400 (Wed, 15 Apr 2020).

Package 1355/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qusage 2.20.0
Christopher Bolen
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/qusage
Branch: RELEASE_3_10
Last Commit: 81a68e6
Last Changed Date: 2019-10-29 13:08:46 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qusage
Version: 2.20.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qusage.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings qusage_2.20.0.tar.gz
StartedAt: 2020-04-15 05:50:16 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:52:56 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 159.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: qusage.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qusage.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings qusage_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/qusage.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 'qusage/DESCRIPTION' ... OK
* this is package 'qusage' version '2.20.0'
* 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 'qusage' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-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 20.75   0.29   21.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
      user system elapsed
qgen 19.03   0.17    19.2
* 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-3.10-bioc/meat/qusage.Rcheck/00check.log'
for details.



Installation output

qusage.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/qusage_2.20.0.tar.gz && rm -rf qusage.buildbin-libdir && mkdir qusage.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qusage.buildbin-libdir qusage_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL qusage_2.20.0.zip && rm qusage_2.20.0.tar.gz qusage_2.20.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 8777k  100 8777k    0     0  53.0M      0 --:--:-- --:--:-- --:--:-- 53.9M

install for i386

* installing *source* package 'qusage' ...
** using staged installation
** 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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/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 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 'qusage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qusage' as qusage_2.20.0.zip
* DONE (qusage)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'qusage' successfully unpacked and MD5 sums checked

Tests output


Example timings

qusage.Rcheck/examples_i386/qusage-Ex.timings

nameusersystemelapsed
aggregateGeneSet0.190.060.25
calcVIF0.220.010.23
combinePDFs2.580.072.64
getXcoords0.350.010.36
makeComparison0.010.000.01
pVal0.630.000.63
plotCIs0.980.000.98
plotCIsGenes0.170.020.19
plotCombinedPDF2.490.002.48
plotDensityCurves0.260.000.27
plotGeneSetDistributions2.600.002.59
qgen20.75 0.2921.05
qsTable1.530.001.53
qusage1.290.021.31

qusage.Rcheck/examples_x64/qusage-Ex.timings

nameusersystemelapsed
aggregateGeneSet0.160.000.16
calcVIF0.220.020.23
combinePDFs2.470.072.55
getXcoords0.160.000.15
makeComparison0.010.000.02
pVal0.490.000.48
plotCIs0.910.020.92
plotCIsGenes0.180.000.19
plotCombinedPDF3.270.033.30
plotDensityCurves0.250.000.25
plotGeneSetDistributions2.620.022.64
qgen19.03 0.1719.20
qsTable0.960.000.96
qusage0.670.000.67