qusage 2.4.0
Christopher Bolen
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/qusage | | Last Changed Rev: 117189 / Revision: 122332 | | Last Changed Date: 2016-05-06 08:27:41 -0700 (Fri, 06 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf qusage.buildbin-libdir qusage.Rcheck && mkdir qusage.buildbin-libdir qusage.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qusage.buildbin-libdir qusage_2.4.0.tar.gz >qusage.Rcheck\00install.out 2>&1 && cp qusage.Rcheck\00install.out qusage-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=qusage.buildbin-libdir --install="check:qusage-install.out" --force-multiarch --no-vignettes --timings qusage_2.4.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/qusage.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.4.0'
* 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 ... OK
* checking installed package size ... NOTE
installed size is 9.9Mb
sub-directories of 1Mb or more:
data 8.5Mb
doc 1.2Mb
* 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'
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 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")
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 installed files from 'inst/doc' ... 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 25.09 0.16 25.27
combinePDFs 7.56 0.03 7.60
plotCombinedPDF 5.85 0.05 5.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qgen 27.45 0.19 27.72
* 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: 4 NOTEs
See
'E:/biocbld/bbs-3.3-bioc/meat/qusage.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'qusage' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'head' from package 'utils' in package 'qusage'
Creating a generic function for 'summary' from package 'base' in package 'qusage'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'qusage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qusage' as qusage_2.4.0.zip
* DONE (qusage)