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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qusage.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qusage_2.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/qusage.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qusage/DESCRIPTION’ ... OK
* this is package ‘qusage’ version ‘2.36.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘qusage’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.8Mb
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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘qusage-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCombinedPDF
> ### Title: Plot combined PDF for an individual pathway
> ### Aliases: plotCombinedPDF
>
> ### ** Examples
>
> ##create 5 example datasets of different sizes
> esets = lapply(1:5, function(i){
+ n = 20 + i*5
+ eset = matrix(rnorm(500*n),500,n, dimnames=list(1:500,1:n))
+
+ labels = c(rep("A",10+5*floor(i/2)),
+ rep("B",10+5*ceiling(i/2))
+ )
+
+ ##genes 1:30 are differentially expressed
+ eset[1:30, labels=="B"] = eset[1:30, labels=="B"] + rnorm(30,rnorm(1,0.5,0.5),1)
+
+ return(list(eset=eset, labels=labels))
+ })
>
> ##gene sets
> geneSets = list(diff.set=1:30, baseline.set=31:60)
>
> ##Run qusage on each dataset
> set.results = lapply(esets, function(dat){
+ qusage(dat$eset, dat$labels, "B-A", geneSets)
+ })
Calculating gene-by-gene comparisons...Done.
Aggregating gene data for gene sets.Done.
Calculating variance inflation factors...Done.
Calculating gene-by-gene comparisons...Done.
Aggregating gene data for gene sets.Done.
Calculating variance inflation factors...Done.
Calculating gene-by-gene comparisons...Done.
Aggregating gene data for gene sets.Done.
Calculating variance inflation factors...Done.
Calculating gene-by-gene comparisons...Done.
Aggregating gene data for gene sets.Done.
Calculating variance inflation factors...Done.
Calculating gene-by-gene comparisons...Done.
Aggregating gene data for gene sets.Done.
Calculating variance inflation factors...Done.
>
> ##run the combinePDFs function
> combined = combinePDFs(set.results)
>
> ##plot the combined PDF result for "diff.set"
> plotCombinedPDF(combined, path.index="diff.set")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in max(QScomb$path.PDF[, path.index]/comb.scaleFactor[path.index], :
no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plotCombinedPDF ... plot -> plot -> plot.default -> localWindow -> plot.window
Execution halted
* 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 ERROR, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/qusage.Rcheck/00check.log’
for details.