TPP 2.2.6
Dorothee Childs
| 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/TPP | | Last Changed Rev: 122034 / Revision: 122332 | | Last Changed Date: 2016-10-07 03:36:12 -0700 (Fri, 07 Oct 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TPP_2.2.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TPP.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘2.2.6’
* 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 ‘TPP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘TPP/R/TPP.R’:
.onLoad calls:
packageStartupMessage(msgText, "\n")
See section ‘Good practice’ in '?.onAttach'.
addTableToPlot: no visible binding for global variable ‘variable’
addTableToPlot: no visible binding for global variable ‘condition’
addTableToPlot: no visible binding for global variable ‘value’
analyzeTPPCCR: no visible global function definition for
‘packageVersion’
analyzeTPPTR: no visible global function definition for
‘packageVersion’
analyzeTPPTR: no visible global function definition for ‘pdf’
analyzeTPPTR: no visible global function definition for ‘dev.off’
assignBins: no visible global function definition for ‘quantile’
checkResultCols_tpptr: no visible binding for global variable
‘refIsVehicle’
checkResultCols_tpptr: no visible binding for global variable
‘testIsVehicle’
computeNormFactors : <anonymous>: no visible binding for global
variable ‘median’
computePvalues: no visible global function definition for ‘p.adjust’
eSetsToLongTable_fData: no visible global function definition for
‘reshape’
eSetsToLongTable_fc: no visible global function definition for
‘reshape’
fitMeltCurves: no visible global function definition for ‘setNames’
fitSigmoidCCR: no visible global function definition for ‘as.formula’
fitSigmoidCCR: no visible global function definition for ‘nls’
fitSigmoidCCR: no visible binding for global variable ‘na.exclude’
fitSigmoidTR: no visible global function definition for ‘as.formula’
fitSigmoidTR: no visible global function definition for ‘runif’
fitSigmoidTR: no visible global function definition for ‘nls’
fitSigmoidTR: no visible binding for global variable ‘na.exclude’
guessInitialDRslope: no visible global function definition for ‘lm’
guessInitialDRslope: no visible global function definition for
‘quantile’
importCheckConfigTable: no visible binding for global variable
‘Experiment’
importFct_readConfigTable: no visible global function definition for
‘read.table’
importFct_readConfigTable: no visible binding for global variable
‘infoTable’
importFct_readFiles: no visible global function definition for
‘read.delim’
inflectionPoint: no visible global function definition for ‘uniroot’
meltingPoint: no visible global function definition for ‘uniroot’
merge_cols : <anonymous>: no visible global function definition for
‘na.omit’
pValsCurrentBin: no visible global function definition for ‘quantile’
plotColors: no visible global function definition for
‘colorRampPalette’
plotDRCurve: no visible binding for global variable ‘experiment’
plotDRCurve: no visible binding for global variable ‘param’
plotDRCurve: no visible binding for global variable ‘concentration’
plotDRCurve: no visible binding for global variable ‘foldChange’
plotDRCurve: no visible binding for global variable ‘x’
plotDRCurve: no visible binding for global variable ‘y’
plotDRCurve: no visible global function definition for ‘pdf’
plotDRCurve: no visible global function definition for ‘dev.off’
plotMeltingCurve: no visible binding for global variable ‘meltPoint’
qcPlotFct_MeltPointHist: no visible binding for global variable
‘resultTable’
qcPlotFct_MeltPointHist: no visible global function definition for
‘combn’
qcPlotFct_MeltPointHist: no visible global function definition for
‘median’
qcPlotFct_MeltPointHist: no visible global function definition for
‘quantile’
qcPlotFct_MeltPointHist: no visible binding for global variable
‘comparison’
qcPlotFct_invokeBottleplots: no visible binding for global variable ‘x’
qcPlotFct_invokeBottleplots: no visible binding for global variable ‘y’
resultTabFromList: no visible binding for global variable ‘Protein_ID’
retrieveDataFromESets_CCR: no visible binding for global variable
‘Protein_ID’
retrieveDataFromESets_TR: no visible binding for global variable
‘Protein_ID’
storeDRCurveParams: no visible binding for global variable ‘expName’
storeDRCurveParams: no visible binding for global variable ‘protID’
storeMeltCurveParams: no visible binding for global variable ‘expName’
storeMeltCurveParams: no visible binding for global variable ‘protID’
tppQCPlotsCorrelateExperiments: no visible binding for global variable
‘x’
tppQCPlotsCorrelateExperiments: no visible binding for global variable
‘y’
tppQCPlotsCorrelateExperiments: no visible global function definition
for ‘reshape’
tppccrCurveFit: no visible binding for global variable ‘variable’
tppccrCurveFit: no visible binding for global variable ‘experiment’
tppccrCurveFit: no visible binding for global variable ‘i’
tppccrNormalize: no visible binding for global variable ‘median’
tppccrPlotCurves: no visible binding for global variable ‘variable’
tppccrPlotCurves: no visible binding for global variable ‘pID’
tpptrCurveFit: no visible binding for global variable ‘p’
tpptrHelperFitandPlot: no visible binding for global variable ‘protID’
tpptrHelperFitandPlot: no visible global function definition for ‘pdf’
tpptrHelperFitandPlot: no visible global function definition for
‘dev.off’
tpptrNormalize: no visible global function definition for ‘pdf’
tpptrNormalize: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
Experiment Protein_ID as.formula colorRampPalette combn comparison
concentration condition dev.off expName experiment foldChange i
infoTable lm median meltPoint na.exclude na.omit nls p p.adjust pID
packageVersion param pdf protID quantile read.delim read.table
refIsVehicle reshape resultTable runif setNames testIsVehicle uniroot
value variable x y
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
importFrom("stats", "as.formula", "lm", "median", "na.exclude",
"na.omit", "nls", "p.adjust", "quantile", "reshape",
"runif", "setNames", "uniroot")
importFrom("utils", "combn", "packageVersion", "read.delim",
"read.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeTPPTR 43.570 0.050 43.923
tppQCPlotsCorrelateExperiments 10.271 0.040 10.366
analyzeTPPCCR 5.461 0.035 5.603
tppccrPlotCurves 5.208 0.054 5.263
tppccrCurveFit 5.085 0.026 5.148
tppccrResultTable 4.983 0.033 5.059
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/TPP.Rcheck/00check.log’
for details.