TPP 3.0.3
Dorothee Childs
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/TPP | | Last Changed Rev: 124878 / Revision: 128728 | | Last Changed Date: 2016-12-07 05:13:45 -0500 (Wed, 07 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TPP_3.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TPP.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘3.0.3’
* 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 ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
example_data 3.4Mb
* 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’
analyze2DTPP: no visible binding for global variable ‘verbose’
analyze2DTPP: possible error in tpp2dCreateReport(resultPath =
resultPath, configFile = configFile, normalize = normalize,
configTable = configTable, resultTable = analysisResults, idVar =
"Protein_ID", fcStr = fcStr, fcStrUpdated = fcStrUpdated,
documentType = createReport, intensityStr = intensityStr, addCol =
addCol, fcTolerance = fcTolerance, r2Cutoff = r2Cutoff, fcCutoff =
fcCutoff, slopeBounds = slopeBounds, trRef = trRef): unused argument
(resultTable = analysisResults)
analyzeTPPTR: no visible binding for global variable ‘Protein_ID’
checkResultCols_tpptr: no visible binding for global variable
‘refIsVehicle’
checkResultCols_tpptr: no visible binding for global variable
‘testIsVehicle’
configTableListToLong: no visible binding for global variable
‘experiment’
convert_2dData_wide_to_long: no visible binding for global variable
‘columnName’
convert_2dData_wide_to_long: no visible binding for global variable
‘fc’
convert_2dData_wide_to_long: no visible binding for global variable
‘Protein_ID’
convert_trData_wide_to_long: no visible binding for global variable
‘key’
convert_trData_wide_to_long: no visible binding for global variable
‘lbl’
convert_trData_wide_to_long: no visible binding for global variable
‘temp’
convert_trData_wide_to_long: no visible binding for global variable
‘temperature’
convert_trData_wide_to_long: no visible binding for global variable
‘label’
convert_trData_wide_to_long: no visible binding for global variable
‘experiment’
createTPP_TPdataset : <anonymous>: no visible binding for global
variable ‘consist.prot.indizes’
create_spline_plots: no visible binding for global variable ‘uniqueID’
create_spline_plots: no visible binding for global variable ‘y’
create_spline_plots: no visible binding for global variable ‘x’
create_spline_plots: no visible binding for global variable ‘colorCol’
create_spline_plots: no visible binding for global variable ‘textStr’
create_spline_plots: no visible binding for global variable ‘highlight’
eSetsToLongTable_fData: no visible binding for global variable
‘experiment’
eSetsToLongTable_fData: no visible binding for global variable
‘variable’
eSetsToLongTable_fc: no visible binding for global variable
‘concentration’
eSetsToLongTable_fc: no visible binding for global variable
‘temperature’
eSetsToLongTable_fc: no visible binding for global variable
‘labelValue’
eSetsToLongTable_fc: no visible binding for global variable ‘labelName’
eval_spline_model: no visible global function definition for ‘ranef’
eval_spline_model: no visible global function definition for ‘fixef’
importCheckConfigTable: no visible binding for global variable
‘Experiment’
importFct_reportValidValues: no visible binding for global variable
‘uniqueID’
importFct_reportValidValues: no visible binding for global variable ‘y’
importFct_reportValidValues: no visible binding for global variable
‘yIsNotNA’
importFct_reportValidValues: no visible binding for global variable
‘sumOfNotNA’
importTR_tidy: no visible binding for global variable ‘experiment’
importTR_tidy: no visible binding for global variable ‘uniqueID’
importTR_tidy: no visible binding for global variable ‘x’
importTR_tidy: no visible binding for global variable ‘fcListAll’
importTidyFoldChanges: no visible binding for global variable ‘key’
inferApparentStabilities: no visible binding for global variable
‘tppRefData’
inferApparentStabilities: no visible binding for global variable
‘Protein_ID’
inferApparentStabilities: no visible binding for global variable
‘temperature’
inferApparentStabilities: no visible binding for global variable
‘relConc’
inferApparentStabilities: no visible binding for global variable ‘x’
inferApparentStabilities: no visible binding for global variable ‘fc’
inferApparentStabilities: no visible binding for global variable
‘splinePrediction’
mergeOutputTables_CCR: no visible binding for global variable
‘Protein_ID’
mergeOutputTables_TR: no visible binding for global variable
‘Protein_ID’
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’
plotMeltingCurve: no visible binding for global variable ‘meltPoint’
plotSplines : <anonymous>: no visible binding for global variable
‘Protein_ID’
plotSplines : <anonymous>: no visible binding for global variable
‘experiment’
plotSplines : <anonymous>: no visible binding for global variable
‘temperature’
plotSplines : <anonymous>: no visible binding for global variable
‘relConc’
plotSplines : <anonymous>: no visible binding for global variable
‘condition’
plotSplines : <anonymous>: no visible binding for global variable
‘fcNormalized’
plotSplines : <anonymous>: no visible binding for global variable
‘drugConc’
plot_fSta_distribution: no visible binding for global variable
‘uniqueID’
plot_fSta_distribution: no visible binding for global variable
‘staType’
plot_fSta_distribution: no visible binding for global variable
‘staValue’
plot_fSta_distribution: no visible binding for global variable ‘df1’
plot_fSta_distribution: no visible binding for global variable ‘df2’
plot_fSta_distribution: no visible binding for global variable
‘df2_moderated’
plot_fSta_distribution: no visible binding for global variable ‘DF1’
plot_fSta_distribution: no visible binding for global variable
‘..density..’
plot_fSta_distribution: no visible binding for global variable ‘label’
plot_pVal_distribution: no visible binding for global variable
‘uniqueID’
plot_pVal_distribution: no visible binding for global variable
‘p_NPARC’
plot_pVal_distribution: no visible binding for global variable
‘p_adj_NPARC’
plot_pVal_distribution: no visible binding for global variable ‘df1’
plot_pVal_distribution: no visible binding for global variable ‘df2’
plot_pVal_distribution: no visible binding for global variable
‘df2_moderated’
plot_pVal_distribution: no visible binding for global variable
‘pValType’
plot_pVal_distribution: no visible binding for global variable ‘pValue’
plot_pVal_distribution: no visible binding for global variable
‘..density..’
plot_pVal_distribution: no visible binding for global variable ‘label’
plot_splines_to_file: no visible binding for global variable ‘uniqueID’
plot_splines_to_file: no visible binding for global variable ‘idx’
plot_splines_to_file: no visible binding for global variable ‘pageNum’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘uniqueID’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘experiment’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘colName’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘newColName’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘y’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘variable’
prepare_NPARC_results_for_export: no visible binding for global
variable ‘value’
qcPlotFct_MeltPointHist: no visible binding for global variable
‘resultTable’
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’
tpp2dAddAdditionalInfo: no visible binding for global variable
‘compound_effect’
tpp2dMerge2dRef: no visible binding for global variable ‘tppRefData’
tpp2dMerge2dRef: no visible binding for global variable ‘clustername’
tpp2dPlotQChist: no visible binding for global variable ‘concentration’
tpp2dPlotQChist : <anonymous>: no visible binding for global variable
‘experiment’
tpp2dPlotQChist : <anonymous>: no visible binding for global variable
‘intercept’
tpp2dPlotQChist : <anonymous>: no visible binding for global variable
‘slope’
tpp2dPlotQChist : <anonymous>: no visible binding for global variable
‘stats’
tpp2dPlotQChist: no visible binding for global variable ‘R2’
tpp2dPlotQChist: no visible binding for global variable ‘temperature’
tpp2dPlotQChist: no visible binding for global variable ‘stddev’
tpp2dPlotQChist: no visible binding for global variable
‘dmso1_vs_dmso2’
tpp2dPlotQChist: no visible binding for global variable ‘marked’
tpp2dPlotQChist: no visible binding for global variable ‘experiment’
tpp2dPlotQChist: no visible binding for global variable ‘Var1’
tpp2dPlotQChist: no visible binding for global variable ‘Freq’
tpp2dPlotQChist: no visible binding for global variable ‘Var2’
tpp2dPlotQChist: no visible binding for global variable
‘median_meltPoint’
tpp2dPlotQChist: no visible binding for global variable ‘rev_cumsum’
tpp2dSplineFitAndTest: no visible binding for global variable ‘plotDir’
tpp2dSplineFitAndTest: no visible binding for global variable
‘Protein_ID’
tpp2dSplineFitAndTest: no visible binding for global variable
‘temperature’
tpp2dSplineFitAndTest: no visible binding for global variable
‘fcNormalized’
tppExport: no visible binding for global variable ‘Protein_ID’
tppQCPlotsCorrelateExperiments: no visible binding for global variable
‘x’
tppQCPlotsCorrelateExperiments: no visible binding for global variable
‘y’
tppccrCurveFit: no visible binding for global variable ‘variable’
tppccrCurveFit: no visible binding for global variable ‘experiment’
tppccrCurveFit: no visible binding for global variable ‘i’
tppccrPlotCurves: no visible binding for global variable ‘variable’
tppccrPlotCurves: no visible binding for global variable ‘foldChange’
tppccrPlotCurves: no visible binding for global variable ‘pID’
tpptrCurveFit: no visible binding for global variable ‘p’
tpptrFTest: no visible binding for global variable ‘testHypothesis’
tpptrFTest: no visible binding for global variable ‘rssH0’
tpptrFTest: no visible binding for global variable ‘rssH1’
tpptrFTest: no visible binding for global variable ‘nObsH1’
tpptrFTest: no visible binding for global variable ‘nCoeffsH1’
tpptrFTest: no visible binding for global variable ‘sigmaH1’
tpptrFTest: no visible binding for global variable ‘residual_df_H1’
tpptrFTest: no visible binding for global variable ‘posterior_var_H1’
tpptrFTest: no visible binding for global variable ‘nCoeffsH0’
tpptrFTest: no visible binding for global variable ‘df2’
tpptrFTest: no visible binding for global variable ‘prior_df_H1’
tpptrFTest: no visible binding for global variable ‘F_moderated’
tpptrFTest: no visible binding for global variable ‘df1’
tpptrFTest: no visible binding for global variable ‘F_scaled’
tpptrFTest: no visible binding for global variable ‘df2_moderated’
tpptrFTest: no visible binding for global variable ‘p_NPARC’
tpptrFTest: no visible binding for global variable ‘uniqueID’
tpptrFTest: no visible binding for global variable ‘F_statistic’
tpptrFTest: no visible binding for global variable ‘p_adj_NPARC’
tpptrFTest: no visible binding for global variable ‘staType’
tpptrFTest: no visible binding for global variable ‘staValue’
tpptrFitSplines: no visible binding for global variable ‘uniqueID’
tpptrFitSplines: no visible binding for global variable
‘testHypothesis’
tpptrFitSplines: no visible binding for global variable ‘fittedModel’
tpptrFitSplines: no visible binding for global variable ‘successfulFit’
tpptrFitSplines: no visible global function definition for
‘tpptrSplineAUCs’
tpptrHelperFitandPlot: no visible binding for global variable ‘protID’
tpptrPlotSplines: no visible binding for global variable ‘colorCol’
tpptrPlotSplines: no visible binding for global variable
‘successfulFit’
tpptrPlotSplines: no visible binding for global variable ‘uniqueID’
tpptrPlotSplines: no visible binding for global variable
‘testHypothesis’
tpptrPlotSplines: no visible binding for global variable ‘p_NPARC’
tpptrPlotSplines: no visible binding for global variable ‘p_adj_NPARC’
tpptrPlotSplines: no visible binding for global variable ‘p.adjStr’
tpptrPlotSplines: no visible binding for global variable ‘pageByP’
tpptrPlotSplines: no visible binding for global variable ‘pageByID’
tpptrSplineFitAndTest: no visible binding for global variable
‘uniqueID’
tpptrTidyUpESets: no visible binding for global variable ‘experiment’
tpptrTidyUpESets: no visible binding for global variable ‘testGroup’
tpptrTidyUpESets: no visible binding for global variable ‘refGroup’
tpptrTidyUpESets: no visible binding for global variable
‘comparisonFactor’
tpptrTidyUpESets: no visible binding for global variable ‘labelValue’
tpptrTidyUpESets: no visible binding for global variable ‘foldChange’
Undefined global functions or variables:
..density.. DF1 Experiment F_moderated F_scaled F_statistic Freq
Protein_ID R2 Var1 Var2 clustername colName colorCol columnName
comparison comparisonFactor compound_effect concentration condition
consist.prot.indizes df1 df2 df2_moderated dmso1_vs_dmso2 drugConc
expName experiment fc fcListAll fcNormalized fittedModel fixef
foldChange highlight i idx intercept key label labelName labelValue
lbl marked median_meltPoint meltPoint nCoeffsH0 nCoeffsH1 nObsH1
newColName p p.adjStr pID pValType pValue p_NPARC p_adj_NPARC
pageByID pageByP pageNum param plotDir posterior_var_H1 prior_df_H1
protID ranef refGroup refIsVehicle relConc residual_df_H1 resultTable
rev_cumsum rssH0 rssH1 sigmaH1 slope splinePrediction staType
staValue stats stddev successfulFit sumOfNotNA temp temperature
testGroup testHypothesis testIsVehicle textStr tppRefData
tpptrSplineAUCs uniqueID value variable verbose x y yIsNotNA
* 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
tppQCPlotsCorrelateExperiments 18.513 0.111 18.683
tpptrPlotSplines 14.851 0.095 14.958
tpptrSplineFitAndTest 12.845 0.078 12.930
tpp2dPlotCCRGoodCurves 12.746 0.091 12.850
tpp2dPlotCCRAllCurves 11.554 0.081 11.646
tpp2dPlotCCRSingleCurves 10.816 0.100 10.928
tpp2dExport 10.676 0.206 11.113
analyze2DTPP 8.079 0.102 8.195
tppccrPlotCurves 7.343 0.051 7.406
analyzeTPPTR 6.987 0.049 7.105
tpptrFTest 6.940 0.047 6.992
tpp2dCurveFit 6.518 0.062 6.587
tppccrCurveFit 5.704 0.041 5.751
analyzeTPPCCR 5.406 0.041 5.451
tppccrResultTable 5.237 0.042 5.284
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/TPP.Rcheck/00check.log’
for details.