BioC 3.2: CHECK report for TPP on oaxaca

Package: TPP

Version: 2.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TPP_2.0.4.tar.gz

StartedAt: 2016-04-23 05:03:23 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:06:01 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 158.9 seconds

RetCode: 0

Status:  OK

CheckDir: TPP.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TPP_2.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TPP.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.0.4’
* 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 ... [5s/5s] 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’
checkResultCols_tpptr: no visible binding for global variable
  ‘refIsVehicle’
checkResultCols_tpptr: no visible binding for global variable
  ‘testIsVehicle’
importCheckConfigTable: no visible binding for global variable
  ‘Experiment’
importFct_readConfigTable: no visible binding for global variable
  ‘infoTable’
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’
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’
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 ‘pID’
tpptrCurveFit: no visible binding for global variable ‘p’
tpptrHelperFitandPlot: no visible binding for global variable ‘protID’
* 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 ... [94s/94s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
analyzeTPPTR                   48.645  0.115  48.792
tppQCPlotsCorrelateExperiments 12.185  0.112  12.354
tppccrPlotCurves                6.709  0.124   6.839
tppccrCurveFit                  6.270  0.107   6.384
analyzeTPPCCR                   6.061  0.106   6.172
tppccrResultTable               6.042  0.101   6.147
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [3s/3s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/TPP.Rcheck/00check.log’
for details.

* installing *source* package ‘TPP’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TPP)

name	user	system	elapsed
analyzeTPPCCR	6.061	0.106	6.172
analyzeTPPTR	48.645	0.115	48.792
tppDefaultTheme	0.516	0.003	0.519
tppExport	0.427	0.025	0.453
tppQCPlotsCorrelateExperiments	12.185	0.112	12.354
tppccrCurveFit	6.270	0.107	6.384
tppccrImport	0.191	0.002	0.194
tppccrNormalize	0.214	0.002	0.217
tppccrNormalizeToReference	0.273	0.002	0.275
tppccrPlotCurves	6.709	0.124	6.839
tppccrResultTable	6.042	0.101	6.147
tppccrTransform	0.251	0.002	0.254
tpptrAnalyzeMeltingCurves	0.554	0.002	0.557
tpptrCurveFit	1.056	0.006	1.063
tpptrDefaultNormReqs	0.536	0.002	0.538
tpptrImport	0.262	0.002	0.264
tpptrNormalize	0.574	0.006	0.580