BioC 3.3: CHECK report for TPP on linux2.bioconductor.org

Package: TPP

Version: 2.1.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TPP_2.1.1.tar.gz

StartedAt: 2015-10-27 08:41:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:43:49 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 121.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TPP.Rcheck

Warnings: 1

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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_2.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TPP.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.1.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘ggplot2’ ‘openxlsx’ ‘plyr’ ‘gridExtra’ ‘grid’
  ‘VennDiagram’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [3s/3s] 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’
importFct_readConfigTable: no visible binding for global variable
  ‘infoTable’
importFct_readConfigTable: no visible binding for global variable
  ‘Experiment’
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’
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’
Undefined global functions or variables:
  Experiment Protein_ID comparison concentration condition expName
  experiment foldChange i infoTable meltPoint p pID param protID
  refIsVehicle resultTable testIsVehicle value variable x y
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                         old_size new_size compress
  hdacCCR_smallExample.RData                 62Kb     47Kb       xz
  hdacTR_fittedData_smallExample.RData      267Kb    226Kb       xz
  hdacTR_resultsTable_smallExample.RData    233Kb    208Kb       xz
  hdacTR_smallExample.RData                 146Kb    112Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [72s/72s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
analyzeTPPTR                   38.403  0.022  38.432
tppQCPlotsCorrelateExperiments 11.157  0.052  11.209
analyzeTPPCCR                   5.108  0.039   5.151
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [2s/2s]
 [2s/2s] 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	5.108	0.039	5.151
analyzeTPPTR	38.403	0.022	38.432
tppDefaultTheme	0.52	0.00	0.52
tppExport	0.689	0.030	0.722
tppQCPlotsCorrelateExperiments	11.157	0.052	11.209
tppccrCurveFit	4.160	0.020	4.179
tppccrImport	0.124	0.000	0.125
tppccrNormalize	0.123	0.000	0.123
tppccrNormalizeToReference	0.146	0.000	0.147
tppccrPlotCurves	4.721	0.061	4.781
tppccrResultTable	3.762	0.025	3.787
tppccrTransform	0.129	0.004	0.133
tpptrAnalyzeMeltingCurves	0.16	0.00	0.16
tpptrCurveFit	0.682	0.028	0.713
tpptrDefaultNormReqs	0.317	0.000	0.317
tpptrImport	0.142	0.000	0.142
tpptrNormalize	0.322	0.008	0.331