TPP 2.0.1
Dorothee Childs
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TPP | | Last Changed Rev: 109686 / Revision: 110496 | | Last Changed Date: 2015-10-16 05:58:05 -0700 (Fri, 16 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | 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_2.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TPP.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.0.1’
* 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 ... [5s/6s] 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_invokeBottleplots: no visible binding for global variable ‘x’
qcPlotFct_invokeBottleplots: no visible binding for global variable ‘y’
qcPlotFct_MeltPointHist: no visible binding for global variable
‘resultTable’
qcPlotFct_MeltPointHist: no visible binding for global variable
‘comparison’
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’
* 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 227Kb xz
hdacTR_resultsTable_smallExample.RData 233Kb 208Kb xz
hdacTR_smallExample.RData 146Kb 112Kb xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [100s/100s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeTPPTR 53.610 0.033 53.645
tppQCPlotsCorrelateExperiments 11.899 0.103 12.105
tppccrPlotCurves 6.900 0.119 7.022
analyzeTPPCCR 6.868 0.109 6.979
tppccrCurveFit 6.391 0.105 6.498
tppccrResultTable 6.271 0.090 6.360
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [3s/3s]
[4s/4s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/TPP.Rcheck/00check.log’
for details.