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BioC 3.5: CHECK report for compcodeR on veracruz2

This page was generated on 2017-10-18 14:31:59 -0400 (Wed, 18 Oct 2017).

Package 265/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.12.0
Charlotte Soneson
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/compcodeR
Branch: RELEASE_3_5
Last Commit: 2564789
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.12.0.tar.gz
StartedAt: 2017-10-18 02:04:25 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:08:22 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 237.7 seconds
RetCode: 0
Status:  OK 
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/compcodeR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rpanel’
* 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 ‘compcodeR’ 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
'library' or 'require' call to ‘rpanel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DESeq.GLM.createRmd: no visible global function definition for
  ‘packageVersion’
DESeq.nbinom.createRmd: no visible global function definition for
  ‘packageVersion’
DESeq2.createRmd: no visible global function definition for
  ‘packageVersion’
DSS.createRmd: no visible global function definition for
  ‘packageVersion’
EBSeq.createRmd: no visible global function definition for
  ‘packageVersion’
NBPSeq.createRmd: no visible global function definition for
  ‘packageVersion’
NOISeq.prenorm.createRmd: no visible global function definition for
  ‘packageVersion’
SAMseq.createRmd: no visible global function definition for
  ‘packageVersion’
TCC.createRmd: no visible global function definition for
  ‘packageVersion’
baySeq.createRmd: no visible global function definition for
  ‘packageVersion’
computeCorrelation: no visible global function definition for ‘cor’
computeCorrelation: no visible global function definition for ‘hclust’
computeCorrelation: no visible global function definition for ‘as.dist’
computeCorrelation: no visible global function definition for
  ‘heat.colors’
computeOverlap: no visible global function definition for ‘hclust’
computeOverlap: no visible global function definition for ‘as.dist’
computeOverlap: no visible global function definition for ‘heat.colors’
computeSignal: no visible binding for global variable ‘sd’
createResultsRmdFile: no visible global function definition for
  ‘packageVersion’
edgeR.GLM.createRmd: no visible global function definition for
  ‘packageVersion’
edgeR.exact.createRmd: no visible global function definition for
  ‘packageVersion’
generateSyntheticData: no visible global function definition for
  ‘runif’
generateSyntheticData: no visible global function definition for ‘rexp’
generateSyntheticData: no visible global function definition for
  ‘rnbinom’
generateSyntheticData: no visible global function definition for
  ‘rpois’
generateSyntheticData: no visible binding for global variable ‘median’
logcpm.limma.createRmd: no visible global function definition for
  ‘packageVersion’
makeFalseDiscoveryCurves: no visible global function definition for
  ‘par’
makeFalseDiscoveryCurves: no visible global function definition for
  ‘lines’
makeFalseDiscoveryCurves: no visible global function definition for
  ‘legend’
makeROCcurves: no visible global function definition for ‘par’
makeROCcurves: no visible global function definition for ‘lines’
makeROCcurves: no visible global function definition for ‘legend’
plotMASignificant: no visible global function definition for ‘par’
plotResultTable: no visible global function definition for ‘par’
plotScoreVsExpr: no visible global function definition for ‘par’
plotScoreVsExpr: no visible global function definition for ‘loess’
plotScoreVsExpr: no visible global function definition for ‘lines’
plotScoreVsExpr: no visible global function definition for ‘predict’
plotScoreVsOutlierEvidence: no visible global function definition for
  ‘par’
plotScoreVsOutlierEvidence: no visible global function definition for
  ‘loess’
plotScoreVsOutlierEvidence: no visible global function definition for
  ‘lines’
plotScoreVsOutlierEvidence: no visible global function definition for
  ‘predict’
plotScoreVsOutliers: no visible global function definition for ‘par’
plotScoreVsOutliers: no visible binding for global variable ‘na.omit’
plotScoreVsOutliers: no visible global function definition for ‘title’
plotScoreVsOutliers: no visible global function definition for ‘axis’
plotSignalForZeroCounts: no visible global function definition for
  ‘par’
sqrtcpm.limma.createRmd: no visible global function definition for
  ‘packageVersion’
ttest.createRmd: no visible global function definition for
  ‘packageVersion’
voom.limma.createRmd: no visible global function definition for
  ‘packageVersion’
voom.ttest.createRmd: no visible global function definition for
  ‘packageVersion’
vst.limma.createRmd: no visible global function definition for
  ‘packageVersion’
vst.ttest.createRmd: no visible global function definition for
  ‘packageVersion’
show,compData: no visible global function definition for ‘head’
Undefined global functions or variables:
  as.dist axis cor hclust head heat.colors legend lines loess median
  na.omit packageVersion par predict rexp rnbinom rpois runif sd title
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "legend", "lines", "par", "title")
  importFrom("stats", "as.dist", "cor", "hclust", "loess", "median",
             "na.omit", "predict", "rexp", "rnbinom", "rpois", "runif",
             "sd")
  importFrom("utils", "head", "packageVersion")
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 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
DESeq.nbinom.createRmd   50.372  2.768  55.090
NBPSeq.createRmd         32.528  2.214  35.814
DESeq.GLM.createRmd      13.919  0.923  15.389
convertcompDataToList     7.172  5.285  12.815
show-compData-method      6.869  5.126  12.300
DESeq2.createRmd          7.458  0.730   8.357
EBSeq.createRmd           6.931  0.315   7.427
runComparison             5.380  0.409   5.995
baySeq.createRmd          5.359  0.333   5.772
NOISeq.prenorm.createRmd  5.121  0.445   5.684
* 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-3.5-bioc/meat/compcodeR.Rcheck/00check.log’
for details.

compcodeR.Rcheck/00install.out:

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

compcodeR.Rcheck/compcodeR-Ex.timings:

nameusersystemelapsed
DESeq.GLM.createRmd13.919 0.92315.389
DESeq.nbinom.createRmd50.372 2.76855.090
DESeq2.createRmd7.4580.7308.357
DSS.createRmd1.8100.1462.001
EBSeq.createRmd6.9310.3157.427
NBPSeq.createRmd32.528 2.21435.814
NOISeq.prenorm.createRmd5.1210.4455.684
SAMseq.createRmd1.1390.1331.287
TCC.createRmd2.6210.1622.827
baySeq.createRmd5.3590.3335.772
checkDataObject0.1840.0300.221
checkTableConsistency1.3900.1161.529
check_compData0.2130.0220.239
check_compData_results1.0790.1081.206
compData0.0020.0000.003
convertListTocompData0.0050.0000.006
convertcompDataToList 7.172 5.28512.815
edgeR.GLM.createRmd1.3560.1001.497
edgeR.exact.createRmd0.6820.0480.741
generateCodeHTMLs0.5240.0490.591
generateSyntheticData0.1910.0190.215
listcreateRmd0.0120.0010.012
logcpm.limma.createRmd0.4210.0460.476
runComparison5.3800.4095.995
runComparisonGUI0.0010.0000.001
runDiffExp0.5950.0490.675
show-compData-method 6.869 5.12612.300
sqrtcpm.limma.createRmd0.3880.0400.437
summarizeSyntheticDataSet2.0630.1762.334
ttest.createRmd0.4290.0480.511
voom.limma.createRmd0.5240.0480.591
voom.ttest.createRmd0.4670.0530.529
vst.limma.createRmd0.6660.0500.730
vst.ttest.createRmd0.7350.0560.803