BioC 3.4: CHECK report for compcodeR on malbec1

Package: compcodeR

Version: 1.10.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.10.0.tar.gz

StartedAt: 2017-04-14 21:44:44 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:48:08 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 203.9 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/compcodeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 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 51.808  0.236  52.607
NBPSeq.createRmd       31.692  0.156  31.886
DESeq.GLM.createRmd    11.472  0.456  12.054
EBSeq.createRmd         8.360  0.160   8.565
show-compData-method    7.540  0.188   7.758
convertcompDataToList   6.136  0.212   6.363
DESeq2.createRmd        5.600  0.448   6.065
baySeq.createRmd        5.396  0.292   5.695
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/compcodeR.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
DESeq.GLM.createRmd	11.472	0.456	12.054
DESeq.nbinom.createRmd	51.808	0.236	52.607
DESeq2.createRmd	5.600	0.448	6.065
DSS.createRmd	2.260	0.196	2.461
EBSeq.createRmd	8.360	0.160	8.565
NBPSeq.createRmd	31.692	0.156	31.886
NOISeq.prenorm.createRmd	3.828	0.240	4.054
SAMseq.createRmd	1.204	0.144	1.352
TCC.createRmd	2.724	0.136	2.904
baySeq.createRmd	5.396	0.292	5.695
checkDataObject	0.216	0.040	0.259
checkTableConsistency	1.084	0.148	1.250
check_compData	0.304	0.032	0.335
check_compData_results	0.676	0.084	0.762
compData	0.004	0.000	0.002
convertListTocompData	0.000	0.004	0.004
convertcompDataToList	6.136	0.212	6.363
edgeR.GLM.createRmd	1.404	0.112	1.531
edgeR.exact.createRmd	0.808	0.096	0.921
generateCodeHTMLs	0.584	0.080	0.683
generateSyntheticData	0.260	0.028	0.287
listcreateRmd	0.012	0.000	0.010
logcpm.limma.createRmd	0.428	0.072	0.501
runComparison	3.016	0.288	3.321
runComparisonGUI	0.000	0.000	0.001
runDiffExp	0.728	0.108	0.849
show-compData-method	7.540	0.188	7.758
sqrtcpm.limma.createRmd	0.456	0.056	0.517
summarizeSyntheticDataSet	1.476	0.084	1.555
ttest.createRmd	0.440	0.100	0.525
voom.limma.createRmd	0.552	0.096	0.651
voom.ttest.createRmd	0.420	0.124	0.542
vst.limma.createRmd	0.660	0.128	0.788
vst.ttest.createRmd	0.676	0.092	0.782