Package: compcodeR

Version: 1.18.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings compcodeR_1.18.1.tar.gz

StartedAt: 2019-04-15 23:05:55 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:11:36 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 341.5 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings compcodeR_1.18.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/compcodeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.1’
* 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 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.
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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’
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   62.848  0.616  63.661
NBPSeq.createRmd         38.312  0.508  38.987
DESeq.GLM.createRmd      10.020  0.540  11.160
NOISeq.prenorm.createRmd  9.528  0.776  10.277
EBSeq.createRmd           9.056  0.332   9.550
DESeq2.createRmd          7.752  0.476   8.228
convertcompDataToList     6.324  0.388   6.731
show-compData-method      5.872  0.340   6.227
DSS.createRmd             5.276  0.508   5.864
* 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-3.8-bioc/meat/compcodeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL compcodeR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘compcodeR’ ...
** R
** inst
** byte-compile and prepare 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	10.02	0.54	11.16
DESeq.nbinom.createRmd	62.848	0.616	63.661
DESeq2.createRmd	7.752	0.476	8.228
DSS.createRmd	5.276	0.508	5.864
EBSeq.createRmd	9.056	0.332	9.550
NBPSeq.createRmd	38.312	0.508	38.987
NOISeq.prenorm.createRmd	9.528	0.776	10.277
TCC.createRmd	2.740	0.300	3.093
baySeq.createRmd	4.292	0.428	4.750
checkDataObject	0.272	0.080	0.354
checkTableConsistency	1.212	0.352	1.595
check_compData	0.300	0.088	0.390
check_compData_results	0.760	0.132	0.902
compData	0.000	0.004	0.004
convertListTocompData	0.008	0.000	0.007
convertcompDataToList	6.324	0.388	6.731
edgeR.GLM.createRmd	1.196	0.204	1.412
edgeR.exact.createRmd	0.624	0.188	0.815
generateCodeHTMLs	0.528	0.180	0.711
generateSyntheticData	0.204	0.060	0.263
listcreateRmd	0.008	0.000	0.008
logcpm.limma.createRmd	0.516	0.188	0.714
runComparison	3.276	0.544	3.861
runComparisonGUI	0.000	0.000	0.001
runDiffExp	0.796	0.212	1.048
show-compData-method	5.872	0.340	6.227
sqrtcpm.limma.createRmd	0.524	0.120	0.661
summarizeSyntheticDataSet	1.940	0.128	2.081
ttest.createRmd	0.452	0.132	0.596
voom.limma.createRmd	0.756	0.256	1.033
voom.ttest.createRmd	0.660	0.232	0.908
vst.limma.createRmd	0.724	0.180	0.906
vst.ttest.createRmd	0.648	0.184	0.836