Package: compcodeR

Version: 1.19.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.19.3.tar.gz

StartedAt: 2019-04-09 00:04:54 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:13:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 507.1 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.19.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/compcodeR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.19.3’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   54.788  3.066  58.261
convertcompDataToList    45.153  8.068  53.426
show-compData-method     40.785  7.614  48.540
NBPSeq.createRmd         39.436  2.425  42.223
NOISeq.prenorm.createRmd 13.876  1.471  15.175
DESeq2.createRmd         13.069  1.158  14.168
EBSeq.createRmd          12.069  0.498  12.629
DESeq.GLM.createRmd      11.560  0.918  12.407
DSS.createRmd             7.597  0.676   8.272
baySeq.createRmd          7.582  0.489   8.048
* 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-3.9-bioc/meat/compcodeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL compcodeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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	11.560	0.918	12.407
DESeq.nbinom.createRmd	54.788	3.066	58.261
DESeq2.createRmd	13.069	1.158	14.168
DSS.createRmd	7.597	0.676	8.272
EBSeq.createRmd	12.069	0.498	12.629
NBPSeq.createRmd	39.436	2.425	42.223
NOISeq.prenorm.createRmd	13.876	1.471	15.175
TCC.createRmd	4.208	0.315	4.495
baySeq.createRmd	7.582	0.489	8.048
checkDataObject	1.232	0.136	1.364
checkTableConsistency	2.151	0.139	2.298
check_compData	1.071	0.045	1.114
check_compData_results	1.582	0.103	1.680
compData	0.003	0.001	0.004
convertListTocompData	0.006	0.001	0.006
convertcompDataToList	45.153	8.068	53.426
edgeR.GLM.createRmd	2.487	0.159	2.647
edgeR.exact.createRmd	1.899	0.096	1.992
generateCodeHTMLs	1.767	0.111	1.877
generateSyntheticData	1.186	0.050	1.235
listcreateRmd	0.014	0.000	0.014
logcpm.limma.createRmd	1.539	0.092	1.632
runComparison	4.126	0.337	4.468
runComparisonGUI	0	0	0
runDiffExp	0.913	0.091	0.998
show-compData-method	40.785	7.614	48.540
sqrtcpm.limma.createRmd	0.690	0.089	0.774
summarizeSyntheticDataSet	3.270	0.301	3.672
ttest.createRmd	0.675	0.085	0.754
voom.limma.createRmd	0.851	0.082	0.926
voom.ttest.createRmd	1.470	0.084	1.554
vst.limma.createRmd	1.674	0.101	1.777
vst.ttest.createRmd	1.655	0.097	1.752