BioC 3.5: CHECK report for EBSeq on oaxaca

Package: EBSeq

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeq_1.15.0.tar.gz

StartedAt: 2017-03-04 02:09:10 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:10:07 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 57.0 seconds

RetCode: 0

Status:  OK

CheckDir: EBSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeq_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EBSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘1.15.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘EBSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DenNHist: no visible global function definition for ‘hist’
DenNHist: no visible global function definition for ‘lines’
DenNHist: no visible global function definition for ‘dbeta’
DenNHist: no visible global function definition for ‘legend’
EBMultiTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBMultiTest: no visible global function definition for ‘quantile’
EBMultiTest : <anonymous>: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘var’
EBTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest: no visible global function definition for ‘quantile’
EBTest: no visible binding for global variable ‘var’
GetDEResults: no visible binding for global variable ‘median’
LogN: no visible global function definition for ‘optim’
LogNMulti: no visible global function definition for ‘optim’
MedianNorm : <anonymous>: no visible global function definition for
  ‘median’
MedianNorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
PlotPattern: no visible global function definition for ‘par’
PlotPattern: no visible global function definition for ‘rainbow’
PlotPattern: no visible global function definition for ‘heatmap’
PlotPostVsRawFC: no visible global function definition for ‘par’
PlotPostVsRawFC: no visible global function definition for ‘plot’
PlotPostVsRawFC: no visible global function definition for ‘abline’
PlotPostVsRawFC: no visible global function definition for ‘rect’
PolyFitPlot: no visible global function definition for ‘lm’
PolyFitPlot: no visible global function definition for ‘smoothScatter’
PolyFitPlot: no visible global function definition for ‘axis’
PolyFitPlot: no visible global function definition for ‘lines’
QQP: no visible global function definition for ‘rbeta’
QQP: no visible global function definition for ‘qqplot’
QQP: no visible global function definition for ‘lm’
QQP: no visible global function definition for ‘abline’
QuantileNorm : <anonymous>: no visible global function definition for
  ‘quantile’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis dbeta heatmap hist legend lines lm median optim par plot
  qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "plot", "rect", "smoothScatter")
  importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
             "qqplot", "quantile", "rbeta", "var")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
GetMultiFC  6.475  0.015   6.495
EBMultiTest 5.842  0.022   5.866
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/EBSeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DenNHist	2.010	0.030	2.039
EBMultiTest	5.842	0.022	5.866
EBSeq_NingLeng-package	1.142	0.013	1.154
EBTest	0.423	0.009	0.432
GeneMat	0.002	0.001	0.002
GetDEResults	0.438	0.005	0.444
GetMultiFC	6.475	0.015	6.495
GetMultiPP	4.748	0.006	4.756
GetNg	0.005	0.001	0.006
GetNormalizedMat	0.006	0.001	0.007
GetPP	0.359	0.005	0.365
GetPPMat	0.490	0.011	0.500
GetPatterns	0.001	0.000	0.001
IsoList	0.004	0.001	0.005
IsoMultiList	0.003	0.001	0.003
Likefun	0.000	0.000	0.001
LikefunMulti	0.000	0.000	0.001
LogN	0	0	0
LogNMulti	0.001	0.000	0.001
MedianNorm	0.006	0.001	0.007
MultiGeneMat	0.002	0.001	0.004
PlotPattern	0.013	0.002	0.015
PlotPostVsRawFC	0.623	0.012	0.635
PolyFitPlot	0.035	0.002	0.037
PostFC	0.481	0.010	0.492
QQP	1.821	0.005	1.828
QuantileNorm	0.004	0.000	0.005
RankNorm	0.014	0.001	0.015
beta.mom	0	0	0
crit_fun	0.493	0.007	0.500
f0	0.001	0.000	0.001
f1	0.000	0.000	0.001