Package: sSeq

Version: 1.21.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sSeq_1.21.1.tar.gz

StartedAt: 2019-04-09 03:56:47 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:02:09 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 321.6 seconds

RetCode: 0

Status:  OK

CheckDir: sSeq.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:sSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sSeq_1.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sSeq.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 ‘sSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sSeq’ version ‘1.21.1’
* 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 ‘sSeq’ 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 ‘caTools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘caTools’
  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
drawMA_vol: no visible global function definition for ‘par’
drawMA_vol: no visible global function definition for ‘plot’
drawMA_vol: no visible global function definition for ‘points’
drawMA_vol: no visible global function definition for ‘abline’
ecdfAUC: no visible global function definition for ‘ecdf’
ecdfAUC: no visible global function definition for ‘trapz’
ecdfAUC: no visible global function definition for ‘plot’
ecdfAUC: no visible global function definition for ‘mtext’
ecdfAUC: no visible global function definition for ‘axis’
ecdfAUC: no visible global function definition for ‘box’
ecdfAUC: no visible global function definition for ‘lines’
ecdfAUC: no visible global function definition for ‘abline’
ecdfAUC: no visible global function definition for ‘legend’
exactNBtest1: no visible global function definition for ‘dnbinom’
getAdjustDisp: no visible global function definition for ‘quantile’
getAdjustDisp: no visible global function definition for ‘var’
getNormFactor : <anonymous>: no visible global function definition for
  ‘median’
getQ: no visible global function definition for ‘quantile’
getQ: no visible global function definition for ‘cov’
getQ: no visible global function definition for ‘var’
getQ: no visible global function definition for ‘plot’
getQ: no visible global function definition for ‘abline’
getQ: no visible global function definition for ‘mtext’
getT: no visible global function definition for ‘quantile’
getT: no visible global function definition for ‘sd’
getT: no visible global function definition for ‘cov’
getT: no visible global function definition for ‘var’
getT: no visible global function definition for ‘plot’
getT: no visible global function definition for ‘mtext’
getT: no visible global function definition for ‘axis’
getT: no visible global function definition for ‘abline’
getTgroup: no visible global function definition for ‘quantile’
getTgroup: no visible global function definition for ‘cov’
getTgroup: no visible global function definition for ‘var’
getTgroup: no visible global function definition for ‘plot’
getTgroup: no visible global function definition for ‘mtext’
getTgroup: no visible global function definition for ‘box’
getTgroup: no visible global function definition for ‘axis’
getTgroup: no visible global function definition for ‘abline’
nbinomTestForMatricesSH : int.func: no visible global function
  definition for ‘median’
nbinomTestForMatricesSH: no visible global function definition for
  ‘dnbinom’
nbinomTestForMatricesSH: no visible global function definition for
  ‘pchisq’
plotDispersion: no visible global function definition for ‘brewer.pal’
plotDispersion: no visible global function definition for
  ‘smoothScatter’
plotDispersion: no visible binding for global variable ‘blues9’
plotDispersion: no visible global function definition for ‘points’
plotDispersion: no visible global function definition for ‘legend’
plotDispersion: no visible global function definition for ‘plot’
rnbinomMV: no visible global function definition for ‘rnbinom’
rowVars: no visible binding for global variable ‘var’
sim: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis blues9 box brewer.pal cov dnbinom ecdf legend lines
  median mtext par pchisq plot points quantile rnbinom rnorm sd
  smoothScatter trapz var
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "mtext", "par", "plot", "points", "smoothScatter")
  importFrom("stats", "cov", "dnbinom", "ecdf", "median", "pchisq",
             "quantile", "rnbinom", "rnorm", "sd", "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
nbTestSH       92.680  3.813  97.519
sSeq-package   86.063  3.399  90.285
getTgroup      84.630  3.082  88.655
plotDispersion  6.972  0.304   7.325
* 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-3.9-bioc/meat/sSeq.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 sSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘sSeq’ ...
** R
** data
** 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 (sSeq)

name	user	system	elapsed
Hammer2months	0.082	0.010	0.092
Sultan	0.074	0.007	0.085
Tuch	0.029	0.004	0.036
countsTable	0.020	0.005	0.026
drawMA_vol	0.524	0.002	0.538
ecdfAUC	0.014	0.000	0.015
equalSpace	0.961	0.011	0.990
exactNBtest1	0	0	0
getAdjustDisp	1.043	0.014	1.071
getNormFactor	0.028	0.006	0.035
getQ	2.075	0.211	2.313
getT	1.816	0.154	1.996
getTgroup	84.630	3.082	88.655
nbTestSH	92.680	3.813	97.519
plotDispersion	6.972	0.304	7.325
rnbinomMV	0.003	0.000	0.003
rowVars	0.001	0.000	0.001
sSeq-package	86.063	3.399	90.285
sim	0.326	0.028	0.355