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 05:45:34 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:51:17 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 343.4 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) (2019-03-18 r76245)
* 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     92.235  7.320 102.085
sSeq-package 88.938  6.434  98.075
getTgroup    87.675  6.222  94.010
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sSeq)

name	user	system	elapsed
Hammer2months	0.071	0.012	0.084
Sultan	0.077	0.012	0.089
Tuch	0.035	0.007	0.042
countsTable	0.016	0.006	0.021
drawMA_vol	0.530	0.006	0.536
ecdfAUC	0.023	0.004	0.027
equalSpace	0.401	0.015	0.416
exactNBtest1	0.001	0.001	0.001
getAdjustDisp	0.406	0.011	0.415
getNormFactor	0.020	0.008	0.028
getQ	1.314	0.333	1.648
getT	1.117	0.292	1.432
getTgroup	87.675	6.222	94.010
nbTestSH	92.235	7.320	102.085
plotDispersion	3.198	0.552	3.809
rnbinomMV	0.003	0.000	0.003
rowVars	0.000	0.000	0.001
sSeq-package	88.938	6.434	98.075
sim	0.319	0.053	0.372