Package: NOISeq

Version: 2.27.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NOISeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NOISeq_2.27.1.tar.gz

StartedAt: 2019-04-09 02:32:01 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:34:49 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 167.7 seconds

RetCode: 0

Status:  OK

CheckDir: NOISeq.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:NOISeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NOISeq_2.27.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/NOISeq.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 ‘NOISeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NOISeq’ version ‘2.27.1’
* 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 ‘NOISeq’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcFactorQuantile : <anonymous>: no visible global function
  definition for ‘quantile’
CV: no visible global function definition for ‘sd’
DE.plot: no visible global function definition for ‘par’
DE.plot: no visible global function definition for ‘plot’
DE.plot: no visible global function definition for ‘points’
DE.plot: no visible global function definition for ‘axis’
DE.plot: no visible global function definition for ‘na.omit’
DE.plot: no visible global function definition for ‘aggregate’
DE.plot: no visible global function definition for ‘abline’
DE.plot: no visible global function definition for ‘rect’
DE.plot: no visible global function definition for ‘segments’
DE.plot: no visible global function definition for ‘text’
DE.plot: no visible global function definition for ‘layout’
DE.plot: no visible global function definition for ‘barplot’
DE.plot: no visible global function definition for ‘legend’
GC.dat: no visible global function definition for ‘quantile’
GC.dat: no visible global function definition for ‘aggregate’
GC.dat: no visible global function definition for ‘lm’
GC.plot: no visible global function definition for ‘par’
GC.plot: no visible global function definition for ‘matplot’
GC.plot: no visible global function definition for ‘text’
GC.plot: no visible global function definition for ‘pf’
GC.plot: no visible global function definition for ‘legend’
GC.plot: no visible global function definition for ‘layout’
MD: no visible global function definition for ‘combn’
MD.plot: no visible global function definition for ‘quantile’
MD.plot: no visible global function definition for ‘plot’
MD.plot: no visible global function definition for ‘points’
MD.plot: no visible global function definition for ‘legend’
MDbio: no visible global function definition for ‘combn’
MDbio: no visible global function definition for ‘quantile’
PCA.plot: no visible global function definition for ‘plot’
PCA.plot: no visible global function definition for ‘colors’
PCA.plot: no visible global function definition for ‘points’
PCA.plot: no visible global function definition for ‘legend’
QCreport: no visible global function definition for ‘pdf’
QCreport: no visible global function definition for ‘layout’
QCreport: no visible global function definition for ‘par’
QCreport: no visible global function definition for ‘plot’
QCreport: no visible global function definition for ‘text’
QCreport: no visible global function definition for ‘abline’
QCreport : <anonymous>: no visible global function definition for ‘pf’
QCreport: no visible global function definition for ‘dev.off’
allMDbio: no visible binding for global variable ‘sd’
biodetection.plot: no visible global function definition for ‘par’
biodetection.plot: no visible global function definition for ‘barplot’
biodetection.plot: no visible global function definition for ‘axis’
biodetection.plot: no visible global function definition for ‘abline’
biodetection.plot: no visible global function definition for ‘legend’
biodetection.plot: no visible global function definition for
  ‘prop.test’
biodetection.plot: no visible global function definition for ‘lines’
cd.dat : <anonymous>: no visible binding for global variable ‘median’
cd.dat: no visible binding for global variable ‘quantile’
cd.plot: no visible binding for global variable ‘density’
cd.plot: no visible global function definition for ‘plot’
cd.plot: no visible global function definition for ‘abline’
cd.plot: no visible global function definition for ‘median’
cd.plot: no visible global function definition for ‘lines’
cd.plot: no visible global function definition for ‘legend’
countsbio.plot: no visible global function definition for ‘par’
countsbio.plot: no visible global function definition for ‘barplot’
countsbio.plot: no visible global function definition for ‘abline’
countsbio.plot: no visible global function definition for ‘mtext’
countsbio.plot: no visible global function definition for ‘legend’
countsbio.plot: no visible global function definition for ‘boxplot’
countsbio.plot: no visible global function definition for ‘axis’
degenes: no visible global function definition for ‘na.omit’
filtered.data : <anonymous>: no visible global function definition for
  ‘wilcox.test’
filtered.data: no visible global function definition for ‘p.adjust’
filtered.data : <anonymous>: no visible global function definition for
  ‘prop.test’
length.dat: no visible global function definition for ‘quantile’
length.dat: no visible global function definition for ‘aggregate’
length.dat: no visible global function definition for ‘lm’
length.plot: no visible global function definition for ‘par’
length.plot: no visible global function definition for ‘matplot’
length.plot: no visible global function definition for ‘text’
length.plot: no visible global function definition for ‘pf’
length.plot: no visible global function definition for ‘legend’
length.plot: no visible global function definition for ‘layout’
noiseqbio: no visible global function definition for ‘density’
noiseqbio: no visible global function definition for ‘approxfun’
noiseqbio: no visible global function definition for ‘lines’
noiseqbio: no visible global function definition for ‘legend’
plot.y2: no visible global function definition for ‘plot’
plot.y2: no visible global function definition for ‘axis’
plot.y2: no visible global function definition for ‘points’
plot.y2: no visible global function definition for ‘lines’
plot.y2: no visible global function definition for ‘supsmu’
plot.y2: no visible global function definition for ‘mtext’
plot.y2: no visible global function definition for ‘par’
plot.y2: no visible global function definition for ‘box’
probdeg: no visible global function definition for ‘na.omit’
rpkm: no visible global function definition for ‘na.omit’
saturation.dat: no visible global function definition for ‘rmultinom’
saturation.plot: no visible global function definition for ‘par’
saturation.plot: no visible global function definition for ‘colors’
saturation.plot: no visible global function definition for ‘plot’
saturation.plot: no visible global function definition for ‘lines’
saturation.plot: no visible global function definition for ‘points’
saturation.plot: no visible global function definition for ‘na.omit’
saturation.plot: no visible global function definition for ‘layout’
saturation.plot: no visible global function definition for ‘rect’
saturation.plot: no visible global function definition for ‘text’
share.info: no visible global function definition for ‘kmeans’
share.info : <anonymous>: no visible global function definition for
  ‘sd’
share.info: no visible global function definition for ‘quantile’
sim.samples: no visible global function definition for ‘runif’
sim.samples: no visible global function definition for ‘rmultinom’
tmm: no visible global function definition for ‘na.omit’
uqua: no visible binding for global variable ‘quantile’
uqua: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  abline aggregate approxfun axis barplot box boxplot colors combn
  density dev.off kmeans layout legend lines lm matplot median mtext
  na.omit p.adjust par pdf pf plot points prop.test quantile rect
  rmultinom runif sd segments supsmu text wilcox.test
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "layout", "legend", "lines", "matplot", "mtext", "par",
             "plot", "points", "rect", "segments", "text")
  importFrom("stats", "aggregate", "approxfun", "density", "kmeans",
             "lm", "median", "na.omit", "p.adjust", "pf", "prop.test",
             "quantile", "rmultinom", "runif", "sd", "supsmu",
             "wilcox.test")
  importFrom("utils", "combn")
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
noiseqbio 37.320  0.158  37.813
noiseq    21.236  8.645  31.386
QCreport   8.509  0.732   9.366
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/NOISeq.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 NOISeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NOISeq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘NOISeq.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (NOISeq)

name	user	system	elapsed
ARSyNSeq	2.997	0.137	3.173
DE.plot	0.255	0.019	0.276
PCA.GENES	0.007	0.000	0.007
QCreport	8.509	0.732	9.366
dat	0.282	0.007	0.308
dat2save	0.196	0.003	0.210
degenes	0.089	0.009	0.102
explo.plot	0.238	0.006	0.250
filter.low.counts	0.998	0.003	1.047
noiseq	21.236	8.645	31.386
noiseqbio	37.320	0.158	37.813
normalization	0.005	0.000	0.005
readData	0.242	0.006	0.250