Package: snm

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:snm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings snm_1.34.0.tar.gz

StartedAt: 2020-04-15 05:49:13 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:54:56 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 343.7 seconds

RetCode: 0

Status:  OK

CheckDir: snm.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:snm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings snm_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/snm.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘snm’ version ‘1.34.0’
* 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 ‘snm’ 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
buildBasisSplineMatrix : <anonymous>: no visible global function
  definition for ‘predict’
calcArrayEffects : <anonymous>: no visible global function definition
  for ‘predict’
edge.glr: no visible global function definition for ‘pf’
edge.qvalue: no visible global function definition for ‘smooth.spline’
edge.qvalue: no visible global function definition for ‘predict’
fit.model: no visible binding for global variable ‘weighted.mean’
fit.model: no visible global function definition for ‘residuals’
getSpanningSet: no visible global function definition for ‘quantile’
make.ref.model.matrices: no visible global function definition for
  ‘model.matrix’
make.ref.model.matrices: no visible global function definition for
  ‘as.formula’
make.snm.obj: no visible global function definition for ‘model.matrix’
sim.doubleChannel: no visible global function definition for ‘rchisq’
sim.doubleChannel: no visible global function definition for ‘runif’
sim.doubleChannel: no visible global function definition for ‘rnorm’
sim.doubleChannel: no visible binding for global variable ‘rnorm’
sim.doubleChannel: no visible global function definition for
  ‘model.matrix’
sim.function.var: no visible global function definition for
  ‘model.matrix’
sim.intensity.dep: no visible global function definition for
  ‘model.matrix’
sim.intensity.dep: no visible global function definition for ‘predict’
sim.preProcessed: no visible global function definition for ‘rchisq’
sim.preProcessed: no visible global function definition for ‘runif’
sim.preProcessed: no visible global function definition for ‘rnorm’
sim.preProcessed: no visible binding for global variable ‘rnorm’
sim.preProcessed: no visible global function definition for
  ‘model.matrix’
sim.probe.specific: no visible global function definition for
  ‘model.matrix’
sim.refDesign: no visible global function definition for ‘rchisq’
sim.refDesign: no visible global function definition for ‘runif’
sim.refDesign: no visible binding for global variable ‘rnorm’
sim.refDesign: no visible global function definition for ‘rnorm’
sim.refDesign: no visible global function definition for ‘model.matrix’
sim.singleChannel: no visible global function definition for ‘rchisq’
sim.singleChannel: no visible global function definition for ‘runif’
sim.singleChannel: no visible global function definition for ‘rnorm’
sim.singleChannel: no visible binding for global variable ‘rnorm’
sim.singleChannel: no visible global function definition for
  ‘model.matrix’
snm.diagnostic.plot: no visible global function definition for ‘par’
snm.diagnostic.plot: no visible global function definition for ‘plot’
snm.diagnostic.plot: no visible global function definition for ‘axis’
snm.diagnostic.plot : <anonymous>: no visible global function
  definition for ‘points’
snm.diagnostic.plot: no visible global function definition for ‘hist’
snm.diagnostic.plot: no visible global function definition for ‘abline’
snm.diagnostic.plot: no visible global function definition for ‘mtext’
snm.diagnostic.plot: no visible global function definition for ‘title’
snm.plot: no visible global function definition for ‘model.matrix’
snm.plot: no visible global function definition for ‘rainbow’
snm.plot: no visible global function definition for ‘plot’
snm.plot: no visible global function definition for ‘points’
snm.plot: no visible global function definition for ‘par’
snm.plot: no visible global function definition for ‘abline’
snm.plot: no visible global function definition for ‘fitted’
snm.plot: no visible global function definition for ‘hist’
snm.plot: no visible global function definition for ‘mtext’
snm.plot: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline as.formula axis fitted hist model.matrix mtext par pf plot
  points predict quantile rainbow rchisq residuals rnorm runif
  smooth.spline title weighted.mean
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
             "plot", "points", "title")
  importFrom("stats", "as.formula", "fitted", "model.matrix", "pf",
             "predict", "quantile", "rchisq", "residuals", "rnorm",
             "runif", "smooth.spline", "weighted.mean")
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
sim.refDesign 139.397 14.757 155.896
snm           116.657  7.693 125.555
* 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-3.10-bioc/meat/snm.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 snm
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘snm’ ...
** using staged installation
** 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 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 (snm)

name	user	system	elapsed
fitted.snm	0.000	0.000	0.001
plot.snm	0	0	0
sim.doubleChannel	0	0	0
sim.preProcessed	3.417	0.197	3.647
sim.refDesign	139.397	14.757	155.896
sim.singleChannel	0	0	0
snm	116.657	7.693	125.555
summary.snm	0.000	0.000	0.001