BioC 3.5: CHECK report for Rnits on oaxaca

Package: Rnits

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rnits_1.9.0.tar.gz

StartedAt: 2017-03-04 08:25:49 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:27:18 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 89.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rnits.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 Rnits_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rnits.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 ‘Rnits/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rnits’ version ‘1.9.0’
* 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 ‘Rnits’ 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 loading without being on the library search path ... 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
build.Rnits: no visible global function definition for ‘median’
build.Rnits: no visible global function definition for ‘sd’
finds0: no visible global function definition for ‘rnorm’
finds0: no visible global function definition for ‘quantile’
finds0: no visible global function definition for ‘mad’
finds0 : <anonymous>: no visible global function definition for ‘sd’
modelfit: no visible global function definition for ‘hat’
ranknormalization: no visible binding for global variable ‘median’
ranknormalization: no visible global function definition for
  ‘smooth.spline’
ranknormalization: no visible global function definition for ‘predict’
ranknormalization: no visible global function definition for ‘par’
solvemat: no visible global function definition for ‘hat’
tsFit: no visible global function definition for ‘txtProgressBar’
tsFit: no visible global function definition for ‘setTxtProgressBar’
calculateGCV,Rnits: no visible global function definition for ‘glm’
calculateGCV,Rnits: no visible binding for global variable ‘gaussian’
fit,Rnits: no visible global function definition for ‘kmeans’
fit,Rnits : <anonymous>: no visible global function definition for
  ‘p.adjust’
fit,Rnits: no visible global function definition for ‘par’
fit,Rnits: no visible global function definition for ‘hist’
getCID,Rnits: no visible global function definition for ‘setNames’
getPval,Rnits: no visible global function definition for ‘setNames’
getStat,Rnits: no visible global function definition for ‘setNames’
plotResults,Rnits: no visible global function definition for ‘aes’
plotResults,Rnits: no visible binding for global variable ‘Time’
plotResults,Rnits: no visible binding for global variable ‘value’
plotResults,Rnits: no visible global function definition for
  ‘geom_point’
plotResults,Rnits: no visible binding for global variable ‘Sample’
plotResults,Rnits: no visible global function definition for
  ‘geom_smooth’
plotResults,Rnits: no visible global function definition for ‘ylab’
plotResults,Rnits: no visible global function definition for ‘theme_bw’
plotResults,Rnits: no visible global function definition for ‘theme’
plotResults,Rnits: no visible global function definition for
  ‘scale_color_brewer’
plotResults,Rnits: no visible global function definition for
  ‘facet_wrap’
plotResults,Rnits: no visible global function definition for ‘dev.off’
summary,Rnits: no visible global function definition for ‘hist’
timeAlign,Rnits: no visible global function definition for ‘quantile’
timeAlign,Rnits: no visible global function definition for ‘mvfft’
timeAlign,Rnits: no visible global function definition for ‘abline’
Undefined global functions or variables:
  Sample Time abline aes dev.off facet_wrap gaussian geom_point
  geom_smooth glm hat hist kmeans mad median mvfft p.adjust par predict
  quantile rnorm scale_color_brewer sd setNames setTxtProgressBar
  smooth.spline theme theme_bw txtProgressBar value ylab
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "gaussian", "glm", "hat", "kmeans", "mad",
             "median", "mvfft", "p.adjust", "predict", "quantile",
             "rnorm", "sd", "setNames", "smooth.spline")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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
calculateGCV-methods 6.63   0.11   6.741
* 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/Rnits.Rcheck/00check.log’
for details.

* installing *source* package ‘Rnits’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rnits)

name	user	system	elapsed
build.Rnits	0.805	0.025	0.830
calculateGCV-methods	6.630	0.110	6.741
fit-methods	0.316	0.019	0.335
getCID-methods	0.335	0.025	0.359
getFitModel-methods	0.380	0.018	0.398
getLR-methods	0.288	0.011	0.299
getPval-methods	0.406	0.024	0.429
getStat-methods	0.317	0.021	0.338
plotResults-methods	0.430	0.014	0.445
summarizeProbes-methods	0.348	0.005	0.353
summary-methods	0.306	0.021	0.327
timeAlign-methods	1.291	0.227	1.519
topData-methods	0.220	0.016	0.237