BioC 3.4: CHECK report for rHVDM on morelia

Package: rHVDM

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rHVDM_1.40.0.tar.gz

StartedAt: 2017-04-15 07:17:53 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:19:36 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 102.7 seconds

RetCode: 0

Status:  OK

CheckDir: rHVDM.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 rHVDM_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rHVDM.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rHVDM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rHVDM’ version ‘1.40.0’
* 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 ‘rHVDM’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* 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
.bin.ut: no visible global function definition for ‘quantile’
.binb.ut: no visible global function definition for ‘quantile’
.geneoutput: no visible global function definition for ‘png’
.geneoutput: no visible global function definition for ‘par’
.geneoutput: no visible global function definition for ‘plot’
.geneoutput: no visible global function definition for ‘arrows’
.geneoutput: no visible global function definition for ‘lines’
.geneoutput: no visible global function definition for ‘dev.off’
.greport: no visible global function definition for ‘runif’
.parameteroutput: no visible global function definition for ‘png’
.parameteroutput: no visible global function definition for ‘par’
.parameteroutput: no visible global function definition for ‘arrows’
.parameteroutput: no visible global function definition for ‘dev.off’
.parameteroutput: no visible global function definition for ‘plot’
.parameteroutput: no visible global function definition for ‘lines’
.parameteroutput: no visible global function definition for ‘cov2cor’
.parameteroutputg: no visible global function definition for ‘png’
.parameteroutputg: no visible global function definition for ‘par’
.parameteroutputg: no visible global function definition for ‘arrows’
.parameteroutputg: no visible global function definition for ‘dev.off’
.parameteroutputg: no visible global function definition for ‘cov2cor’
.parameteroutputg.nl: no visible global function definition for ‘png’
.parameteroutputg.nl: no visible global function definition for ‘par’
.parameteroutputg.nl: no visible global function definition for
  ‘arrows’
.parameteroutputg.nl: no visible global function definition for
  ‘dev.off’
.parameteroutputg.nl: no visible global function definition for
  ‘cov2cor’
.scoreoutput: no visible global function definition for ‘qchisq’
.scoreoutput: no visible global function definition for ‘png’
.scoreoutput: no visible global function definition for ‘par’
.scoreoutput: no visible global function definition for ‘plot’
.scoreoutput: no visible global function definition for ‘dchisq’
.scoreoutput: no visible global function definition for ‘points’
.scoreoutput: no visible global function definition for ‘qnorm’
.scoreoutput: no visible global function definition for ‘lines’
.scoreoutput: no visible global function definition for ‘dev.off’
.scorout: no visible global function definition for ‘pchisq’
.screenoutput: no visible global function definition for ‘png’
.screenoutput: no visible global function definition for ‘plot’
.screenoutput: no visible global function definition for ‘lines’
.screenoutput: no visible global function definition for ‘dev.off’
.sreport: no visible global function definition for ‘runif’
.treport: no visible global function definition for ‘runif’
Undefined global functions or variables:
  arrows cov2cor dchisq dev.off lines par pchisq plot png points qchisq
  qnorm quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "arrows", "lines", "par", "plot", "points")
  importFrom("stats", "cov2cor", "dchisq", "pchisq", "qchisq", "qnorm",
             "quantile", "runif")
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
screening.nl 10.048  0.084  10.135
training.nl   8.471  0.073   8.545
fitgene.nl    8.421  0.087   8.510
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/rHVDM.Rcheck/00check.log’
for details.

* installing *source* package ‘rHVDM’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rHVDM)

name	user	system	elapsed
HVDMcheck	0.324	0.017	0.340
HVDMreport	0.709	0.027	0.736
estimerrors	2.039	0.110	2.149
fitgene	0.724	0.029	0.754
fitgene.lin	0.705	0.023	0.727
fitgene.nl	8.421	0.087	8.510
screening	1.012	0.026	1.038
screening.nl	10.048	0.084	10.135
training	0.643	0.020	0.663
training.nl	8.471	0.073	8.545