Package: rHVDM

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rHVDM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rHVDM_1.46.0.tar.gz

StartedAt: 2018-10-16 23:42:21 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:44:06 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 105.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rHVDM.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rHVDM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rHVDM_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/rHVDM.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.46.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/rHVDM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
screening.nl 13.632  0.106  13.908
fitgene.nl   13.300  0.114  16.720
training.nl  12.777  0.100  13.103
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/rHVDM.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 rHVDM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rHVDM’ ...
** R
** data
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rHVDM)

name	user	system	elapsed
HVDMcheck	0.271	0.022	0.294
HVDMreport	0.919	0.037	0.960
estimerrors	1.930	0.093	2.035
fitgene	0.958	0.031	0.995
fitgene.lin	0.850	0.025	0.880
fitgene.nl	13.300	0.114	16.720
screening	1.259	0.027	1.296
screening.nl	13.632	0.106	13.908
training	0.910	0.026	0.953
training.nl	12.777	0.100	13.103