BioC 3.4: CHECK report for DMRcate on zin1

Package: DMRcate

Version: 1.9.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DMRcate_1.9.2.tar.gz

StartedAt: 2016-09-20 05:40:24 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:46:37 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 373.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DMRcate.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DMRcate_1.9.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DMRcate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘1.9.2’
* 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 ‘DMRcate’ 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 ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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
DMR.plot: no visible global function definition for 'subjectHits'
DMR.plot: no visible binding for global variable 'tx.hg19'
DMR.plot: no visible binding for global variable 'tx.hg38'
DMR.plot: no visible binding for global variable 'tx.mm10'
KernelTest: no visible global function definition for 'pchisq'
SparseDeltas: no visible global function definition for 'approx'
dmrcate: no visible global function definition for 'p.adjust'
dmrcate : <anonymous>: no visible global function definition for
  'pnorm'
dmrcate : <anonymous>: no visible global function definition for
  'qnorm'
extractRanges: no visible binding for global variable 'tx.hg19'
extractRanges: no visible binding for global variable 'tx.hg38'
extractRanges: no visible binding for global variable 'tx.mm10'
rmSNPandCH: no visible global function definition for 'data'
rmSNPandCH: no visible binding for global variable 'dmrcatedata'
Undefined global functions or variables:
  approx data dmrcatedata p.adjust pchisq pnorm qnorm subjectHits
  tx.hg19 tx.hg38 tx.mm10
Consider adding
  importFrom("stats", "approx", "p.adjust", "pchisq", "pnorm", "qnorm")
  importFrom("utils", "data")
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
DMRcate-package 38.248  1.568  60.268
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DMRcate.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DMR.plot	0.000	0.000	0.001
DMRcate-package	38.248	1.568	60.268
cpg.annotate	0.000	0.000	0.001
dmrcate	0	0	0
extractRanges	0.004	0.000	0.001
rmSNPandCH	0	0	0