BioC 3.5: CHECK report for MethTargetedNGS on malbec2

Package: MethTargetedNGS

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MethTargetedNGS_1.8.0.tar.gz

StartedAt: 2017-10-18 00:44:07 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:45:24 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 77.1 seconds

RetCode: 0

Status:  OK

CheckDir: MethTargetedNGS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MethTargetedNGS_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MethTargetedNGS.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethTargetedNGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethTargetedNGS’ version ‘1.8.0’
* 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 ‘MethTargetedNGS’ 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 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
compare_samples: no visible global function definition for ‘par’
compare_samples: no visible global function definition for ‘plot’
compare_samples: no visible global function definition for ‘lines’
fishertest_cpg: no visible global function definition for ‘fisher.test’
fishertest_cpg: no visible global function definition for ‘p.adjust’
fishertest_cpg: no visible global function definition for ‘barplot’
fishertest_cpg: no visible global function definition for ‘abline’
methAlign: no visible global function definition for ‘subject’
methAlign: no visible global function definition for ‘pattern’
nhmmer: no visible global function definition for ‘read.table’
nhmmer: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  abline barplot fisher.test lines p.adjust par pattern plot read.table
  setNames subject
Consider adding
  importFrom("graphics", "abline", "barplot", "lines", "par", "plot")
  importFrom("stats", "fisher.test", "p.adjust", "setNames")
  importFrom("utils", "read.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/MethTargetedNGS.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
bconv	0.000	0.000	0.002
compare_samples	4.244	0.016	4.262
fishertest_cpg	3.616	0.000	3.619
hmmbuild	0.004	0.000	0.001
methAlign	1.740	0.000	1.741
methAvg	1.812	0.000	1.812
methEntropy	1.812	0.000	1.812
methHeatmap	1.812	0.000	1.814
nhmmer	0.000	0.000	0.001
odd_ratio	3.604	0.000	3.605