Package: MethTargetedNGS

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MethTargetedNGS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MethTargetedNGS_1.12.0.tar.gz

StartedAt: 2018-10-16 22:32:31 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:34:19 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 108.3 seconds

RetCode: 0

Status:  OK

CheckDir: MethTargetedNGS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MethTargetedNGS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MethTargetedNGS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MethTargetedNGS.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 ‘MethTargetedNGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethTargetedNGS’ version ‘1.12.0’
* 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 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 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
compare_samples 6.054  0.117   6.303
odd_ratio       5.653  0.044   5.753
fishertest_cpg  5.132  0.054   5.270
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/MethTargetedNGS.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MethTargetedNGS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MethTargetedNGS’ ...
** R
** inst
** byte-compile and prepare 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	0.003	0.001	0.003
compare_samples	6.054	0.117	6.303
fishertest_cpg	5.132	0.054	5.270
hmmbuild	0.002	0.000	0.002
methAlign	2.467	0.030	2.548
methAvg	2.778	0.030	2.846
methEntropy	2.751	0.035	2.848
methHeatmap	2.825	0.049	2.921
nhmmer	0.003	0.000	0.003
odd_ratio	5.653	0.044	5.753