Package: MethTargetedNGS

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2019-04-09 03:26:28 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:28:40 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 132.7 seconds

RetCode: 0

Status:  OK

CheckDir: MethTargetedNGS.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MethTargetedNGS.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.0’
* 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 6.491  0.184   6.678
odd_ratio       5.787  0.057   5.844
fishertest_cpg  4.969  0.050   5.019
* 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-3.9-bioc/meat/MethTargetedNGS.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 MethTargetedNGS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MethTargetedNGS’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MethTargetedNGS)

name	user	system	elapsed
bconv	0.003	0.001	0.005
compare_samples	6.491	0.184	6.678
fishertest_cpg	4.969	0.050	5.019
hmmbuild	0.001	0.001	0.002
methAlign	3.147	0.034	3.180
methAvg	2.828	0.026	2.854
methEntropy	3.300	0.028	3.329
methHeatmap	3.071	0.124	3.195
nhmmer	0.003	0.001	0.003
odd_ratio	5.787	0.057	5.844