Package: iASeq

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iASeq_1.31.0.tar.gz

StartedAt: 2020-01-16 05:29:41 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 05:30:20 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 39.1 seconds

RetCode: 0

Status:  OK

CheckDir: iASeq.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:iASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iASeq_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/iASeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iASeq’ version ‘1.31.0’
* 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 ‘iASeq’ 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
ASErawfit: no visible global function definition for ‘var’
fdown.loglike: no visible global function definition for ‘pbeta’
fup.loglike: no visible global function definition for ‘pbeta’
iASeqmotiffit: no visible global function definition for ‘runif’
iASeqmotiffit: no visible global function definition for ‘var’
plotBIC: no visible global function definition for ‘lines’
plotMotif: no visible global function definition for ‘image’
singleEMfit: no visible global function definition for ‘var’
Undefined global functions or variables:
  image lines pbeta runif var
Consider adding
  importFrom("graphics", "image", "lines")
  importFrom("stats", "pbeta", "runif", "var")
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
* 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-3.11-bioc/meat/iASeq.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 iASeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘iASeq’ ...
** using staged installation
** R
** data
** 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 (iASeq)

name	user	system	elapsed
ASErawfit	0.043	0.016	0.060
iASeqmotif	0.775	0.144	0.919
plotBIC	0.702	0.081	0.783
plotMotif	0.773	0.069	0.843
sampleASE	0.669	0.070	0.740
singleEMfit	0.236	0.046	0.282