Package: SemDist

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SemDist.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SemDist_1.17.0.tar.gz

StartedAt: 2019-04-09 05:22:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:26:14 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 224.2 seconds

RetCode: 0

Status:  OK

CheckDir: SemDist.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:SemDist.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SemDist_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SemDist.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 ‘SemDist/DESCRIPTION’ ... OK
* this is package ‘SemDist’ version ‘1.17.0’
* 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 ‘SemDist’ 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
RUMIcurve : IA_sum: no visible global function definition for ‘na.omit’
computeIA: no visible global function definition for ‘read.table’
findRUMI : IA_sum: no visible global function definition for ‘na.omit’
getPredictions: no visible global function definition for ‘read.table’
getTrues: no visible global function definition for ‘read.table’
loadIA: no visible global function definition for ‘data’
readOntology: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  data na.omit read.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data", "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 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
Examples with CPU or elapsed time > 5s
           user system elapsed
RUMIcurve 6.593  1.388   7.986
* 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/SemDist.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 SemDist
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SemDist’ ...
** 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 (SemDist)

name	user	system	elapsed
IAccr	0.025	0.009	0.034
RUMIcurve	6.593	1.388	7.986
computeIA	0.747	0.088	0.837
findRUMI	0.885	0.172	1.057
parentcnt	0.008	0.002	0.011
termcnt	0.007	0.001	0.009