BioC 3.3: CHECK report for SemDist on morelia

Package: SemDist

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SemDist_1.5.0.tar.gz

StartedAt: 2016-04-21 07:24:16 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:25:53 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 96.7 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 --no-vignettes --timings SemDist_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SemDist.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SemDist/DESCRIPTION’ ... OK
* this is package ‘SemDist’ version ‘1.5.0’
* 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 ... [9s/12s] 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘introduction.bbl’
Please remove them from your package.
* checking examples ... [13s/13s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
RUMIcurve 6.813  0.278   7.235
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/SemDist.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
IAccr	0.029	0.005	0.034
RUMIcurve	6.813	0.278	7.235
computeIA	1.002	0.013	1.023
findRUMI	1.060	0.033	1.099
parentcnt	0.004	0.001	0.005
termcnt	0.004	0.001	0.005