Package: SPIA

Version: 2.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SPIA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPIA_2.34.0.tar.gz

StartedAt: 2019-04-16 02:56:23 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:04:44 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 501.1 seconds

RetCode: 0

Status:  OK

CheckDir: SPIA.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:SPIA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPIA_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SPIA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPIA/DESCRIPTION’ ... OK
* this is package ‘SPIA’ version ‘2.34.0’
* 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 ‘SPIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’
A package should be listed in only one of these fields.
* 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 ... NOTE
Package in Depends field not imported from: ‘KEGGgraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combfunc: no visible global function definition for ‘na.omit’
combfunc: no visible global function definition for ‘pnorm’
combfunc: no visible global function definition for ‘qnorm’
getP2: no visible global function definition for ‘qchisq’
getP2: no visible global function definition for ‘pnorm’
getP2: no visible global function definition for ‘qnorm’
makeSPIAdata: no visible global function definition for ‘parseKGML’
makeSPIAdata: no visible global function definition for ‘nodes’
makeSPIAdata: no visible global function definition for ‘na.omit’
makeSPIAdata: no visible global function definition for ‘edges’
plotP: no visible global function definition for ‘na.omit’
plotP: no visible global function definition for ‘pnorm’
plotP: no visible global function definition for ‘qnorm’
plotP: no visible global function definition for ‘text’
spia: no visible global function definition for ‘pdf’
spia: no visible global function definition for ‘par’
spia: no visible global function definition for ‘phyper’
spia: no visible global function definition for ‘median’
spia: no visible global function definition for ‘sd’
spia: no visible global function definition for ‘density’
spia: no visible global function definition for ‘dev.off’
spia: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  density dev.off edges median na.omit nodes p.adjust par parseKGML pdf
  phyper pnorm qchisq qnorm sd text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "text")
  importFrom("stats", "density", "median", "na.omit", "p.adjust",
             "phyper", "pnorm", "qchisq", "qnorm", "sd")
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
spia         353.523 21.688 382.055
plotP         69.731  5.654  76.019
makeSPIAdata   5.897  0.452   6.397
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/SPIA.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 SPIA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SPIA’ ...
** 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
* DONE (SPIA)

name	user	system	elapsed
combfunc	0.001	0.000	0.001
makeSPIAdata	5.897	0.452	6.397
plotP	69.731	5.654	76.019
spia	353.523	21.688	382.055