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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPIA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPIA_2.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SPIA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPIA/DESCRIPTION’ ... OK
* this is package ‘SPIA’ version ‘2.58.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 (user + system) or elapsed time > 5s
         user system elapsed
spia  115.249  5.144 120.393
plotP  25.436  1.181  26.617
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/SPIA.Rcheck/00check.log’
for details.