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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qvalue.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qvalue_2.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/qvalue.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 ‘qvalue/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qvalue’ version ‘2.38.0’
* 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 ‘qvalue’ 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hist.qvalue: no visible binding for global variable ‘density’
lfdr: no visible global function definition for ‘qnorm’
lfdr: no visible global function definition for ‘density’
lfdr: no visible global function definition for ‘smooth.spline’
lfdr: no visible global function definition for ‘predict’
lfdr: no visible global function definition for ‘dnorm’
pi0est: no visible global function definition for ‘smooth.spline’
pi0est: no visible global function definition for ‘predict’
pi0est: no visible global function definition for ‘quantile’
plot.qvalue: no visible global function definition for ‘quantile’
write.qvalue: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  density dnorm predict qnorm quantile smooth.spline write.table
Consider adding
  importFrom("stats", "density", "dnorm", "predict", "qnorm", "quantile",
             "smooth.spline")
  importFrom("utils", "write.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’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/qvalue.Rcheck/00check.log’
for details.