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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:qvalue.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings qvalue_2.33.0.tar.gz
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* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/qvalue.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
    GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘qvalue/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qvalue’ version ‘2.33.0’
* 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 ‘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 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘qvalue.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/hpages/bbs-3.18-bioc-testing/meat/qvalue.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL qvalue
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘qvalue’ ...
** 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 (qvalue)