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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:hierGWAS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings hierGWAS_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hierGWAS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘hierGWAS/DESCRIPTION’ ... OK
* this is package ‘hierGWAS’ version ‘1.36.0’
* 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 ‘hierGWAS’ 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 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
MEL: no visible global function definition for ‘glm’
MEL: no visible binding for global variable ‘binomial’
MEL: no visible global function definition for ‘glm.control’
MEL: no visible global function definition for ‘coef’
adj.pval: no visible global function definition for ‘quantile’
cluster.snp: no visible global function definition for ‘cor’
cluster.snp: no visible global function definition for ‘as.dist’
cluster.snp: no visible global function definition for ‘as.dendrogram’
return.r2: no visible global function definition for ‘lm’
test.hierarchy: no visible global function definition for
  ‘order.dendrogram’
test.snp: no visible global function definition for ‘anova’
test.snp: no visible global function definition for ‘lm’
Undefined global functions or variables:
  anova as.dendrogram as.dist binomial coef cor glm glm.control lm
  order.dendrogram quantile
Consider adding
  importFrom("stats", "anova", "as.dendrogram", "as.dist", "binomial",
             "coef", "cor", "glm", "glm.control", "lm",
             "order.dendrogram", "quantile")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) simGWAS.Rd:14: \item in \describe must have non-empty label
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/hierGWAS.Rcheck/00check.log’
for details.