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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IHW.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings IHW_1.28.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/IHW.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'IHW/DESCRIPTION' ... OK
* this is package 'IHW' version '1.28.0'
* 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 whether package 'IHW' 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 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
filter_pvals_for_optim: no visible global function definition for
  'p.adjust'
groups_by_filter: no visible global function definition for 'runif'
ihw.DESeqResults: no visible global function definition for 'mcols'
ihw.DESeqResults: no visible global function definition for 'mcols<-'
ihw.DESeqResults: no visible global function definition for 'metadata'
ihw.DESeqResults: no visible global function definition for
  'metadata<-'
ihw.default: no visible global function definition for 'runif'
ihw.default: no visible global function definition for 'p.adjust'
ihw_convex: no visible global function definition for 'gurobi'
ihw_internal: no visible global function definition for 'p.adjust'
ihw_milp: no visible global function definition for 'str'
ihw_milp: no visible global function definition for 'gurobi'
plot_decisionboundary: no visible binding for global variable 'stratum'
plot_decisionboundary: no visible binding for global variable
  'covariate'
plot_decisionboundary: no visible binding for global variable 'pvalue'
plot_decisionboundary: no visible binding for global variable 'fold'
thresholds_ihwResult: no visible global function definition for
  'na.exclude'
thresholds,ihwResult: no visible global function definition for
  'na.exclude'
Undefined global functions or variables:
  covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude
  p.adjust pvalue runif str stratum
Consider adding
  importFrom("stats", "na.exclude", "p.adjust", "runif")
  importFrom("utils", "str")
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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'IHW-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ihwResult-class
> ### Title: An S4 class to represent the ihw output.
> ### Aliases: ihwResult-class ihwResult adj_pvalues
> ###   adj_pvalues,ihwResult-method weights,ihwResult-method thresholds
> ###   thresholds,ihwResult-method pvalues pvalues,ihwResult-method
> ###   weighted_pvalues weighted_pvalues,ihwResult-method covariates
> ###   covariates,ihwResult-method covariate_type
> ###   covariate_type,ihwResult-method groups_factor
> ###   groups_factor,ihwResult-method nfolds nfolds,ihwResult-method nbins
> ###   nbins,ihwResult-method alpha alpha,ihwResult-method rejections
> ###   rejections,ihwResult-method rejected_hypotheses
> ###   rejected_hypotheses,ihwResult-method regularization_term
> ###   regularization_term,ihwResult-method m_groups
> ###   m_groups,ihwResult-method as.data.frame_ihwResult
> ###   as.data.frame,ihwResult-method nrow,ihwResult-method
> ###   show,ihwResult-method
> 
> ### ** Examples
> 
> 
> save.seed <- .Random.seed; set.seed(1)
> X   <- runif(n = 20000, min = 0.5, max = 4.5)       # Covariate
> # Is the null hypothesis (mean=0) true or false ?
> H   <- rbinom(n = length(X), size = 1, prob = 0.1)  
> Z   <- rnorm(n = length(X), mean = H * X)           # Z-score
> .Random.seed <- save.seed
> 
> pvalue <- 1 - pnorm(Z)                              # pvalue
> ihw_res <- ihw(pvalue, covariates = X, alpha = 0.1)
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/IHW.Rcheck/00check.log'
for details.