##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:concordexR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings concordexR_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/concordexR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘concordexR/DESCRIPTION’ ... OK
* this is package ‘concordexR’ version ‘1.9.1’
* package encoding: UTF-8
* 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 ‘concordexR’ 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
.concordex_nbhd_consolidation: no visible global function definition
  for ‘bpvec’
calculateConcordex,ANY: no visible global function definition for
  ‘NNGraphParam’
Undefined global functions or variables:
  NNGraphParam bpvec
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculateConcordex.Rd: SpatialExperiment, SingleCellExperiment,
    SummarizedExperiment, SummarizedExperiment-class, reducedDimNames,
    BlusterParam-class, BiocNeighborIndex, findKNN, BiocNeighborParam,
    BiocParallelParam, bpparam, reducedDims
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'calculateConcordex.Rd':
\S4method{calculateConcordex}{ANY}
  Code: function(x, labels, ..., n_neighbors = 30, compute_similarity =
                 FALSE, BNINDEX, BLUSPARAM = NNGraphParam(cluster.fun =
                 "louvain"), BNPARAM = KmknnParam(), BPPARAM =
                 SerialParam())
  Docs: function(x, labels, ..., n_neighbors = 30, compute_similarity =
                 FALSE, BLUSPARAM, BNINDEX, BNPARAM = KmknnParam(),
                 BPPARAM = NNGraphParam(cluster.fun = "louvain"))
  Mismatches in argument names:
    Position: 6 Code: BNINDEX Docs: BLUSPARAM
    Position: 7 Code: BLUSPARAM Docs: BNINDEX
  Mismatches in argument default values:
    Name: 'BLUSPARAM' Code: NNGraphParam(cluster.fun = "louvain") Docs: 
    Name: 'BPPARAM' Code: SerialParam() Docs: NNGraphParam(cluster.fun = "louvain")

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/concordexR.Rcheck/00check.log’
for details.