##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClusterFoldSimilarity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClusterFoldSimilarity_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClusterFoldSimilarity.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClusterFoldSimilarity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClusterFoldSimilarity’ version ‘1.3.0’
* package encoding: UTF-8
* 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 ‘ClusterFoldSimilarity’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘SeuratObject’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterFoldSimilarity: no visible global function definition for ‘show’
findCommunitiesSimmilarity: no visible global function definition for
  ‘hcl.colors’
similarityHeatmap : <anonymous>: no visible binding for global variable
  ‘datasetL’
similarityHeatmap : <anonymous>: no visible binding for global variable
  ‘datasetR’
similarityHeatmap : <anonymous>: no visible global function definition
  for ‘desc’
similarityHeatmap : <anonymous>: no visible binding for global variable
  ‘clusterL’
similarityHeatmap : <anonymous>: no visible binding for global variable
  ‘clusterR’
similarityHeatmap : <anonymous>: no visible binding for global variable
  ‘similarityValue’
Undefined global functions or variables:
  clusterL clusterR datasetL datasetR desc hcl.colors show
  similarityValue
Consider adding
  importFrom("grDevices", "hcl.colors")
  importFrom("methods", "show")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'findCommunitiesSimmilarity.Rd':
findCommunitiesSimmilarity
  Code: function(similarityTable = NULL, nIterations = 10,
                 leidenResolution = 1)
  Docs: function(similarityTable = NULL)
  Argument names in code not in docs:
    nIterations leidenResolution

* 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 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClusterFoldSimilarity.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ClusterFoldSimilarity
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ClusterFoldSimilarity’ ...
** using staged installation
** R
** 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 (ClusterFoldSimilarity)