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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings evaluomeR_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/evaluomeR.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 ‘evaluomeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘evaluomeR’ version ‘1.22.0’
* 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'
 NOTE
Depends: includes the non-default packages:
  'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc',
  'randomForest', 'flexmix', 'RSKC', 'sparcl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘evaluomeR’ 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 ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RSKC’ ‘sparcl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getMetricRangeByCluster: no visible global function definition for
  ‘%>%’
getMetricRangeByCluster: no visible binding for global variable
  ‘cluster’
getMetricsRelevancy: no visible global function definition for ‘RSKC’
kmeansruns: no visible global function definition for ‘pairs’
kmeansruns: no visible global function definition for ‘calinhara’
kmeansruns: no visible global function definition for ‘dudahart2’
plotMetricsCluster: no visible global function definition for
  ‘as.dendrogram’
rskcCBI: no visible global function definition for ‘RSKC’
speccCBI: no visible global function definition for ‘specc’
Undefined global functions or variables:
  %>% RSKC as.dendrogram calinhara cluster dudahart2 pairs specc
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "as.dendrogram")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'getMetricRangeByCluster':
  ‘getMetricRangeByCluster.Rd’ ‘getMetricsRelevancy.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘clusterbootWrapper’ ‘standardizeQualityData’
  ‘standardizeStabilityData’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'quality.Rd'
  ‘...’

Undocumented arguments in Rd file 'qualityRange.Rd'
  ‘...’

Undocumented arguments in Rd file 'qualitySet.Rd'
  ‘...’

Undocumented arguments in Rd file 'stability.Rd'
  ‘...’

Undocumented arguments in Rd file 'stabilityRange.Rd'
  ‘...’

Undocumented arguments in Rd file 'stabilitySet.Rd'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ‘testAll.R’
  Running ‘testAnalysis.R’
  Running ‘testCBI.R’
  Running ‘testMetricsRelevancy.R’
  Running ‘testQuality.R’
  Running ‘testStability.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: 3 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/evaluomeR.Rcheck/00check.log’
for details.