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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:M3C.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings M3C_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/M3C.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘M3C/DESCRIPTION’ ... OK
* this is package ‘M3C’ version ‘1.28.0’
* 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 ‘M3C’ 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
CDF: no visible global function definition for ‘ecdf’
CDF: no visible global function definition for ‘complete.cases’
CDF: no visible binding for global variable ‘consensusindex’
CDF: no visible binding for global variable ‘k’
CDF: no visible binding for global variable ‘K’
CDF: no visible binding for global variable ‘PAC_SCORE’
M3C: no visible global function definition for ‘exprs’
M3C: no visible global function definition for ‘is’
M3C: no visible global function definition for ‘capture.output’
M3C: no visible global function definition for ‘txtProgressBar’
M3C : progress: no visible global function definition for
  ‘setTxtProgressBar’
M3C: no visible global function definition for ‘prcomp’
M3C: no visible global function definition for ‘cov’
M3C: no visible global function definition for ‘rnorm’
M3C: no visible binding for global variable ‘sd’
M3C: no visible binding for global variable ‘var’
M3C : <anonymous>: no visible global function definition for ‘pbeta’
M3C : <anonymous>: no visible global function definition for ‘pnorm’
M3C: no visible binding for global variable ‘K’
M3C: no visible binding for global variable ‘RCSI’
M3C: no visible global function definition for ‘qnorm’
M3C: no visible binding for global variable ‘RCSI_SE’
M3C: no visible binding for global variable ‘P_SCORE’
M3Creal: no visible global function definition for ‘hclust’
M3Creal: no visible global function definition for ‘as.dist’
M3Creal: no visible global function definition for ‘cutree’
M3Creal: no visible global function definition for ‘is’
PCSI_plot: no visible binding for global variable ‘K’
PCSI_plot: no visible binding for global variable ‘PCSI’
ccRun: no visible global function definition for ‘dist’
ccRun: no visible global function definition for ‘as.dist’
ccRun: no visible global function definition for ‘kmeans’
ccRun: no visible global function definition for ‘hclust’
ccRun: no visible global function definition for ‘cutree’
clustersim : addnoise: no visible global function definition for
  ‘rnorm’
clustersim: no visible global function definition for ‘rnorm’
clustersim: no visible binding for global variable ‘X3’
clustersim: no visible global function definition for ‘prcomp’
clustersim: no visible global function definition for ‘kmeans’
clustersim: no visible binding for global variable ‘PC1’
clustersim: no visible binding for global variable ‘PC2’
featurefilter: no visible binding for global variable ‘sd’
featurefilter: no visible global function definition for ‘quantile’
featurefilter: no visible binding for global variable ‘mad’
getl: no visible global function definition for ‘kmeans’
getl: no visible global function definition for ‘dist’
getl: no visible global function definition for ‘hclust’
getl: no visible global function definition for ‘cutree’
pca: no visible global function definition for ‘prcomp’
pca: no visible global function definition for ‘png’
pca: no visible global function definition for ‘dev.off’
pca: no visible binding for global variable ‘label’
rbfkernel: no visible global function definition for ‘dist’
tsne: no visible binding for global variable ‘X1’
tsne: no visible binding for global variable ‘X2’
tsne: no visible global function definition for ‘png’
tsne: no visible global function definition for ‘dev.off’
tsne: no visible binding for global variable ‘label’
umap: no visible binding for global variable ‘X1’
umap: no visible binding for global variable ‘X2’
umap: no visible global function definition for ‘png’
umap: no visible global function definition for ‘dev.off’
umap: no visible binding for global variable ‘label’
Undefined global functions or variables:
  K PAC_SCORE PC1 PC2 PCSI P_SCORE RCSI RCSI_SE X1 X2 X3 as.dist
  capture.output complete.cases consensusindex cov cutree dev.off dist
  ecdf exprs hclust is k kmeans label mad pbeta png pnorm prcomp qnorm
  quantile rnorm sd setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "complete.cases", "cov", "cutree",
             "dist", "ecdf", "hclust", "kmeans", "mad", "pbeta", "pnorm",
             "prcomp", "qnorm", "quantile", "rnorm", "sd", "var")
  importFrom("utils", "capture.output", "setTxtProgressBar",
             "txtProgressBar")
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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
M3C 1.427  0.079  20.253
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/M3C.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL M3C
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘M3C’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (M3C)