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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MesKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MesKit_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.20.0’
* 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 ‘MesKit’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘MesKit’
  Warning: replacing previous import ‘dplyr::count’ by ‘mclust::count’ when loading ‘MesKit’
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
* 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 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
calJSI : processJSI: no visible binding for global variable ‘CCF’
cna2gene: no visible global function definition for ‘genes’
cna2gene: no visible binding for global variable ‘org.Hs.eg.db’
cna2gene: no visible binding for global variable ‘seqnames’
cna2gene: no visible binding for global variable ‘Chromosome’
cna2gene: no visible binding for global variable ‘Hugo_Symbol’
cna2gene: no visible binding for global variable ‘Start_Position’
cna2gene: no visible binding for global variable ‘End_Position’
cna2gene: no visible binding for global variable ‘i.End_Position’
cna2gene: no visible binding for global variable ‘i.Start_Position’
cna2gene: no visible binding for global variable ‘Patient_ID’
cna2gene: no visible binding for global variable ‘Tumor_Sample_Barcode’
cna2gene: no visible binding for global variable ‘seg_id’
cna2gene: no visible binding for global variable ‘overlap_width’
copyNumberFilter: no visible binding for global variable ‘Patient_ID’
drawVAFCombine: no visible binding for global variable ‘V’
drawVAFCombineVline: no visible binding for global variable ‘V’
fitSignatures : processFitSig: no visible binding for global variable
  ‘Branch’
fitSignatures : processFitSig: no visible binding for global variable
  ‘Original’
fitSignatures : processFitSig: no visible binding for global variable
  ‘Reconstructed’
mutCluster : processVafcluster_sample: no visible binding for global
  variable ‘cluster’
plotCNA: no visible binding for global variable ‘Cytoband’
plotCNA: no visible binding for global variable ‘Cytoband_pos’
plotCNA: no visible binding for global variable ‘gene_id’
plotCNA: no visible binding for global variable ‘gene_pos’
plotCNA: no visible binding for global variable ‘Hugo_Symbol’
plotTree: no visible binding for global variable ‘is.match’
plotTree: no visible binding for global variable ‘x’
plotTree: no visible binding for global variable ‘y’
plotTree: no visible binding for global variable ‘xend’
plotTree: no visible binding for global variable ‘yend’
Undefined global functions or variables:
  Branch CCF Chromosome Cytoband Cytoband_pos End_Position Hugo_Symbol
  Original Patient_ID Reconstructed Start_Position Tumor_Sample_Barcode
  V cluster gene_id gene_pos genes i.End_Position i.Start_Position
  is.match org.Hs.eg.db overlap_width seg_id seqnames x xend y yend
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
cna2gene             39.149  1.863  46.704
calFst               40.348  0.412  46.526
plotMutSigProfile    37.625  0.679  47.767
mutHeatmap           37.477  0.199  42.441
getPhyloTreeTsbLabel 36.956  0.202  42.013
getMutBranches       36.564  0.593  46.501
getCCFMatrix         36.388  0.691  50.522
getBinaryMatrix      35.896  0.628  44.529
getPhyloTreePatient  36.032  0.431  41.516
getBootstrapValue    36.027  0.348  45.529
getBranchType        35.771  0.290  48.367
getPhyloTree         35.778  0.222  41.706
getPhyloTreeRef      35.812  0.160  40.718
getTreeMethod        35.078  0.451  40.399
getTree              34.241  0.213  39.335
compareCCF           29.258  3.185  38.306
compareTree          29.883  0.408  37.264
calNeiDist           29.261  0.188  33.716
mutCluster           27.753  1.157  32.749
calJSI               27.999  0.181  32.536
ccfAUC               27.614  0.158  31.562
testNeutral          26.639  0.174  36.789
mutTrunkBranch       25.680  0.340  30.169
triMatrix            25.484  0.376  33.637
fitSignatures        25.122  0.463  31.248
plotPhyloTree        24.330  0.187  30.854
plotMutProfile       24.169  0.120  28.597
classifyMut          22.764  1.234  27.624
getMafPatient        20.226  0.252  27.460
readMaf              20.185  0.149  25.662
getMafRef            19.875  0.098  25.568
subMaf               19.799  0.165  28.418
getMafData           19.825  0.133  25.951
getNonSyn_vc         19.808  0.096  25.249
mathScore            19.492  0.104  22.306
getSampleInfo        18.616  0.081  21.253
plotCNA               7.623  0.068   8.722
* 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/MesKit.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MesKit
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MesKit’ ...
** this is package ‘MesKit’ version ‘1.20.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘MesKit’
Warning: replacing previous import ‘dplyr::count’ by ‘mclust::count’ when loading ‘MesKit’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘MesKit’
Warning: replacing previous import ‘dplyr::count’ by ‘mclust::count’ when loading ‘MesKit’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘MesKit’
Warning: replacing previous import ‘dplyr::count’ by ‘mclust::count’ when loading ‘MesKit’
** testing if installed package keeps a record of temporary installation path
* DONE (MesKit)