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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MesKit_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.19.0’
* 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’
See ‘/home/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  6.0Mb
  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 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
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
calFst               23.626  0.366  24.807
cna2gene             22.276  0.515  22.852
getCCFMatrix         21.257  0.168  21.750
getPhyloTreeRef      20.534  0.789  21.552
plotMutSigProfile    21.106  0.188  21.456
getTree              20.710  0.259  21.020
getTreeMethod        20.817  0.132  21.010
mutHeatmap           20.618  0.167  21.049
getBinaryMatrix      20.669  0.096  20.849
getBranchType        20.648  0.048  22.826
getPhyloTreeTsbLabel 20.235  0.411  20.944
getPhyloTreePatient  20.266  0.204  20.669
getPhyloTree         20.129  0.060  20.241
getBootstrapValue    19.966  0.067  20.499
getMutBranches       19.814  0.131  20.190
compareTree          17.446  0.111  17.643
calNeiDist           17.373  0.136  17.553
mutCluster           16.536  0.247  16.839
calJSI               16.280  0.044  16.365
compareCCF           15.771  0.331  16.210
ccfAUC               15.705  0.028  15.774
testNeutral          15.471  0.100  15.624
triMatrix            15.118  0.124  15.293
fitSignatures        15.001  0.084  15.124
mutTrunkBranch       14.004  0.136  14.210
plotPhyloTree        13.806  0.051  13.980
plotMutProfile       13.198  0.055  13.652
classifyMut          12.640  0.120  12.790
mathScore            11.630  0.056  11.718
getSampleInfo        11.332  0.148  11.512
readMaf              11.409  0.016  11.513
subMaf               11.363  0.032  11.519
getNonSyn_vc         10.795  0.032  11.093
getMafRef            10.584  0.076  10.848
getMafPatient        10.516  0.028  10.678
getMafData           10.358  0.024  10.403
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MesKit
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘MesKit’ ...
** this is package ‘MesKit’ version ‘1.19.0’
** 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’
** 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’
** 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’
** testing if installed package keeps a record of temporary installation path
* DONE (MesKit)