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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_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.18.0’
* 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-3.21-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
cna2gene             23.797  0.300  24.100
calFst               23.652  0.327  24.048
getCCFMatrix         21.028  0.119  21.183
getBinaryMatrix      20.873  0.183  21.092
getBootstrapValue    20.774  0.124  20.938
getMutBranches       20.649  0.184  20.873
getBranchType        20.703  0.056  20.798
getPhyloTreeTsbLabel 20.638  0.095  20.768
getTreeMethod        20.352  0.140  20.516
getTree              20.369  0.060  20.453
getPhyloTreePatient  20.192  0.088  20.312
getPhyloTreeRef      19.940  0.104  20.078
getPhyloTree         19.843  0.144  20.022
plotMutSigProfile    18.792  0.363  19.198
mutHeatmap           18.405  0.055  18.501
calNeiDist           17.320  0.091  17.445
compareCCF           16.496  0.247  16.767
compareTree          16.628  0.012  16.672
calJSI               15.858  0.040  15.928
plotMutProfile       14.895  0.650  15.574
mutTrunkBranch       14.650  0.647  15.331
ccfAUC               14.706  0.031  14.761
fitSignatures        14.625  0.080  14.734
mutCluster           14.111  0.080  14.217
triMatrix            13.592  0.152  13.757
testNeutral          13.558  0.108  13.679
plotPhyloTree        13.125  0.248  13.393
classifyMut          12.993  0.120  13.129
getNonSyn_vc         12.273  0.111  12.405
getMafData           11.210  0.080  11.309
mathScore            11.116  0.068  11.189
getMafPatient        11.056  0.024  11.102
subMaf               10.912  0.132  11.055
getMafRef            11.005  0.023  11.044
readMaf              10.783  0.139  10.926
getSampleInfo        10.664  0.012  10.696
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘MesKit’ ...
** this is package ‘MesKit’ version ‘1.18.0’
** 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)