##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.17.0’
* 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 ... 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 ... 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             17.694  0.691  18.216
calFst               14.718  0.364  15.036
getTree              13.711  0.049  13.709
getTreeMethod        13.671  0.028  13.645
getPhyloTreeTsbLabel 13.058  0.093  13.103
getCCFMatrix         12.965  0.093  13.002
getPhyloTreeRef      12.816  0.089  12.857
getBranchType        12.821  0.077  12.851
getBinaryMatrix      12.630  0.183  12.761
getPhyloTreePatient  12.765  0.034  12.752
getBootstrapValue    12.683  0.079  12.708
getPhyloTree         12.701  0.052  12.696
getMutBranches       12.564  0.123  12.644
mutHeatmap           12.095  0.093  12.126
plotMutSigProfile    11.939  0.148  12.025
compareCCF           10.629  1.020  11.599
mutTrunkBranch       10.541  0.334  10.830
calNeiDist           10.670  0.045  10.665
calJSI                9.899  0.116   9.974
compareTree           9.929  0.077   9.960
mutCluster            9.150  0.314   9.425
ccfAUC                9.146  0.048   9.142
fitSignatures         8.743  0.200   8.904
triMatrix             8.726  0.210   8.885
plotPhyloTree         8.806  0.031   8.773
testNeutral           8.744  0.053   8.743
classifyMut           8.071  0.439   8.458
plotMutProfile        8.305  0.004   8.244
getMafData            8.079  0.086   8.132
readMaf               7.155  0.042   7.128
mathScore             7.121  0.023   7.082
getSampleInfo         7.028  0.073   7.060
subMaf                6.763  0.054   6.763
getMafPatient         6.647  0.001   6.615
getMafRef             6.585  0.001   6.558
getNonSyn_vc          6.547  0.003   6.522
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘MesKit’ ...
** this is package ‘MesKit’ version ‘1.17.0’
** 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)