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This page was generated on 2025-12-06 11:34 -0500 (Sat, 06 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4869
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4576
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1221/2331HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.21.0  (landing page)
Mengni Liu
Snapshot Date: 2025-12-05 13:40 -0500 (Fri, 05 Dec 2025)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: devel
git_last_commit: 15660f6
git_last_commit_date: 2025-10-29 11:01:00 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for MesKit on nebbiolo1

To the developers/maintainers of the MesKit package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MesKit.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MesKit
Version: 1.21.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MesKit_1.21.0.tar.gz
StartedAt: 2025-12-06 01:08:40 -0500 (Sat, 06 Dec 2025)
EndedAt: 2025-12-06 01:18:36 -0500 (Sat, 06 Dec 2025)
EllapsedTime: 595.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MesKit_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.21.0’
* 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 ‘/home/biocbuild/bbs-3.23-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             22.634  0.977  23.454
calFst               15.121  0.267  15.345
getPhyloTreePatient  13.913  0.196  14.043
plotMutSigProfile    13.398  0.222  13.581
getPhyloTree         13.105  0.129  13.186
mutHeatmap           13.091  0.042  13.069
getCCFMatrix         12.977  0.149  13.077
getMutBranches       12.954  0.167  13.072
getBranchType        12.897  0.128  12.972
getPhyloTreeRef      13.021  0.003  12.977
getTree              12.950  0.046  12.951
getPhyloTreeTsbLabel 12.991  0.002  12.946
getTreeMethod        12.743  0.077  12.770
getBootstrapValue    12.615  0.074  12.627
getBinaryMatrix      12.504  0.139  12.581
compareCCF           10.472  1.017  11.443
calNeiDist           10.421  0.053  10.416
calJSI               10.253  0.158  10.356
compareTree          10.293  0.007  10.269
ccfAUC               10.186  0.086  10.210
mutCluster            9.639  0.277   9.863
testNeutral           9.785  0.051   9.782
mutTrunkBranch        8.848  0.185   8.993
fitSignatures         8.835  0.190   8.972
triMatrix             8.762  0.164   8.893
plotMutProfile        8.551  0.050   8.552
plotPhyloTree         8.475  0.052   8.488
classifyMut           7.455  0.473   7.881
readMaf               6.931  0.012   6.881
getNonSyn_vc          6.820  0.045   6.823
getMafData            6.835  0.007   6.811
subMaf                6.783  0.006   6.749
getSampleInfo         6.759  0.022   6.749
getMafPatient         6.742  0.022   6.731
mathScore             6.709  0.007   6.667
getMafRef             6.654  0.004   6.622
* 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-3.23-bioc/meat/MesKit.Rcheck/00check.log’
for details.


Installation output

MesKit.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘MesKit’ ...
** this is package ‘MesKit’ version ‘1.21.0’
** 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)

Tests output


Example timings

MesKit.Rcheck/MesKit-Ex.timings

nameusersystemelapsed
calFst15.121 0.26715.345
calJSI10.253 0.15810.356
calNeiDist10.421 0.05310.416
ccfAUC10.186 0.08610.210
classifyMut7.4550.4737.881
cna2gene22.634 0.97723.454
compareCCF10.472 1.01711.443
compareTree10.293 0.00710.269
fitSignatures8.8350.1908.972
getBinaryMatrix12.504 0.13912.581
getBootstrapValue12.615 0.07412.627
getBranchType12.897 0.12812.972
getCCFMatrix12.977 0.14913.077
getMafData6.8350.0076.811
getMafPatient6.7420.0226.731
getMafRef6.6540.0046.622
getMutBranches12.954 0.16713.072
getNonSyn_vc6.8200.0456.823
getPhyloTree13.105 0.12913.186
getPhyloTreePatient13.913 0.19614.043
getPhyloTreeRef13.021 0.00312.977
getPhyloTreeTsbLabel12.991 0.00212.946
getSampleInfo6.7590.0226.749
getTree12.950 0.04612.951
getTreeMethod12.743 0.07712.770
mathScore6.7090.0076.667
mutCluster9.6390.2779.863
mutHeatmap13.091 0.04213.069
mutTrunkBranch8.8480.1858.993
plotCNA3.5200.0413.462
plotMutProfile8.5510.0508.552
plotMutSigProfile13.398 0.22213.581
plotPhyloTree8.4750.0528.488
readMaf6.9310.0126.881
readSegment0.4710.0010.413
runMesKit000
subMaf6.7830.0066.749
testNeutral9.7850.0519.782
triMatrix8.7620.1648.893