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This page was generated on 2025-10-15 12:07 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4866
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4653
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1226/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.19.0  (landing page)
Mengni Liu
Snapshot Date: 2025-10-14 13:45 -0400 (Tue, 14 Oct 2025)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: devel
git_last_commit: 70ad035
git_last_commit_date: 2025-04-15 12:05:40 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for MesKit on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MesKit
Version: 1.19.0
Command: /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
StartedAt: 2025-10-14 09:55:41 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 10:08:48 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 787.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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
cna2gene             25.732  0.471  26.237
calFst               24.069  0.653  24.820
getPhyloTreeTsbLabel 21.296  0.208  21.552
plotMutSigProfile    21.180  0.112  21.338
mutHeatmap           20.953  0.131  21.126
getPhyloTreeRef      20.901  0.103  21.049
getPhyloTreePatient  20.891  0.112  21.049
getBootstrapValue    20.561  0.100  20.699
getPhyloTree         20.548  0.096  20.692
getMutBranches       20.436  0.168  20.653
getCCFMatrix         20.538  0.064  20.661
getBinaryMatrix      20.420  0.163  20.626
getBranchType        20.531  0.044  20.618
getTreeMethod        20.211  0.096  20.351
getTree              19.751  0.091  19.885
calNeiDist           17.392  0.115  17.552
calJSI               17.080  0.203  17.330
compareTree          17.130  0.115  17.286
compareCCF           16.508  0.264  16.801
ccfAUC               16.497  0.184  16.721
testNeutral          15.510  0.080  15.621
mutCluster           15.506  0.080  15.619
fitSignatures        14.503  0.164  14.704
mutTrunkBranch       14.380  0.128  14.536
triMatrix            14.080  0.167  14.273
plotPhyloTree        13.630  0.095  13.756
plotMutProfile       13.314  0.080  13.416
classifyMut          12.228  0.151  12.399
readMaf              11.420  0.036  11.470
mathScore            11.223  0.108  11.348
getMafData           11.156  0.087  11.271
subMaf               11.165  0.056  11.236
getNonSyn_vc         11.092  0.091  11.212
getMafPatient        11.130  0.028  11.185
getMafRef            11.055  0.048  11.128
getSampleInfo        10.821  0.004  10.848
* 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.


Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* 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)

Tests output


Example timings

MesKit.Rcheck/MesKit-Ex.timings

nameusersystemelapsed
calFst24.069 0.65324.820
calJSI17.080 0.20317.330
calNeiDist17.392 0.11517.552
ccfAUC16.497 0.18416.721
classifyMut12.228 0.15112.399
cna2gene25.732 0.47126.237
compareCCF16.508 0.26416.801
compareTree17.130 0.11517.286
fitSignatures14.503 0.16414.704
getBinaryMatrix20.420 0.16320.626
getBootstrapValue20.561 0.10020.699
getBranchType20.531 0.04420.618
getCCFMatrix20.538 0.06420.661
getMafData11.156 0.08711.271
getMafPatient11.130 0.02811.185
getMafRef11.055 0.04811.128
getMutBranches20.436 0.16820.653
getNonSyn_vc11.092 0.09111.212
getPhyloTree20.548 0.09620.692
getPhyloTreePatient20.891 0.11221.049
getPhyloTreeRef20.901 0.10321.049
getPhyloTreeTsbLabel21.296 0.20821.552
getSampleInfo10.821 0.00410.848
getTree19.751 0.09119.885
getTreeMethod20.211 0.09620.351
mathScore11.223 0.10811.348
mutCluster15.506 0.08015.619
mutHeatmap20.953 0.13121.126
mutTrunkBranch14.380 0.12814.536
plotCNA4.6630.0204.678
plotMutProfile13.314 0.08013.416
plotMutSigProfile21.180 0.11221.338
plotPhyloTree13.630 0.09513.756
readMaf11.420 0.03611.470
readSegment0.5350.0080.538
runMesKit000
subMaf11.165 0.05611.236
testNeutral15.510 0.08015.621
triMatrix14.080 0.16714.273