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This page was generated on 2025-10-06 11:39 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 1220/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.18.0  (landing page)
Mengni Liu
Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_21
git_last_commit: 9981ad5
git_last_commit_date: 2025-04-15 12:05:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for MesKit on merida1

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: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MesKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MesKit_1.18.0.tar.gz
StartedAt: 2025-10-03 06:01:41 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 06:24:41 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 1380.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MesKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MesKit_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  5.9Mb
  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 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               39.017  0.416  41.379
plotMutSigProfile    37.022  0.433  39.128
mutHeatmap           37.027  0.171  38.157
getCCFMatrix         36.045  0.554  40.842
getBootstrapValue    35.919  0.245  39.574
getBinaryMatrix      35.592  0.560  39.318
getBranchType        35.732  0.218  39.403
getTreeMethod        35.420  0.310  36.850
getPhyloTreeTsbLabel 35.079  0.245  35.662
getPhyloTreeRef      34.553  0.366  35.896
getTree              34.590  0.248  35.509
getPhyloTreePatient  34.616  0.218  36.031
getPhyloTree         34.416  0.359  36.377
getMutBranches       33.894  0.568  36.160
cna2gene             32.609  1.589  34.855
compareCCF           28.697  3.130  32.324
compareTree          29.863  0.400  32.605
calNeiDist           27.862  0.146  28.512
mutCluster           26.721  1.276  28.308
mutTrunkBranch       26.834  0.402  28.684
calJSI               26.903  0.154  27.603
ccfAUC               26.486  0.150  27.086
testNeutral          25.931  0.131  26.363
fitSignatures        25.197  0.342  28.684
triMatrix            24.401  0.248  25.567
plotPhyloTree        23.944  0.208  24.354
classifyMut          22.639  1.270  24.508
plotMutProfile       23.515  0.122  24.385
getMafRef            19.988  0.120  21.059
readMaf              19.614  0.099  19.962
subMaf               19.590  0.086  20.008
mathScore            19.390  0.082  19.988
getMafData           19.086  0.087  20.098
getMafPatient        18.993  0.081  22.197
getSampleInfo        18.733  0.058  18.908
getNonSyn_vc         18.307  0.090  19.170
plotCNA               7.683  0.136   8.555
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00check.log’
for details.


Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

Tests output


Example timings

MesKit.Rcheck/MesKit-Ex.timings

nameusersystemelapsed
calFst39.017 0.41641.379
calJSI26.903 0.15427.603
calNeiDist27.862 0.14628.512
ccfAUC26.486 0.15027.086
classifyMut22.639 1.27024.508
cna2gene32.609 1.58934.855
compareCCF28.697 3.13032.324
compareTree29.863 0.40032.605
fitSignatures25.197 0.34228.684
getBinaryMatrix35.592 0.56039.318
getBootstrapValue35.919 0.24539.574
getBranchType35.732 0.21839.403
getCCFMatrix36.045 0.55440.842
getMafData19.086 0.08720.098
getMafPatient18.993 0.08122.197
getMafRef19.988 0.12021.059
getMutBranches33.894 0.56836.160
getNonSyn_vc18.307 0.09019.170
getPhyloTree34.416 0.35936.377
getPhyloTreePatient34.616 0.21836.031
getPhyloTreeRef34.553 0.36635.896
getPhyloTreeTsbLabel35.079 0.24535.662
getSampleInfo18.733 0.05818.908
getTree34.590 0.24835.509
getTreeMethod35.42 0.3136.85
mathScore19.390 0.08219.988
mutCluster26.721 1.27628.308
mutHeatmap37.027 0.17138.157
mutTrunkBranch26.834 0.40228.684
plotCNA7.6830.1368.555
plotMutProfile23.515 0.12224.385
plotMutSigProfile37.022 0.43339.128
plotPhyloTree23.944 0.20824.354
readMaf19.614 0.09919.962
readSegment0.9810.0120.996
runMesKit0.0000.0010.001
subMaf19.590 0.08620.008
testNeutral25.931 0.13126.363
triMatrix24.401 0.24825.567