Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-09-08 12:05 -0400 (Mon, 08 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1214/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.19.0  (landing page)
Mengni Liu
Snapshot Date: 2025-09-07 13:45 -0400 (Sun, 07 Sep 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 12.7.1 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 lconway

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: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2025-09-07 21:54:38 -0400 (Sun, 07 Sep 2025)
EndedAt: 2025-09-07 22:04:54 -0400 (Sun, 07 Sep 2025)
EllapsedTime: 616.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.19.0’
* 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 ‘/Users/biocbuild/bbs-3.22-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
cna2gene             20.399  0.852  21.356
calFst               18.153  0.295  18.595
getTree              15.765  0.227  16.085
getPhyloTreeTsbLabel 15.759  0.162  15.991
getPhyloTreeRef      15.634  0.276  15.976
getMutBranches       15.405  0.420  15.896
getCCFMatrix         15.545  0.243  15.853
getPhyloTree         15.562  0.182  15.809
getBranchType        15.501  0.171  15.729
getPhyloTreePatient  15.323  0.157  15.530
getBinaryMatrix      14.925  0.308  15.287
compareCCF           13.573  1.482  15.211
getTreeMethod        14.742  0.162  14.978
plotMutSigProfile    14.621  0.248  14.943
getBootstrapValue    14.306  0.304  14.666
mutHeatmap           13.674  0.128  13.872
calNeiDist           13.093  0.118  13.280
compareTree          12.545  0.177  12.771
fitSignatures        11.993  0.266  12.312
calJSI               11.906  0.109  12.081
mutCluster           10.725  0.490  11.290
mutTrunkBranch       10.882  0.174  11.113
testNeutral          10.377  0.078  10.497
triMatrix            10.110  0.164  10.325
plotPhyloTree        10.065  0.082  10.205
plotMutProfile       10.021  0.077  10.148
ccfAUC                9.810  0.106   9.958
classifyMut           8.912  0.456   9.408
getMafData            8.403  0.060   8.506
subMaf                8.348  0.087   8.475
readMaf               8.325  0.071   8.443
mathScore             8.205  0.173   8.426
getSampleInfo         8.155  0.052   8.236
getMafPatient         8.151  0.054   8.231
getNonSyn_vc          8.097  0.056   8.191
getMafRef             7.951  0.055   8.041
* 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-3.22-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 ‘1.19.0’
** 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
calFst18.153 0.29518.595
calJSI11.906 0.10912.081
calNeiDist13.093 0.11813.280
ccfAUC9.8100.1069.958
classifyMut8.9120.4569.408
cna2gene20.399 0.85221.356
compareCCF13.573 1.48215.211
compareTree12.545 0.17712.771
fitSignatures11.993 0.26612.312
getBinaryMatrix14.925 0.30815.287
getBootstrapValue14.306 0.30414.666
getBranchType15.501 0.17115.729
getCCFMatrix15.545 0.24315.853
getMafData8.4030.0608.506
getMafPatient8.1510.0548.231
getMafRef7.9510.0558.041
getMutBranches15.405 0.42015.896
getNonSyn_vc8.0970.0568.191
getPhyloTree15.562 0.18215.809
getPhyloTreePatient15.323 0.15715.530
getPhyloTreeRef15.634 0.27615.976
getPhyloTreeTsbLabel15.759 0.16215.991
getSampleInfo8.1550.0528.236
getTree15.765 0.22716.085
getTreeMethod14.742 0.16214.978
mathScore8.2050.1738.426
mutCluster10.725 0.49011.290
mutHeatmap13.674 0.12813.872
mutTrunkBranch10.882 0.17411.113
plotCNA3.2420.0513.312
plotMutProfile10.021 0.07710.148
plotMutSigProfile14.621 0.24814.943
plotPhyloTree10.065 0.08210.205
readMaf8.3250.0718.443
readSegment0.4950.0070.505
runMesKit000
subMaf8.3480.0878.475
testNeutral10.377 0.07810.497
triMatrix10.110 0.16410.325