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This page was generated on 2025-08-06 13:55 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1209/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.19.0  (landing page)
Mengni Liu
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 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 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 2025-08-05 22:00:21 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 22:10:33 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 612.1 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_1.19.0.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             20.343  0.923  21.438
calFst               18.656  0.292  19.111
getCCFMatrix         15.471  0.233  15.772
plotMutSigProfile    15.224  0.287  15.638
getMutBranches       14.951  0.448  15.471
getPhyloTreeRef      15.029  0.265  15.374
getPhyloTree         14.864  0.167  15.120
getBinaryMatrix      14.476  0.361  14.894
getTreeMethod        14.463  0.308  14.851
getBranchType        14.589  0.178  14.818
getPhyloTreePatient  14.601  0.145  14.801
getPhyloTreeTsbLabel 14.557  0.176  14.809
getBootstrapValue    14.298  0.282  14.645
getTree              14.149  0.182  14.425
compareCCF           12.935  1.167  14.175
mutHeatmap           13.691  0.134  13.905
calNeiDist           13.432  0.128  13.630
compareTree          12.537  0.198  12.790
calJSI               12.106  0.105  12.286
fitSignatures        11.818  0.260  12.150
mutCluster           10.534  0.460  11.067
triMatrix            10.689  0.195  10.947
mutTrunkBranch       10.563  0.182  10.817
testNeutral          10.611  0.088  10.754
plotMutProfile       10.245  0.084  10.401
ccfAUC                9.932  0.094  10.071
plotPhyloTree         9.809  0.067   9.920
classifyMut           9.312  0.413   9.776
getSampleInfo         9.120  0.089   9.262
subMaf                8.509  0.081   8.644
readMaf               8.460  0.069   8.581
getMafData            8.351  0.066   8.465
getMafRef             8.116  0.051   8.203
mathScore             7.993  0.067   8.110
getNonSyn_vc          7.876  0.060   7.988
getMafPatient         7.846  0.057   7.951
* 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
calFst18.656 0.29219.111
calJSI12.106 0.10512.286
calNeiDist13.432 0.12813.630
ccfAUC 9.932 0.09410.071
classifyMut9.3120.4139.776
cna2gene20.343 0.92321.438
compareCCF12.935 1.16714.175
compareTree12.537 0.19812.790
fitSignatures11.818 0.26012.150
getBinaryMatrix14.476 0.36114.894
getBootstrapValue14.298 0.28214.645
getBranchType14.589 0.17814.818
getCCFMatrix15.471 0.23315.772
getMafData8.3510.0668.465
getMafPatient7.8460.0577.951
getMafRef8.1160.0518.203
getMutBranches14.951 0.44815.471
getNonSyn_vc7.8760.0607.988
getPhyloTree14.864 0.16715.120
getPhyloTreePatient14.601 0.14514.801
getPhyloTreeRef15.029 0.26515.374
getPhyloTreeTsbLabel14.557 0.17614.809
getSampleInfo9.1200.0899.262
getTree14.149 0.18214.425
getTreeMethod14.463 0.30814.851
mathScore7.9930.0678.110
mutCluster10.534 0.46011.067
mutHeatmap13.691 0.13413.905
mutTrunkBranch10.563 0.18210.817
plotCNA2.9180.0432.974
plotMutProfile10.245 0.08410.401
plotMutSigProfile15.224 0.28715.638
plotPhyloTree9.8090.0679.920
readMaf8.4600.0698.581
readSegment0.4930.0070.501
runMesKit000
subMaf8.5090.0818.644
testNeutral10.611 0.08810.754
triMatrix10.689 0.19510.947