| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R 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 1221/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MesKit 1.21.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
|
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. |
| 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: 2025-12-05 01:12:42 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 01:22:39 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 596.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MesKit.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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 23.163 0.739 23.745
calFst 14.975 0.318 15.249
getTreeMethod 14.374 0.179 14.503
getBootstrapValue 13.435 0.099 13.490
getCCFMatrix 13.382 0.105 13.442
getBinaryMatrix 13.355 0.108 13.396
plotMutSigProfile 13.182 0.180 13.325
getBranchType 13.303 0.034 13.280
getTree 13.143 0.115 13.209
getPhyloTreeRef 13.136 0.055 13.134
mutHeatmap 12.974 0.071 12.974
getPhyloTreePatient 12.929 0.004 12.885
getPhyloTreeTsbLabel 12.717 0.079 12.726
getMutBranches 12.531 0.220 12.689
getPhyloTree 12.631 0.005 12.578
compareTree 10.936 0.096 10.975
compareCCF 10.042 0.978 10.975
calNeiDist 10.480 0.081 10.517
calJSI 10.091 0.176 10.208
ccfAUC 10.022 0.138 10.116
mutCluster 9.784 0.287 10.009
testNeutral 9.882 0.049 9.870
fitSignatures 9.391 0.206 9.555
triMatrix 8.855 0.164 8.981
mutTrunkBranch 8.669 0.191 8.824
plotPhyloTree 8.702 0.015 8.678
getMafData 8.154 0.167 8.288
plotMutProfile 8.214 0.041 8.196
classifyMut 7.391 0.456 7.799
readMaf 7.366 0.026 7.327
subMaf 7.106 0.014 7.069
getSampleInfo 6.804 0.017 6.787
mathScore 6.771 0.004 6.709
getNonSyn_vc 6.578 0.007 6.558
getMafRef 6.498 0.038 6.498
getMafPatient 6.516 0.019 6.502
* 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.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
MesKit.Rcheck/MesKit-Ex.timings
| name | user | system | elapsed | |
| calFst | 14.975 | 0.318 | 15.249 | |
| calJSI | 10.091 | 0.176 | 10.208 | |
| calNeiDist | 10.480 | 0.081 | 10.517 | |
| ccfAUC | 10.022 | 0.138 | 10.116 | |
| classifyMut | 7.391 | 0.456 | 7.799 | |
| cna2gene | 23.163 | 0.739 | 23.745 | |
| compareCCF | 10.042 | 0.978 | 10.975 | |
| compareTree | 10.936 | 0.096 | 10.975 | |
| fitSignatures | 9.391 | 0.206 | 9.555 | |
| getBinaryMatrix | 13.355 | 0.108 | 13.396 | |
| getBootstrapValue | 13.435 | 0.099 | 13.490 | |
| getBranchType | 13.303 | 0.034 | 13.280 | |
| getCCFMatrix | 13.382 | 0.105 | 13.442 | |
| getMafData | 8.154 | 0.167 | 8.288 | |
| getMafPatient | 6.516 | 0.019 | 6.502 | |
| getMafRef | 6.498 | 0.038 | 6.498 | |
| getMutBranches | 12.531 | 0.220 | 12.689 | |
| getNonSyn_vc | 6.578 | 0.007 | 6.558 | |
| getPhyloTree | 12.631 | 0.005 | 12.578 | |
| getPhyloTreePatient | 12.929 | 0.004 | 12.885 | |
| getPhyloTreeRef | 13.136 | 0.055 | 13.134 | |
| getPhyloTreeTsbLabel | 12.717 | 0.079 | 12.726 | |
| getSampleInfo | 6.804 | 0.017 | 6.787 | |
| getTree | 13.143 | 0.115 | 13.209 | |
| getTreeMethod | 14.374 | 0.179 | 14.503 | |
| mathScore | 6.771 | 0.004 | 6.709 | |
| mutCluster | 9.784 | 0.287 | 10.009 | |
| mutHeatmap | 12.974 | 0.071 | 12.974 | |
| mutTrunkBranch | 8.669 | 0.191 | 8.824 | |
| plotCNA | 3.302 | 0.028 | 3.232 | |
| plotMutProfile | 8.214 | 0.041 | 8.196 | |
| plotMutSigProfile | 13.182 | 0.180 | 13.325 | |
| plotPhyloTree | 8.702 | 0.015 | 8.678 | |
| readMaf | 7.366 | 0.026 | 7.327 | |
| readSegment | 0.519 | 0.003 | 0.446 | |
| runMesKit | 0 | 0 | 0 | |
| subMaf | 7.106 | 0.014 | 7.069 | |
| testNeutral | 9.882 | 0.049 | 9.870 | |
| triMatrix | 8.855 | 0.164 | 8.981 | |