Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-08 12:05 -0400 (Mon, 08 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1214/2322 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.19.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.19.0 |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
MesKit.Rcheck/MesKit-Ex.timings
name | user | system | elapsed | |
calFst | 18.153 | 0.295 | 18.595 | |
calJSI | 11.906 | 0.109 | 12.081 | |
calNeiDist | 13.093 | 0.118 | 13.280 | |
ccfAUC | 9.810 | 0.106 | 9.958 | |
classifyMut | 8.912 | 0.456 | 9.408 | |
cna2gene | 20.399 | 0.852 | 21.356 | |
compareCCF | 13.573 | 1.482 | 15.211 | |
compareTree | 12.545 | 0.177 | 12.771 | |
fitSignatures | 11.993 | 0.266 | 12.312 | |
getBinaryMatrix | 14.925 | 0.308 | 15.287 | |
getBootstrapValue | 14.306 | 0.304 | 14.666 | |
getBranchType | 15.501 | 0.171 | 15.729 | |
getCCFMatrix | 15.545 | 0.243 | 15.853 | |
getMafData | 8.403 | 0.060 | 8.506 | |
getMafPatient | 8.151 | 0.054 | 8.231 | |
getMafRef | 7.951 | 0.055 | 8.041 | |
getMutBranches | 15.405 | 0.420 | 15.896 | |
getNonSyn_vc | 8.097 | 0.056 | 8.191 | |
getPhyloTree | 15.562 | 0.182 | 15.809 | |
getPhyloTreePatient | 15.323 | 0.157 | 15.530 | |
getPhyloTreeRef | 15.634 | 0.276 | 15.976 | |
getPhyloTreeTsbLabel | 15.759 | 0.162 | 15.991 | |
getSampleInfo | 8.155 | 0.052 | 8.236 | |
getTree | 15.765 | 0.227 | 16.085 | |
getTreeMethod | 14.742 | 0.162 | 14.978 | |
mathScore | 8.205 | 0.173 | 8.426 | |
mutCluster | 10.725 | 0.490 | 11.290 | |
mutHeatmap | 13.674 | 0.128 | 13.872 | |
mutTrunkBranch | 10.882 | 0.174 | 11.113 | |
plotCNA | 3.242 | 0.051 | 3.312 | |
plotMutProfile | 10.021 | 0.077 | 10.148 | |
plotMutSigProfile | 14.621 | 0.248 | 14.943 | |
plotPhyloTree | 10.065 | 0.082 | 10.205 | |
readMaf | 8.325 | 0.071 | 8.443 | |
readSegment | 0.495 | 0.007 | 0.505 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 8.348 | 0.087 | 8.475 | |
testNeutral | 10.377 | 0.078 | 10.497 | |
triMatrix | 10.110 | 0.164 | 10.325 | |