Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:09 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 1209/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.19.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 2025-08-03 22:11:32 -0400 (Sun, 03 Aug 2025) |
EndedAt: 2025-08-03 22:21:45 -0400 (Sun, 03 Aug 2025) |
EllapsedTime: 612.3 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 20.530 0.901 21.571 calFst 18.170 0.286 18.608 getTree 15.788 0.214 16.118 getPhyloTreeRef 15.410 0.280 15.752 getPhyloTreePatient 15.426 0.168 15.677 getPhyloTree 15.194 0.227 15.505 getCCFMatrix 15.103 0.263 15.431 getPhyloTreeTsbLabel 15.158 0.144 15.364 getMutBranches 14.857 0.411 15.350 getBinaryMatrix 14.582 0.327 14.956 plotMutSigProfile 14.633 0.268 15.005 getBranchType 14.711 0.166 14.935 getTreeMethod 14.708 0.161 14.953 getBootstrapValue 14.255 0.274 14.574 compareCCF 12.920 1.185 14.179 mutHeatmap 13.522 0.122 13.726 calNeiDist 12.983 0.133 13.183 compareTree 12.338 0.197 12.587 fitSignatures 12.085 0.287 12.435 calJSI 12.240 0.109 12.430 triMatrix 10.900 0.183 11.141 mutCluster 10.520 0.469 11.071 mutTrunkBranch 10.805 0.183 11.062 testNeutral 10.644 0.101 10.794 plotMutProfile 10.320 0.074 10.447 ccfAUC 10.275 0.092 10.405 plotPhyloTree 9.939 0.067 10.056 classifyMut 9.291 0.401 9.734 readMaf 8.310 0.068 8.427 getSampleInfo 8.191 0.057 8.293 getMafData 8.180 0.051 8.263 getMafPatient 8.081 0.055 8.188 mathScore 7.926 0.169 8.143 getMafRef 8.035 0.057 8.136 getNonSyn_vc 7.731 0.051 7.817 subMaf 7.592 0.062 7.689 * 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 | 18.170 | 0.286 | 18.608 | |
calJSI | 12.240 | 0.109 | 12.430 | |
calNeiDist | 12.983 | 0.133 | 13.183 | |
ccfAUC | 10.275 | 0.092 | 10.405 | |
classifyMut | 9.291 | 0.401 | 9.734 | |
cna2gene | 20.530 | 0.901 | 21.571 | |
compareCCF | 12.920 | 1.185 | 14.179 | |
compareTree | 12.338 | 0.197 | 12.587 | |
fitSignatures | 12.085 | 0.287 | 12.435 | |
getBinaryMatrix | 14.582 | 0.327 | 14.956 | |
getBootstrapValue | 14.255 | 0.274 | 14.574 | |
getBranchType | 14.711 | 0.166 | 14.935 | |
getCCFMatrix | 15.103 | 0.263 | 15.431 | |
getMafData | 8.180 | 0.051 | 8.263 | |
getMafPatient | 8.081 | 0.055 | 8.188 | |
getMafRef | 8.035 | 0.057 | 8.136 | |
getMutBranches | 14.857 | 0.411 | 15.350 | |
getNonSyn_vc | 7.731 | 0.051 | 7.817 | |
getPhyloTree | 15.194 | 0.227 | 15.505 | |
getPhyloTreePatient | 15.426 | 0.168 | 15.677 | |
getPhyloTreeRef | 15.410 | 0.280 | 15.752 | |
getPhyloTreeTsbLabel | 15.158 | 0.144 | 15.364 | |
getSampleInfo | 8.191 | 0.057 | 8.293 | |
getTree | 15.788 | 0.214 | 16.118 | |
getTreeMethod | 14.708 | 0.161 | 14.953 | |
mathScore | 7.926 | 0.169 | 8.143 | |
mutCluster | 10.520 | 0.469 | 11.071 | |
mutHeatmap | 13.522 | 0.122 | 13.726 | |
mutTrunkBranch | 10.805 | 0.183 | 11.062 | |
plotCNA | 3.109 | 0.054 | 3.179 | |
plotMutProfile | 10.320 | 0.074 | 10.447 | |
plotMutSigProfile | 14.633 | 0.268 | 15.005 | |
plotPhyloTree | 9.939 | 0.067 | 10.056 | |
readMaf | 8.310 | 0.068 | 8.427 | |
readSegment | 0.426 | 0.007 | 0.433 | |
runMesKit | 0.000 | 0.000 | 0.001 | |
subMaf | 7.592 | 0.062 | 7.689 | |
testNeutral | 10.644 | 0.101 | 10.794 | |
triMatrix | 10.900 | 0.183 | 11.141 | |