Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-29 11:38 -0400 (Mon, 29 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
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 1220/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.18.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | 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: 1.18.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.18.0.tar.gz |
StartedAt: 2025-09-29 00:51:48 -0400 (Mon, 29 Sep 2025) |
EndedAt: 2025-09-29 01:01:37 -0400 (Mon, 29 Sep 2025) |
EllapsedTime: 589.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.18.0’ * 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 ‘/home/biocbuild/bbs-3.21-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 19.391 1.258 20.463 calFst 15.225 0.283 15.467 getBranchType 13.975 0.167 14.108 getBinaryMatrix 13.518 0.186 13.647 plotMutSigProfile 13.549 0.131 13.640 getPhyloTreeTsbLabel 13.377 0.055 13.384 getTreeMethod 12.992 0.211 13.158 getTree 13.066 0.101 13.115 mutHeatmap 13.141 0.018 13.119 getPhyloTreeRef 13.053 0.055 13.060 getBootstrapValue 12.855 0.093 12.894 getMutBranches 12.469 0.276 12.695 getPhyloTree 12.673 0.034 12.659 getCCFMatrix 12.478 0.139 12.560 getPhyloTreePatient 12.461 0.009 12.422 compareCCF 9.965 1.043 10.956 calNeiDist 10.895 0.088 10.916 calJSI 10.799 0.153 10.900 compareTree 10.655 0.266 10.882 ccfAUC 9.786 0.106 9.851 mutCluster 9.326 0.272 9.550 testNeutral 9.418 0.013 9.374 classifyMut 8.669 0.694 9.312 fitSignatures 9.122 0.224 9.312 mutTrunkBranch 8.844 0.180 8.986 triMatrix 8.725 0.139 8.818 plotMutProfile 8.415 0.064 8.432 plotPhyloTree 8.290 0.081 8.329 readMaf 6.993 0.035 6.935 subMaf 6.825 0.037 6.811 getSampleInfo 6.790 0.029 6.791 getMafData 6.649 0.046 6.649 getNonSyn_vc 6.549 0.003 6.519 getMafRef 6.479 0.034 6.471 getMafPatient 6.497 0.005 6.475 mathScore 6.371 0.002 6.324 * 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-3.21-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘MesKit’ ... ** this is package ‘MesKit’ version ‘1.18.0’ ** 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 | 15.225 | 0.283 | 15.467 | |
calJSI | 10.799 | 0.153 | 10.900 | |
calNeiDist | 10.895 | 0.088 | 10.916 | |
ccfAUC | 9.786 | 0.106 | 9.851 | |
classifyMut | 8.669 | 0.694 | 9.312 | |
cna2gene | 19.391 | 1.258 | 20.463 | |
compareCCF | 9.965 | 1.043 | 10.956 | |
compareTree | 10.655 | 0.266 | 10.882 | |
fitSignatures | 9.122 | 0.224 | 9.312 | |
getBinaryMatrix | 13.518 | 0.186 | 13.647 | |
getBootstrapValue | 12.855 | 0.093 | 12.894 | |
getBranchType | 13.975 | 0.167 | 14.108 | |
getCCFMatrix | 12.478 | 0.139 | 12.560 | |
getMafData | 6.649 | 0.046 | 6.649 | |
getMafPatient | 6.497 | 0.005 | 6.475 | |
getMafRef | 6.479 | 0.034 | 6.471 | |
getMutBranches | 12.469 | 0.276 | 12.695 | |
getNonSyn_vc | 6.549 | 0.003 | 6.519 | |
getPhyloTree | 12.673 | 0.034 | 12.659 | |
getPhyloTreePatient | 12.461 | 0.009 | 12.422 | |
getPhyloTreeRef | 13.053 | 0.055 | 13.060 | |
getPhyloTreeTsbLabel | 13.377 | 0.055 | 13.384 | |
getSampleInfo | 6.790 | 0.029 | 6.791 | |
getTree | 13.066 | 0.101 | 13.115 | |
getTreeMethod | 12.992 | 0.211 | 13.158 | |
mathScore | 6.371 | 0.002 | 6.324 | |
mutCluster | 9.326 | 0.272 | 9.550 | |
mutHeatmap | 13.141 | 0.018 | 13.119 | |
mutTrunkBranch | 8.844 | 0.180 | 8.986 | |
plotCNA | 3.405 | 0.018 | 3.280 | |
plotMutProfile | 8.415 | 0.064 | 8.432 | |
plotMutSigProfile | 13.549 | 0.131 | 13.640 | |
plotPhyloTree | 8.290 | 0.081 | 8.329 | |
readMaf | 6.993 | 0.035 | 6.935 | |
readSegment | 0.497 | 0.013 | 0.421 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 6.825 | 0.037 | 6.811 | |
testNeutral | 9.418 | 0.013 | 9.374 | |
triMatrix | 8.725 | 0.139 | 8.818 | |