Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-20 12:03 -0400 (Wed, 20 Aug 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" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1211/2317 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MesKit_1.19.0.tar.gz |
StartedAt: 2025-08-19 23:58:11 -0400 (Tue, 19 Aug 2025) |
EndedAt: 2025-08-20 00:07:38 -0400 (Wed, 20 Aug 2025) |
EllapsedTime: 567.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MesKit_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-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 ‘1.19.0’ * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck/00install.out’ for details. * checking installed package size ... INFO installed size is 6.0Mb 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 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 18.753 0.627 19.216 calFst 14.964 0.369 15.293 getTreeMethod 13.956 0.113 14.006 getBranchType 13.686 0.149 13.785 getBootstrapValue 13.344 0.118 13.420 getBinaryMatrix 13.129 0.091 13.163 getTree 13.085 0.003 13.026 getPhyloTreeTsbLabel 12.537 0.001 12.492 getMutBranches 12.447 0.016 12.414 getPhyloTreeRef 12.437 0.009 12.400 getPhyloTreePatient 12.373 0.008 12.336 plotMutSigProfile 12.211 0.091 12.260 getPhyloTree 12.285 0.003 12.246 getCCFMatrix 12.000 0.094 12.046 mutHeatmap 11.275 0.067 11.295 calNeiDist 10.751 0.109 10.806 compareTree 10.237 0.130 10.319 calJSI 10.106 0.119 10.173 compareCCF 9.808 0.264 10.024 fitSignatures 8.952 0.101 9.013 ccfAUC 8.863 0.101 8.911 mutTrunkBranch 8.862 0.048 8.863 mutCluster 8.610 0.076 8.646 testNeutral 8.609 0.072 8.624 triMatrix 8.374 0.079 8.418 plotMutProfile 8.231 0.022 8.205 plotPhyloTree 8.192 0.053 8.194 classifyMut 7.686 0.073 7.711 subMaf 7.058 0.040 7.060 readMaf 6.828 0.034 6.795 getNonSyn_vc 6.844 0.000 6.803 getSampleInfo 6.651 0.004 6.628 getMafRef 6.586 0.003 6.551 getMafPatient 6.561 0.003 6.532 mathScore 6.451 0.021 6.424 getMafData 6.337 0.034 6.341 * 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-3.22-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 | 14.964 | 0.369 | 15.293 | |
calJSI | 10.106 | 0.119 | 10.173 | |
calNeiDist | 10.751 | 0.109 | 10.806 | |
ccfAUC | 8.863 | 0.101 | 8.911 | |
classifyMut | 7.686 | 0.073 | 7.711 | |
cna2gene | 18.753 | 0.627 | 19.216 | |
compareCCF | 9.808 | 0.264 | 10.024 | |
compareTree | 10.237 | 0.130 | 10.319 | |
fitSignatures | 8.952 | 0.101 | 9.013 | |
getBinaryMatrix | 13.129 | 0.091 | 13.163 | |
getBootstrapValue | 13.344 | 0.118 | 13.420 | |
getBranchType | 13.686 | 0.149 | 13.785 | |
getCCFMatrix | 12.000 | 0.094 | 12.046 | |
getMafData | 6.337 | 0.034 | 6.341 | |
getMafPatient | 6.561 | 0.003 | 6.532 | |
getMafRef | 6.586 | 0.003 | 6.551 | |
getMutBranches | 12.447 | 0.016 | 12.414 | |
getNonSyn_vc | 6.844 | 0.000 | 6.803 | |
getPhyloTree | 12.285 | 0.003 | 12.246 | |
getPhyloTreePatient | 12.373 | 0.008 | 12.336 | |
getPhyloTreeRef | 12.437 | 0.009 | 12.400 | |
getPhyloTreeTsbLabel | 12.537 | 0.001 | 12.492 | |
getSampleInfo | 6.651 | 0.004 | 6.628 | |
getTree | 13.085 | 0.003 | 13.026 | |
getTreeMethod | 13.956 | 0.113 | 14.006 | |
mathScore | 6.451 | 0.021 | 6.424 | |
mutCluster | 8.610 | 0.076 | 8.646 | |
mutHeatmap | 11.275 | 0.067 | 11.295 | |
mutTrunkBranch | 8.862 | 0.048 | 8.863 | |
plotCNA | 2.804 | 0.003 | 2.709 | |
plotMutProfile | 8.231 | 0.022 | 8.205 | |
plotMutSigProfile | 12.211 | 0.091 | 12.260 | |
plotPhyloTree | 8.192 | 0.053 | 8.194 | |
readMaf | 6.828 | 0.034 | 6.795 | |
readSegment | 0.458 | 0.009 | 0.403 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 7.058 | 0.040 | 7.060 | |
testNeutral | 8.609 | 0.072 | 8.624 | |
triMatrix | 8.374 | 0.079 | 8.418 | |