Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:06 -0400 (Sat, 30 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" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1213/2320 | 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: 2025-08-29 21:55:07 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 22:05:08 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 600.8 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 20.131 0.824 21.072 calFst 17.150 0.275 17.579 getPhyloTreeTsbLabel 15.701 0.270 16.044 getCCFMatrix 15.454 0.330 15.857 getMutBranches 15.169 0.322 15.568 getPhyloTreePatient 15.316 0.163 15.535 getPhyloTreeRef 15.256 0.142 15.463 getPhyloTree 15.137 0.154 15.371 plotMutSigProfile 14.892 0.265 15.256 getBinaryMatrix 14.779 0.348 15.179 getTreeMethod 14.890 0.153 15.111 getTree 14.757 0.188 15.028 getBootstrapValue 14.342 0.202 14.600 getBranchType 13.932 0.175 14.147 mutHeatmap 13.522 0.132 13.748 compareCCF 12.469 1.132 13.664 calNeiDist 12.518 0.129 12.710 fitSignatures 11.690 0.356 12.277 calJSI 11.722 0.109 11.908 compareTree 11.648 0.164 11.865 mutCluster 10.526 0.539 11.142 triMatrix 10.717 0.177 10.951 mutTrunkBranch 10.470 0.166 10.677 ccfAUC 10.299 0.096 10.440 testNeutral 10.177 0.084 10.317 plotMutProfile 9.937 0.087 10.088 plotPhyloTree 9.912 0.078 10.037 classifyMut 8.667 0.433 9.146 subMaf 8.379 0.081 8.512 getMafData 8.185 0.055 8.282 readMaf 8.034 0.060 8.132 getMafPatient 8.013 0.049 8.114 getNonSyn_vc 7.927 0.129 8.104 mathScore 7.753 0.055 7.839 getSampleInfo 7.553 0.055 7.646 getMafRef 7.491 0.062 7.576 * 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 | 17.150 | 0.275 | 17.579 | |
calJSI | 11.722 | 0.109 | 11.908 | |
calNeiDist | 12.518 | 0.129 | 12.710 | |
ccfAUC | 10.299 | 0.096 | 10.440 | |
classifyMut | 8.667 | 0.433 | 9.146 | |
cna2gene | 20.131 | 0.824 | 21.072 | |
compareCCF | 12.469 | 1.132 | 13.664 | |
compareTree | 11.648 | 0.164 | 11.865 | |
fitSignatures | 11.690 | 0.356 | 12.277 | |
getBinaryMatrix | 14.779 | 0.348 | 15.179 | |
getBootstrapValue | 14.342 | 0.202 | 14.600 | |
getBranchType | 13.932 | 0.175 | 14.147 | |
getCCFMatrix | 15.454 | 0.330 | 15.857 | |
getMafData | 8.185 | 0.055 | 8.282 | |
getMafPatient | 8.013 | 0.049 | 8.114 | |
getMafRef | 7.491 | 0.062 | 7.576 | |
getMutBranches | 15.169 | 0.322 | 15.568 | |
getNonSyn_vc | 7.927 | 0.129 | 8.104 | |
getPhyloTree | 15.137 | 0.154 | 15.371 | |
getPhyloTreePatient | 15.316 | 0.163 | 15.535 | |
getPhyloTreeRef | 15.256 | 0.142 | 15.463 | |
getPhyloTreeTsbLabel | 15.701 | 0.270 | 16.044 | |
getSampleInfo | 7.553 | 0.055 | 7.646 | |
getTree | 14.757 | 0.188 | 15.028 | |
getTreeMethod | 14.890 | 0.153 | 15.111 | |
mathScore | 7.753 | 0.055 | 7.839 | |
mutCluster | 10.526 | 0.539 | 11.142 | |
mutHeatmap | 13.522 | 0.132 | 13.748 | |
mutTrunkBranch | 10.470 | 0.166 | 10.677 | |
plotCNA | 3.130 | 0.040 | 3.182 | |
plotMutProfile | 9.937 | 0.087 | 10.088 | |
plotMutSigProfile | 14.892 | 0.265 | 15.256 | |
plotPhyloTree | 9.912 | 0.078 | 10.037 | |
readMaf | 8.034 | 0.060 | 8.132 | |
readSegment | 0.483 | 0.008 | 0.494 | |
runMesKit | 0.000 | 0.001 | 0.000 | |
subMaf | 8.379 | 0.081 | 8.512 | |
testNeutral | 10.177 | 0.084 | 10.317 | |
triMatrix | 10.717 | 0.177 | 10.951 | |