Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1220/2333 | 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: 2025-09-19 22:03:25 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 22:14:13 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 647.0 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 Patched (2025-09-10 r88807) * 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 20.889 0.911 21.937 calFst 18.903 0.247 19.314 getMutBranches 17.164 0.446 17.690 mutHeatmap 17.338 0.225 17.682 plotMutSigProfile 16.948 0.254 17.322 getBinaryMatrix 15.900 0.367 16.315 getBootstrapValue 15.986 0.222 16.261 getTreeMethod 16.011 0.174 16.292 getTree 15.784 0.251 16.130 getCCFMatrix 15.624 0.292 15.995 getPhyloTreePatient 15.468 0.183 15.734 getBranchType 15.297 0.170 15.504 getPhyloTree 15.209 0.209 15.506 getPhyloTreeRef 15.079 0.249 15.391 getPhyloTreeTsbLabel 14.995 0.197 15.250 compareCCF 12.989 1.122 14.179 compareTree 13.429 0.225 13.716 mutCluster 12.553 0.497 13.126 calNeiDist 12.638 0.109 12.812 calJSI 12.578 0.105 12.746 ccfAUC 12.285 0.110 12.462 testNeutral 12.103 0.103 12.272 triMatrix 11.310 0.200 11.574 mutTrunkBranch 11.176 0.183 11.437 fitSignatures 10.775 0.241 11.078 plotPhyloTree 10.298 0.083 10.437 plotMutProfile 10.172 0.092 10.313 classifyMut 9.224 0.473 9.742 subMaf 8.655 0.094 8.797 getMafData 8.580 0.057 8.670 mathScore 8.302 0.077 8.433 getMafRef 8.302 0.051 8.388 getMafPatient 8.162 0.058 8.248 readMaf 8.138 0.065 8.244 getSampleInfo 7.988 0.052 8.068 getNonSyn_vc 7.849 0.050 7.931 * 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 | 18.903 | 0.247 | 19.314 | |
calJSI | 12.578 | 0.105 | 12.746 | |
calNeiDist | 12.638 | 0.109 | 12.812 | |
ccfAUC | 12.285 | 0.110 | 12.462 | |
classifyMut | 9.224 | 0.473 | 9.742 | |
cna2gene | 20.889 | 0.911 | 21.937 | |
compareCCF | 12.989 | 1.122 | 14.179 | |
compareTree | 13.429 | 0.225 | 13.716 | |
fitSignatures | 10.775 | 0.241 | 11.078 | |
getBinaryMatrix | 15.900 | 0.367 | 16.315 | |
getBootstrapValue | 15.986 | 0.222 | 16.261 | |
getBranchType | 15.297 | 0.170 | 15.504 | |
getCCFMatrix | 15.624 | 0.292 | 15.995 | |
getMafData | 8.580 | 0.057 | 8.670 | |
getMafPatient | 8.162 | 0.058 | 8.248 | |
getMafRef | 8.302 | 0.051 | 8.388 | |
getMutBranches | 17.164 | 0.446 | 17.690 | |
getNonSyn_vc | 7.849 | 0.050 | 7.931 | |
getPhyloTree | 15.209 | 0.209 | 15.506 | |
getPhyloTreePatient | 15.468 | 0.183 | 15.734 | |
getPhyloTreeRef | 15.079 | 0.249 | 15.391 | |
getPhyloTreeTsbLabel | 14.995 | 0.197 | 15.250 | |
getSampleInfo | 7.988 | 0.052 | 8.068 | |
getTree | 15.784 | 0.251 | 16.130 | |
getTreeMethod | 16.011 | 0.174 | 16.292 | |
mathScore | 8.302 | 0.077 | 8.433 | |
mutCluster | 12.553 | 0.497 | 13.126 | |
mutHeatmap | 17.338 | 0.225 | 17.682 | |
mutTrunkBranch | 11.176 | 0.183 | 11.437 | |
plotCNA | 3.868 | 0.064 | 3.955 | |
plotMutProfile | 10.172 | 0.092 | 10.313 | |
plotMutSigProfile | 16.948 | 0.254 | 17.322 | |
plotPhyloTree | 10.298 | 0.083 | 10.437 | |
readMaf | 8.138 | 0.065 | 8.244 | |
readSegment | 0.555 | 0.011 | 0.572 | |
runMesKit | 0.000 | 0.000 | 0.001 | |
subMaf | 8.655 | 0.094 | 8.797 | |
testNeutral | 12.103 | 0.103 | 12.272 | |
triMatrix | 11.310 | 0.200 | 11.574 | |