Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-07 12:08 -0400 (Thu, 07 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 1209/2315 | 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 | ![]() | ||||||||
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: 2025-08-06 22:16:06 -0400 (Wed, 06 Aug 2025) |
EndedAt: 2025-08-06 22:26:26 -0400 (Wed, 06 Aug 2025) |
EllapsedTime: 620.1 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 20.623 0.791 21.534 calFst 18.403 0.300 18.839 getBranchType 15.888 0.203 16.206 getMutBranches 15.272 0.486 15.863 getCCFMatrix 15.417 0.275 15.805 getPhyloTree 15.457 0.207 15.782 plotMutSigProfile 15.378 0.286 15.786 getPhyloTreePatient 15.327 0.159 15.552 getPhyloTreeTsbLabel 15.263 0.175 15.513 getPhyloTreeRef 15.151 0.269 15.480 getBinaryMatrix 14.742 0.312 15.096 getTree 14.830 0.189 15.114 getBootstrapValue 14.470 0.325 14.874 getTreeMethod 14.293 0.322 14.687 compareCCF 13.070 1.193 14.332 mutHeatmap 13.769 0.150 13.998 calNeiDist 13.534 0.127 13.734 compareTree 12.410 0.190 12.647 calJSI 12.150 0.110 12.342 fitSignatures 11.937 0.274 12.271 testNeutral 10.970 0.099 11.133 mutTrunkBranch 10.774 0.178 11.024 mutCluster 10.390 0.482 10.957 triMatrix 10.491 0.186 10.743 ccfAUC 10.093 0.101 10.246 plotMutProfile 10.043 0.093 10.208 plotPhyloTree 9.767 0.067 9.889 getSampleInfo 9.416 0.145 9.644 classifyMut 9.014 0.405 9.462 getMafData 8.497 0.055 8.593 readMaf 8.459 0.079 8.595 subMaf 8.374 0.092 8.513 mathScore 8.273 0.070 8.395 getNonSyn_vc 8.233 0.065 8.352 getMafRef 8.009 0.064 8.118 getMafPatient 7.935 0.052 8.029 * 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 | 18.403 | 0.300 | 18.839 | |
calJSI | 12.150 | 0.110 | 12.342 | |
calNeiDist | 13.534 | 0.127 | 13.734 | |
ccfAUC | 10.093 | 0.101 | 10.246 | |
classifyMut | 9.014 | 0.405 | 9.462 | |
cna2gene | 20.623 | 0.791 | 21.534 | |
compareCCF | 13.070 | 1.193 | 14.332 | |
compareTree | 12.410 | 0.190 | 12.647 | |
fitSignatures | 11.937 | 0.274 | 12.271 | |
getBinaryMatrix | 14.742 | 0.312 | 15.096 | |
getBootstrapValue | 14.470 | 0.325 | 14.874 | |
getBranchType | 15.888 | 0.203 | 16.206 | |
getCCFMatrix | 15.417 | 0.275 | 15.805 | |
getMafData | 8.497 | 0.055 | 8.593 | |
getMafPatient | 7.935 | 0.052 | 8.029 | |
getMafRef | 8.009 | 0.064 | 8.118 | |
getMutBranches | 15.272 | 0.486 | 15.863 | |
getNonSyn_vc | 8.233 | 0.065 | 8.352 | |
getPhyloTree | 15.457 | 0.207 | 15.782 | |
getPhyloTreePatient | 15.327 | 0.159 | 15.552 | |
getPhyloTreeRef | 15.151 | 0.269 | 15.480 | |
getPhyloTreeTsbLabel | 15.263 | 0.175 | 15.513 | |
getSampleInfo | 9.416 | 0.145 | 9.644 | |
getTree | 14.830 | 0.189 | 15.114 | |
getTreeMethod | 14.293 | 0.322 | 14.687 | |
mathScore | 8.273 | 0.070 | 8.395 | |
mutCluster | 10.390 | 0.482 | 10.957 | |
mutHeatmap | 13.769 | 0.150 | 13.998 | |
mutTrunkBranch | 10.774 | 0.178 | 11.024 | |
plotCNA | 3.055 | 0.050 | 3.127 | |
plotMutProfile | 10.043 | 0.093 | 10.208 | |
plotMutSigProfile | 15.378 | 0.286 | 15.786 | |
plotPhyloTree | 9.767 | 0.067 | 9.889 | |
readMaf | 8.459 | 0.079 | 8.595 | |
readSegment | 0.503 | 0.007 | 0.513 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 8.374 | 0.092 | 8.513 | |
testNeutral | 10.970 | 0.099 | 11.133 | |
triMatrix | 10.491 | 0.186 | 10.743 | |