Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-06 11:39 -0400 (Mon, 06 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
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: /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_1.18.0.tar.gz |
StartedAt: 2025-10-03 06:01:41 -0400 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 06:24:41 -0400 (Fri, 03 Oct 2025) |
EllapsedTime: 1380.3 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_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘1.18.0’ * 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 ‘/Users/biocbuild/bbs-3.21-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 calFst 39.017 0.416 41.379 plotMutSigProfile 37.022 0.433 39.128 mutHeatmap 37.027 0.171 38.157 getCCFMatrix 36.045 0.554 40.842 getBootstrapValue 35.919 0.245 39.574 getBinaryMatrix 35.592 0.560 39.318 getBranchType 35.732 0.218 39.403 getTreeMethod 35.420 0.310 36.850 getPhyloTreeTsbLabel 35.079 0.245 35.662 getPhyloTreeRef 34.553 0.366 35.896 getTree 34.590 0.248 35.509 getPhyloTreePatient 34.616 0.218 36.031 getPhyloTree 34.416 0.359 36.377 getMutBranches 33.894 0.568 36.160 cna2gene 32.609 1.589 34.855 compareCCF 28.697 3.130 32.324 compareTree 29.863 0.400 32.605 calNeiDist 27.862 0.146 28.512 mutCluster 26.721 1.276 28.308 mutTrunkBranch 26.834 0.402 28.684 calJSI 26.903 0.154 27.603 ccfAUC 26.486 0.150 27.086 testNeutral 25.931 0.131 26.363 fitSignatures 25.197 0.342 28.684 triMatrix 24.401 0.248 25.567 plotPhyloTree 23.944 0.208 24.354 classifyMut 22.639 1.270 24.508 plotMutProfile 23.515 0.122 24.385 getMafRef 19.988 0.120 21.059 readMaf 19.614 0.099 19.962 subMaf 19.590 0.086 20.008 mathScore 19.390 0.082 19.988 getMafData 19.086 0.087 20.098 getMafPatient 18.993 0.081 22.197 getSampleInfo 18.733 0.058 18.908 getNonSyn_vc 18.307 0.090 19.170 plotCNA 7.683 0.136 8.555 * 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-3.21-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 ‘1.18.0’ ** 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 | 39.017 | 0.416 | 41.379 | |
calJSI | 26.903 | 0.154 | 27.603 | |
calNeiDist | 27.862 | 0.146 | 28.512 | |
ccfAUC | 26.486 | 0.150 | 27.086 | |
classifyMut | 22.639 | 1.270 | 24.508 | |
cna2gene | 32.609 | 1.589 | 34.855 | |
compareCCF | 28.697 | 3.130 | 32.324 | |
compareTree | 29.863 | 0.400 | 32.605 | |
fitSignatures | 25.197 | 0.342 | 28.684 | |
getBinaryMatrix | 35.592 | 0.560 | 39.318 | |
getBootstrapValue | 35.919 | 0.245 | 39.574 | |
getBranchType | 35.732 | 0.218 | 39.403 | |
getCCFMatrix | 36.045 | 0.554 | 40.842 | |
getMafData | 19.086 | 0.087 | 20.098 | |
getMafPatient | 18.993 | 0.081 | 22.197 | |
getMafRef | 19.988 | 0.120 | 21.059 | |
getMutBranches | 33.894 | 0.568 | 36.160 | |
getNonSyn_vc | 18.307 | 0.090 | 19.170 | |
getPhyloTree | 34.416 | 0.359 | 36.377 | |
getPhyloTreePatient | 34.616 | 0.218 | 36.031 | |
getPhyloTreeRef | 34.553 | 0.366 | 35.896 | |
getPhyloTreeTsbLabel | 35.079 | 0.245 | 35.662 | |
getSampleInfo | 18.733 | 0.058 | 18.908 | |
getTree | 34.590 | 0.248 | 35.509 | |
getTreeMethod | 35.42 | 0.31 | 36.85 | |
mathScore | 19.390 | 0.082 | 19.988 | |
mutCluster | 26.721 | 1.276 | 28.308 | |
mutHeatmap | 37.027 | 0.171 | 38.157 | |
mutTrunkBranch | 26.834 | 0.402 | 28.684 | |
plotCNA | 7.683 | 0.136 | 8.555 | |
plotMutProfile | 23.515 | 0.122 | 24.385 | |
plotMutSigProfile | 37.022 | 0.433 | 39.128 | |
plotPhyloTree | 23.944 | 0.208 | 24.354 | |
readMaf | 19.614 | 0.099 | 19.962 | |
readSegment | 0.981 | 0.012 | 0.996 | |
runMesKit | 0.000 | 0.001 | 0.001 | |
subMaf | 19.590 | 0.086 | 20.008 | |
testNeutral | 25.931 | 0.131 | 26.363 | |
triMatrix | 24.401 | 0.248 | 25.567 | |