Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-23 12:04 -0400 (Sat, 23 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" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 1212/2319 | 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: 2025-08-23 00:01:19 -0400 (Sat, 23 Aug 2025) |
EndedAt: 2025-08-23 00:10:46 -0400 (Sat, 23 Aug 2025) |
EllapsedTime: 567.6 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 18.473 0.459 18.794 calFst 14.823 0.238 15.020 getMutBranches 12.987 0.074 13.009 getPhyloTreeRef 12.930 0.031 12.909 getPhyloTreePatient 12.869 0.083 12.903 getPhyloTreeTsbLabel 12.879 0.008 12.828 getPhyloTree 12.744 0.115 12.809 getBranchType 12.398 0.111 12.459 getBootstrapValue 12.413 0.073 12.438 getTreeMethod 12.412 0.001 12.365 getCCFMatrix 12.313 0.081 12.343 getTree 12.156 0.013 12.110 getBinaryMatrix 11.996 0.119 12.067 plotMutSigProfile 12.028 0.074 12.069 mutHeatmap 11.263 0.024 11.245 calNeiDist 10.878 0.069 10.893 compareCCF 10.329 0.220 10.497 compareTree 10.186 0.117 10.248 calJSI 9.840 0.131 9.923 fitSignatures 9.802 0.040 9.804 mutCluster 8.833 0.035 8.829 triMatrix 8.699 0.059 8.719 testNeutral 8.654 0.013 8.614 ccfAUC 8.649 0.008 8.615 mutTrunkBranch 8.557 0.070 8.570 plotMutProfile 8.303 0.051 8.309 plotPhyloTree 8.212 0.066 8.241 getSampleInfo 7.596 0.091 7.661 classifyMut 7.550 0.051 7.558 readMaf 7.080 0.041 7.058 subMaf 7.085 0.026 7.061 getMafRef 6.744 0.027 6.738 getNonSyn_vc 6.709 0.024 6.701 getMafPatient 6.612 0.007 6.582 getMafData 6.555 0.010 6.524 mathScore 6.558 0.002 6.518 * 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 | 14.823 | 0.238 | 15.020 | |
calJSI | 9.840 | 0.131 | 9.923 | |
calNeiDist | 10.878 | 0.069 | 10.893 | |
ccfAUC | 8.649 | 0.008 | 8.615 | |
classifyMut | 7.550 | 0.051 | 7.558 | |
cna2gene | 18.473 | 0.459 | 18.794 | |
compareCCF | 10.329 | 0.220 | 10.497 | |
compareTree | 10.186 | 0.117 | 10.248 | |
fitSignatures | 9.802 | 0.040 | 9.804 | |
getBinaryMatrix | 11.996 | 0.119 | 12.067 | |
getBootstrapValue | 12.413 | 0.073 | 12.438 | |
getBranchType | 12.398 | 0.111 | 12.459 | |
getCCFMatrix | 12.313 | 0.081 | 12.343 | |
getMafData | 6.555 | 0.010 | 6.524 | |
getMafPatient | 6.612 | 0.007 | 6.582 | |
getMafRef | 6.744 | 0.027 | 6.738 | |
getMutBranches | 12.987 | 0.074 | 13.009 | |
getNonSyn_vc | 6.709 | 0.024 | 6.701 | |
getPhyloTree | 12.744 | 0.115 | 12.809 | |
getPhyloTreePatient | 12.869 | 0.083 | 12.903 | |
getPhyloTreeRef | 12.930 | 0.031 | 12.909 | |
getPhyloTreeTsbLabel | 12.879 | 0.008 | 12.828 | |
getSampleInfo | 7.596 | 0.091 | 7.661 | |
getTree | 12.156 | 0.013 | 12.110 | |
getTreeMethod | 12.412 | 0.001 | 12.365 | |
mathScore | 6.558 | 0.002 | 6.518 | |
mutCluster | 8.833 | 0.035 | 8.829 | |
mutHeatmap | 11.263 | 0.024 | 11.245 | |
mutTrunkBranch | 8.557 | 0.070 | 8.570 | |
plotCNA | 2.742 | 0.005 | 2.579 | |
plotMutProfile | 8.303 | 0.051 | 8.309 | |
plotMutSigProfile | 12.028 | 0.074 | 12.069 | |
plotPhyloTree | 8.212 | 0.066 | 8.241 | |
readMaf | 7.080 | 0.041 | 7.058 | |
readSegment | 0.494 | 0.008 | 0.433 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 7.085 | 0.026 | 7.061 | |
testNeutral | 8.654 | 0.013 | 8.614 | |
triMatrix | 8.699 | 0.059 | 8.719 | |