Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-15 12:07 -0400 (Wed, 15 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4866 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4653 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4598 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1226/2346 | 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 12.7.6 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MesKit |
Version: 1.19.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MesKit_1.19.0.tar.gz |
StartedAt: 2025-10-14 09:55:41 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 10:08:48 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 787.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MesKit_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 ‘/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 25.732 0.471 26.237 calFst 24.069 0.653 24.820 getPhyloTreeTsbLabel 21.296 0.208 21.552 plotMutSigProfile 21.180 0.112 21.338 mutHeatmap 20.953 0.131 21.126 getPhyloTreeRef 20.901 0.103 21.049 getPhyloTreePatient 20.891 0.112 21.049 getBootstrapValue 20.561 0.100 20.699 getPhyloTree 20.548 0.096 20.692 getMutBranches 20.436 0.168 20.653 getCCFMatrix 20.538 0.064 20.661 getBinaryMatrix 20.420 0.163 20.626 getBranchType 20.531 0.044 20.618 getTreeMethod 20.211 0.096 20.351 getTree 19.751 0.091 19.885 calNeiDist 17.392 0.115 17.552 calJSI 17.080 0.203 17.330 compareTree 17.130 0.115 17.286 compareCCF 16.508 0.264 16.801 ccfAUC 16.497 0.184 16.721 testNeutral 15.510 0.080 15.621 mutCluster 15.506 0.080 15.619 fitSignatures 14.503 0.164 14.704 mutTrunkBranch 14.380 0.128 14.536 triMatrix 14.080 0.167 14.273 plotPhyloTree 13.630 0.095 13.756 plotMutProfile 13.314 0.080 13.416 classifyMut 12.228 0.151 12.399 readMaf 11.420 0.036 11.470 mathScore 11.223 0.108 11.348 getMafData 11.156 0.087 11.271 subMaf 11.165 0.056 11.236 getNonSyn_vc 11.092 0.091 11.212 getMafPatient 11.130 0.028 11.185 getMafRef 11.055 0.048 11.128 getSampleInfo 10.821 0.004 10.848 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 | 24.069 | 0.653 | 24.820 | |
calJSI | 17.080 | 0.203 | 17.330 | |
calNeiDist | 17.392 | 0.115 | 17.552 | |
ccfAUC | 16.497 | 0.184 | 16.721 | |
classifyMut | 12.228 | 0.151 | 12.399 | |
cna2gene | 25.732 | 0.471 | 26.237 | |
compareCCF | 16.508 | 0.264 | 16.801 | |
compareTree | 17.130 | 0.115 | 17.286 | |
fitSignatures | 14.503 | 0.164 | 14.704 | |
getBinaryMatrix | 20.420 | 0.163 | 20.626 | |
getBootstrapValue | 20.561 | 0.100 | 20.699 | |
getBranchType | 20.531 | 0.044 | 20.618 | |
getCCFMatrix | 20.538 | 0.064 | 20.661 | |
getMafData | 11.156 | 0.087 | 11.271 | |
getMafPatient | 11.130 | 0.028 | 11.185 | |
getMafRef | 11.055 | 0.048 | 11.128 | |
getMutBranches | 20.436 | 0.168 | 20.653 | |
getNonSyn_vc | 11.092 | 0.091 | 11.212 | |
getPhyloTree | 20.548 | 0.096 | 20.692 | |
getPhyloTreePatient | 20.891 | 0.112 | 21.049 | |
getPhyloTreeRef | 20.901 | 0.103 | 21.049 | |
getPhyloTreeTsbLabel | 21.296 | 0.208 | 21.552 | |
getSampleInfo | 10.821 | 0.004 | 10.848 | |
getTree | 19.751 | 0.091 | 19.885 | |
getTreeMethod | 20.211 | 0.096 | 20.351 | |
mathScore | 11.223 | 0.108 | 11.348 | |
mutCluster | 15.506 | 0.080 | 15.619 | |
mutHeatmap | 20.953 | 0.131 | 21.126 | |
mutTrunkBranch | 14.380 | 0.128 | 14.536 | |
plotCNA | 4.663 | 0.020 | 4.678 | |
plotMutProfile | 13.314 | 0.080 | 13.416 | |
plotMutSigProfile | 21.180 | 0.112 | 21.338 | |
plotPhyloTree | 13.630 | 0.095 | 13.756 | |
readMaf | 11.420 | 0.036 | 11.470 | |
readSegment | 0.535 | 0.008 | 0.538 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 11.165 | 0.056 | 11.236 | |
testNeutral | 15.510 | 0.080 | 15.621 | |
triMatrix | 14.080 | 0.167 | 14.273 | |