Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
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: 2025-09-24 02:05:50 -0400 (Wed, 24 Sep 2025) |
EndedAt: 2025-09-24 02:15:03 -0400 (Wed, 24 Sep 2025) |
EllapsedTime: 552.6 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 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * 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 cna2gene 23.608 0.870 24.609 calFst 15.304 0.228 15.916 getPhyloTreePatient 14.107 0.488 14.629 plotMutSigProfile 13.700 0.208 13.924 mutHeatmap 13.684 0.191 13.964 getPhyloTree 13.188 0.406 13.587 getMutBranches 13.109 0.370 13.596 getTree 13.055 0.362 13.465 getBinaryMatrix 12.832 0.552 13.375 getBranchType 12.909 0.360 13.264 getCCFMatrix 12.947 0.271 13.230 getBootstrapValue 12.731 0.320 13.077 getTreeMethod 12.797 0.231 13.125 getPhyloTreeTsbLabel 12.684 0.182 12.917 getPhyloTreeRef 12.537 0.232 12.780 compareCCF 10.751 0.963 11.760 calNeiDist 10.588 0.110 10.889 calJSI 10.586 0.104 10.871 mutCluster 9.424 0.406 9.844 ccfAUC 9.624 0.099 9.833 compareTree 9.502 0.184 9.754 fitSignatures 8.922 0.250 9.277 mutTrunkBranch 8.724 0.180 8.894 testNeutral 8.438 0.073 8.660 triMatrix 8.229 0.233 8.562 classifyMut 7.702 0.414 8.120 plotMutProfile 8.036 0.054 8.088 plotPhyloTree 8.025 0.064 8.076 readMaf 7.947 0.117 8.059 getMafPatient 6.747 0.054 7.037 getMafData 6.569 0.131 6.875 getMafRef 6.367 0.045 6.416 subMaf 6.273 0.076 6.394 getNonSyn_vc 6.306 0.041 6.331 mathScore 6.133 0.053 6.218 getSampleInfo 5.442 0.039 5.509 * 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-arm64/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 | 15.304 | 0.228 | 15.916 | |
calJSI | 10.586 | 0.104 | 10.871 | |
calNeiDist | 10.588 | 0.110 | 10.889 | |
ccfAUC | 9.624 | 0.099 | 9.833 | |
classifyMut | 7.702 | 0.414 | 8.120 | |
cna2gene | 23.608 | 0.870 | 24.609 | |
compareCCF | 10.751 | 0.963 | 11.760 | |
compareTree | 9.502 | 0.184 | 9.754 | |
fitSignatures | 8.922 | 0.250 | 9.277 | |
getBinaryMatrix | 12.832 | 0.552 | 13.375 | |
getBootstrapValue | 12.731 | 0.320 | 13.077 | |
getBranchType | 12.909 | 0.360 | 13.264 | |
getCCFMatrix | 12.947 | 0.271 | 13.230 | |
getMafData | 6.569 | 0.131 | 6.875 | |
getMafPatient | 6.747 | 0.054 | 7.037 | |
getMafRef | 6.367 | 0.045 | 6.416 | |
getMutBranches | 13.109 | 0.370 | 13.596 | |
getNonSyn_vc | 6.306 | 0.041 | 6.331 | |
getPhyloTree | 13.188 | 0.406 | 13.587 | |
getPhyloTreePatient | 14.107 | 0.488 | 14.629 | |
getPhyloTreeRef | 12.537 | 0.232 | 12.780 | |
getPhyloTreeTsbLabel | 12.684 | 0.182 | 12.917 | |
getSampleInfo | 5.442 | 0.039 | 5.509 | |
getTree | 13.055 | 0.362 | 13.465 | |
getTreeMethod | 12.797 | 0.231 | 13.125 | |
mathScore | 6.133 | 0.053 | 6.218 | |
mutCluster | 9.424 | 0.406 | 9.844 | |
mutHeatmap | 13.684 | 0.191 | 13.964 | |
mutTrunkBranch | 8.724 | 0.180 | 8.894 | |
plotCNA | 3.412 | 0.052 | 3.468 | |
plotMutProfile | 8.036 | 0.054 | 8.088 | |
plotMutSigProfile | 13.700 | 0.208 | 13.924 | |
plotPhyloTree | 8.025 | 0.064 | 8.076 | |
readMaf | 7.947 | 0.117 | 8.059 | |
readSegment | 0.438 | 0.027 | 0.482 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 6.273 | 0.076 | 6.394 | |
testNeutral | 8.438 | 0.073 | 8.660 | |
triMatrix | 8.229 | 0.233 | 8.562 | |