Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1195/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.16.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.16.0 |
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_1.16.0.tar.gz |
StartedAt: 2024-12-21 00:27:20 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 00:36:05 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 525.2 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.16.0’ * 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-3.20-bioc/meat/MesKit.Rcheck/00install.out’ for details. * checking installed package size ... NOTE 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 24.204 0.872 23.784 calFst 15.650 0.258 15.601 getBranchType 15.465 0.443 15.706 getBinaryMatrix 14.253 0.398 14.228 getBootstrapValue 14.407 0.195 14.162 getTreeMethod 13.303 0.366 13.248 getTree 13.226 0.397 13.196 getPhyloTreePatient 13.158 0.386 13.143 getPhyloTreeRef 13.103 0.429 13.107 getPhyloTreeTsbLabel 12.958 0.483 13.047 getPhyloTree 12.982 0.387 12.938 getCCFMatrix 12.909 0.395 13.265 getMutBranches 12.503 0.600 12.686 plotMutSigProfile 11.973 0.287 11.852 mutHeatmap 11.142 0.208 10.943 compareTree 10.762 0.267 10.434 calNeiDist 10.768 0.191 10.583 mutCluster 10.401 0.550 10.521 compareCCF 9.984 0.871 10.450 calJSI 9.710 0.125 9.453 fitSignatures 9.535 0.277 9.397 ccfAUC 9.201 0.165 8.969 triMatrix 8.630 0.254 8.536 testNeutral 8.477 0.125 8.163 classifyMut 7.947 0.362 7.965 plotMutProfile 8.128 0.124 7.816 plotPhyloTree 7.993 0.118 7.697 mutTrunkBranch 6.708 0.176 6.661 mathScore 6.707 0.092 6.468 readMaf 6.583 0.098 6.361 getMafRef 6.397 0.157 6.353 getSampleInfo 6.286 0.053 6.269 getMafPatient 6.218 0.078 6.053 getNonSyn_vc 6.171 0.049 6.180 subMaf 5.851 0.149 5.798 getMafData 5.785 0.083 5.711 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘MesKit’ ... ** 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 | 15.650 | 0.258 | 15.601 | |
calJSI | 9.710 | 0.125 | 9.453 | |
calNeiDist | 10.768 | 0.191 | 10.583 | |
ccfAUC | 9.201 | 0.165 | 8.969 | |
classifyMut | 7.947 | 0.362 | 7.965 | |
cna2gene | 24.204 | 0.872 | 23.784 | |
compareCCF | 9.984 | 0.871 | 10.450 | |
compareTree | 10.762 | 0.267 | 10.434 | |
fitSignatures | 9.535 | 0.277 | 9.397 | |
getBinaryMatrix | 14.253 | 0.398 | 14.228 | |
getBootstrapValue | 14.407 | 0.195 | 14.162 | |
getBranchType | 15.465 | 0.443 | 15.706 | |
getCCFMatrix | 12.909 | 0.395 | 13.265 | |
getMafData | 5.785 | 0.083 | 5.711 | |
getMafPatient | 6.218 | 0.078 | 6.053 | |
getMafRef | 6.397 | 0.157 | 6.353 | |
getMutBranches | 12.503 | 0.600 | 12.686 | |
getNonSyn_vc | 6.171 | 0.049 | 6.180 | |
getPhyloTree | 12.982 | 0.387 | 12.938 | |
getPhyloTreePatient | 13.158 | 0.386 | 13.143 | |
getPhyloTreeRef | 13.103 | 0.429 | 13.107 | |
getPhyloTreeTsbLabel | 12.958 | 0.483 | 13.047 | |
getSampleInfo | 6.286 | 0.053 | 6.269 | |
getTree | 13.226 | 0.397 | 13.196 | |
getTreeMethod | 13.303 | 0.366 | 13.248 | |
mathScore | 6.707 | 0.092 | 6.468 | |
mutCluster | 10.401 | 0.550 | 10.521 | |
mutHeatmap | 11.142 | 0.208 | 10.943 | |
mutTrunkBranch | 6.708 | 0.176 | 6.661 | |
plotCNA | 3.236 | 0.120 | 2.595 | |
plotMutProfile | 8.128 | 0.124 | 7.816 | |
plotMutSigProfile | 11.973 | 0.287 | 11.852 | |
plotPhyloTree | 7.993 | 0.118 | 7.697 | |
readMaf | 6.583 | 0.098 | 6.361 | |
readSegment | 0.760 | 0.061 | 0.453 | |
runMesKit | 0.001 | 0.001 | 0.000 | |
subMaf | 5.851 | 0.149 | 5.798 | |
testNeutral | 8.477 | 0.125 | 8.163 | |
triMatrix | 8.630 | 0.254 | 8.536 | |