Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:42 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1173/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.15.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | 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: 1.15.0 |
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_1.15.0.tar.gz |
StartedAt: 2024-07-15 21:39:25 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 21:50:07 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 641.7 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_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.15.0’ * 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 20.793 0.861 21.747 calFst 19.129 0.262 19.531 getBinaryMatrix 16.565 0.352 16.985 getBootstrapValue 16.665 0.208 16.945 getBranchType 16.549 0.188 16.805 getTree 16.476 0.223 16.802 getCCFMatrix 16.458 0.235 16.771 getPhyloTreeRef 16.288 0.353 16.750 getTreeMethod 16.152 0.192 16.431 getPhyloTreeTsbLabel 16.065 0.182 16.328 compareCCF 14.945 1.069 16.087 plotMutSigProfile 15.776 0.211 16.060 getPhyloTreePatient 15.748 0.207 16.044 getPhyloTree 15.576 0.207 15.840 getMutBranches 15.106 0.446 15.628 mutHeatmap 14.369 0.117 14.559 calNeiDist 13.543 0.140 13.761 calJSI 12.349 0.105 12.522 compareTree 11.868 0.164 12.082 plotPhyloTree 11.503 0.196 11.745 mutTrunkBranch 11.452 0.197 11.720 mutCluster 11.085 0.496 11.636 fitSignatures 11.262 0.254 11.577 ccfAUC 11.293 0.109 11.475 plotMutProfile 10.580 0.093 10.717 triMatrix 10.184 0.202 10.452 classifyMut 9.929 0.438 10.412 testNeutral 10.130 0.085 10.262 getMafPatient 9.585 0.109 9.732 mathScore 8.649 0.175 8.872 getMafData 8.689 0.063 8.796 getSampleInfo 8.607 0.074 8.732 readMaf 8.272 0.064 8.379 subMaf 8.103 0.069 8.216 getNonSyn_vc 8.050 0.068 8.163 getMafRef 7.497 0.044 7.563 * 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-x86_64/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 | 19.129 | 0.262 | 19.531 | |
calJSI | 12.349 | 0.105 | 12.522 | |
calNeiDist | 13.543 | 0.140 | 13.761 | |
ccfAUC | 11.293 | 0.109 | 11.475 | |
classifyMut | 9.929 | 0.438 | 10.412 | |
cna2gene | 20.793 | 0.861 | 21.747 | |
compareCCF | 14.945 | 1.069 | 16.087 | |
compareTree | 11.868 | 0.164 | 12.082 | |
fitSignatures | 11.262 | 0.254 | 11.577 | |
getBinaryMatrix | 16.565 | 0.352 | 16.985 | |
getBootstrapValue | 16.665 | 0.208 | 16.945 | |
getBranchType | 16.549 | 0.188 | 16.805 | |
getCCFMatrix | 16.458 | 0.235 | 16.771 | |
getMafData | 8.689 | 0.063 | 8.796 | |
getMafPatient | 9.585 | 0.109 | 9.732 | |
getMafRef | 7.497 | 0.044 | 7.563 | |
getMutBranches | 15.106 | 0.446 | 15.628 | |
getNonSyn_vc | 8.050 | 0.068 | 8.163 | |
getPhyloTree | 15.576 | 0.207 | 15.840 | |
getPhyloTreePatient | 15.748 | 0.207 | 16.044 | |
getPhyloTreeRef | 16.288 | 0.353 | 16.750 | |
getPhyloTreeTsbLabel | 16.065 | 0.182 | 16.328 | |
getSampleInfo | 8.607 | 0.074 | 8.732 | |
getTree | 16.476 | 0.223 | 16.802 | |
getTreeMethod | 16.152 | 0.192 | 16.431 | |
mathScore | 8.649 | 0.175 | 8.872 | |
mutCluster | 11.085 | 0.496 | 11.636 | |
mutHeatmap | 14.369 | 0.117 | 14.559 | |
mutTrunkBranch | 11.452 | 0.197 | 11.720 | |
plotCNA | 3.143 | 0.063 | 3.225 | |
plotMutProfile | 10.580 | 0.093 | 10.717 | |
plotMutSigProfile | 15.776 | 0.211 | 16.060 | |
plotPhyloTree | 11.503 | 0.196 | 11.745 | |
readMaf | 8.272 | 0.064 | 8.379 | |
readSegment | 0.469 | 0.024 | 0.498 | |
runMesKit | 0.000 | 0.000 | 0.001 | |
subMaf | 8.103 | 0.069 | 8.216 | |
testNeutral | 10.130 | 0.085 | 10.262 | |
triMatrix | 10.184 | 0.202 | 10.452 | |