Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:42 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 1204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.14.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2024-05-29 21:55:19 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 22:06:13 -0400 (Wed, 29 May 2024) |
EllapsedTime: 654.0 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MesKit.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.14.0’ * 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-3.19-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 20.538 0.969 21.668 calFst 18.959 0.349 19.475 getBinaryMatrix 16.981 0.447 17.572 getBranchType 16.972 0.263 17.369 getPhyloTreeRef 16.519 0.411 17.104 getCCFMatrix 16.569 0.350 17.057 getTree 16.602 0.306 17.080 getBootstrapValue 16.479 0.332 16.972 getMutBranches 16.029 0.522 16.704 getTreeMethod 16.260 0.231 16.625 getPhyloTreeTsbLabel 16.215 0.252 16.603 getPhyloTree 15.966 0.282 16.357 compareCCF 14.951 1.236 16.295 getPhyloTreePatient 15.757 0.254 16.146 plotMutSigProfile 15.364 0.280 15.769 mutHeatmap 14.652 0.176 14.948 calNeiDist 13.799 0.175 14.118 calJSI 12.448 0.156 12.705 compareTree 12.221 0.217 12.511 mutTrunkBranch 11.890 0.241 12.261 plotPhyloTree 11.624 0.271 11.997 mutCluster 11.189 0.508 11.782 ccfAUC 11.354 0.162 11.608 fitSignatures 11.137 0.372 11.615 classifyMut 10.311 0.642 11.089 triMatrix 10.649 0.263 11.000 plotMutProfile 10.775 0.128 10.990 testNeutral 10.456 0.114 10.634 getMafPatient 9.534 0.154 9.760 mathScore 8.933 0.237 9.250 getSampleInfo 8.606 0.100 8.788 getMafData 8.459 0.091 8.603 readMaf 8.085 0.105 8.254 subMaf 8.069 0.104 8.231 getNonSyn_vc 8.071 0.101 8.246 getMafRef 8.018 0.093 8.177 * 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-3.19-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 | 18.959 | 0.349 | 19.475 | |
calJSI | 12.448 | 0.156 | 12.705 | |
calNeiDist | 13.799 | 0.175 | 14.118 | |
ccfAUC | 11.354 | 0.162 | 11.608 | |
classifyMut | 10.311 | 0.642 | 11.089 | |
cna2gene | 20.538 | 0.969 | 21.668 | |
compareCCF | 14.951 | 1.236 | 16.295 | |
compareTree | 12.221 | 0.217 | 12.511 | |
fitSignatures | 11.137 | 0.372 | 11.615 | |
getBinaryMatrix | 16.981 | 0.447 | 17.572 | |
getBootstrapValue | 16.479 | 0.332 | 16.972 | |
getBranchType | 16.972 | 0.263 | 17.369 | |
getCCFMatrix | 16.569 | 0.350 | 17.057 | |
getMafData | 8.459 | 0.091 | 8.603 | |
getMafPatient | 9.534 | 0.154 | 9.760 | |
getMafRef | 8.018 | 0.093 | 8.177 | |
getMutBranches | 16.029 | 0.522 | 16.704 | |
getNonSyn_vc | 8.071 | 0.101 | 8.246 | |
getPhyloTree | 15.966 | 0.282 | 16.357 | |
getPhyloTreePatient | 15.757 | 0.254 | 16.146 | |
getPhyloTreeRef | 16.519 | 0.411 | 17.104 | |
getPhyloTreeTsbLabel | 16.215 | 0.252 | 16.603 | |
getSampleInfo | 8.606 | 0.100 | 8.788 | |
getTree | 16.602 | 0.306 | 17.080 | |
getTreeMethod | 16.260 | 0.231 | 16.625 | |
mathScore | 8.933 | 0.237 | 9.250 | |
mutCluster | 11.189 | 0.508 | 11.782 | |
mutHeatmap | 14.652 | 0.176 | 14.948 | |
mutTrunkBranch | 11.890 | 0.241 | 12.261 | |
plotCNA | 3.084 | 0.071 | 3.194 | |
plotMutProfile | 10.775 | 0.128 | 10.990 | |
plotMutSigProfile | 15.364 | 0.280 | 15.769 | |
plotPhyloTree | 11.624 | 0.271 | 11.997 | |
readMaf | 8.085 | 0.105 | 8.254 | |
readSegment | 0.494 | 0.014 | 0.512 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 8.069 | 0.104 | 8.231 | |
testNeutral | 10.456 | 0.114 | 10.634 | |
triMatrix | 10.649 | 0.263 | 11.000 | |