Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -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: 2024-12-20 05:41:13 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:04:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1376.6 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_1.16.0.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: 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 12.7.6 * 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 calFst 39.805 0.480 41.798 getBinaryMatrix 37.617 0.545 41.689 getCCFMatrix 37.622 0.338 42.223 getBranchType 37.393 0.206 40.032 getBootstrapValue 37.090 0.326 39.118 getMutBranches 35.678 1.013 37.881 getTreeMethod 36.257 0.251 37.444 getPhyloTreeTsbLabel 36.030 0.375 37.041 getTree 36.115 0.276 37.093 getPhyloTree 35.836 0.375 37.443 getPhyloTreeRef 35.926 0.238 36.803 getPhyloTreePatient 35.576 0.293 35.880 plotMutSigProfile 34.891 0.380 37.207 cna2gene 32.526 1.488 34.585 mutHeatmap 31.954 0.181 32.478 compareCCF 28.002 2.962 31.597 compareTree 29.598 0.267 30.998 calNeiDist 28.919 0.194 29.589 calJSI 27.183 0.222 28.121 mutCluster 25.219 1.152 26.691 fitSignatures 25.861 0.336 28.310 mutTrunkBranch 25.890 0.292 26.699 ccfAUC 25.419 0.201 26.148 testNeutral 25.134 0.181 27.325 plotMutProfile 24.879 0.130 25.886 triMatrix 24.683 0.264 28.276 plotPhyloTree 24.223 0.120 25.282 classifyMut 22.589 1.216 23.638 mathScore 21.614 0.287 22.430 getMafData 20.651 0.306 21.376 readMaf 20.744 0.126 22.150 subMaf 20.637 0.113 22.579 getSampleInfo 19.601 0.090 19.854 getMafRef 19.141 0.076 19.415 getMafPatient 19.001 0.073 19.286 getNonSyn_vc 18.948 0.080 19.232 plotCNA 6.186 0.091 6.341 * 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 | 39.805 | 0.480 | 41.798 | |
calJSI | 27.183 | 0.222 | 28.121 | |
calNeiDist | 28.919 | 0.194 | 29.589 | |
ccfAUC | 25.419 | 0.201 | 26.148 | |
classifyMut | 22.589 | 1.216 | 23.638 | |
cna2gene | 32.526 | 1.488 | 34.585 | |
compareCCF | 28.002 | 2.962 | 31.597 | |
compareTree | 29.598 | 0.267 | 30.998 | |
fitSignatures | 25.861 | 0.336 | 28.310 | |
getBinaryMatrix | 37.617 | 0.545 | 41.689 | |
getBootstrapValue | 37.090 | 0.326 | 39.118 | |
getBranchType | 37.393 | 0.206 | 40.032 | |
getCCFMatrix | 37.622 | 0.338 | 42.223 | |
getMafData | 20.651 | 0.306 | 21.376 | |
getMafPatient | 19.001 | 0.073 | 19.286 | |
getMafRef | 19.141 | 0.076 | 19.415 | |
getMutBranches | 35.678 | 1.013 | 37.881 | |
getNonSyn_vc | 18.948 | 0.080 | 19.232 | |
getPhyloTree | 35.836 | 0.375 | 37.443 | |
getPhyloTreePatient | 35.576 | 0.293 | 35.880 | |
getPhyloTreeRef | 35.926 | 0.238 | 36.803 | |
getPhyloTreeTsbLabel | 36.030 | 0.375 | 37.041 | |
getSampleInfo | 19.601 | 0.090 | 19.854 | |
getTree | 36.115 | 0.276 | 37.093 | |
getTreeMethod | 36.257 | 0.251 | 37.444 | |
mathScore | 21.614 | 0.287 | 22.430 | |
mutCluster | 25.219 | 1.152 | 26.691 | |
mutHeatmap | 31.954 | 0.181 | 32.478 | |
mutTrunkBranch | 25.890 | 0.292 | 26.699 | |
plotCNA | 6.186 | 0.091 | 6.341 | |
plotMutProfile | 24.879 | 0.130 | 25.886 | |
plotMutSigProfile | 34.891 | 0.380 | 37.207 | |
plotPhyloTree | 24.223 | 0.120 | 25.282 | |
readMaf | 20.744 | 0.126 | 22.150 | |
readSegment | 1.088 | 0.027 | 1.383 | |
runMesKit | 0.000 | 0.001 | 0.000 | |
subMaf | 20.637 | 0.113 | 22.579 | |
testNeutral | 25.134 | 0.181 | 27.325 | |
triMatrix | 24.683 | 0.264 | 28.276 | |