Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 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" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 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: 1.14.0 |
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: 2024-06-24 07:08:44 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 07:35:54 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1630.3 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 12.7.4 * 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 calFst 40.592 0.677 45.960 getCCFMatrix 39.513 0.652 47.536 getBinaryMatrix 39.027 0.589 46.014 getBranchType 38.916 0.368 50.165 getPhyloTreeTsbLabel 38.420 0.779 45.789 getMutBranches 38.041 1.105 45.853 getBootstrapValue 38.481 0.401 48.646 getTreeMethod 38.263 0.283 43.392 getPhyloTreeRef 37.732 0.557 40.684 getTree 37.964 0.286 43.196 plotMutSigProfile 37.753 0.475 43.478 getPhyloTreePatient 37.825 0.314 41.866 getPhyloTree 37.299 0.317 40.295 mutHeatmap 35.863 0.503 42.359 cna2gene 32.196 1.641 40.299 compareCCF 30.505 2.944 39.121 calNeiDist 31.951 0.340 37.411 compareTree 30.427 0.375 36.913 calJSI 29.572 0.395 34.435 mutCluster 27.691 1.385 34.363 mutTrunkBranch 28.038 0.460 33.204 fitSignatures 27.582 0.428 34.710 ccfAUC 27.124 0.276 32.294 plotMutProfile 27.031 0.237 31.480 testNeutral 26.423 0.355 32.977 classifyMut 25.092 1.390 32.735 triMatrix 25.757 0.347 32.928 plotPhyloTree 24.892 0.189 28.908 mathScore 21.871 0.142 24.841 getSampleInfo 21.014 0.324 25.207 readMaf 21.091 0.182 25.343 subMaf 20.959 0.167 24.818 getNonSyn_vc 20.735 0.145 23.702 getMafPatient 20.592 0.142 24.994 getMafData 20.538 0.158 24.574 getMafRef 20.208 0.284 22.482 plotCNA 6.189 0.073 7.256 * 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 | 40.592 | 0.677 | 45.960 | |
calJSI | 29.572 | 0.395 | 34.435 | |
calNeiDist | 31.951 | 0.340 | 37.411 | |
ccfAUC | 27.124 | 0.276 | 32.294 | |
classifyMut | 25.092 | 1.390 | 32.735 | |
cna2gene | 32.196 | 1.641 | 40.299 | |
compareCCF | 30.505 | 2.944 | 39.121 | |
compareTree | 30.427 | 0.375 | 36.913 | |
fitSignatures | 27.582 | 0.428 | 34.710 | |
getBinaryMatrix | 39.027 | 0.589 | 46.014 | |
getBootstrapValue | 38.481 | 0.401 | 48.646 | |
getBranchType | 38.916 | 0.368 | 50.165 | |
getCCFMatrix | 39.513 | 0.652 | 47.536 | |
getMafData | 20.538 | 0.158 | 24.574 | |
getMafPatient | 20.592 | 0.142 | 24.994 | |
getMafRef | 20.208 | 0.284 | 22.482 | |
getMutBranches | 38.041 | 1.105 | 45.853 | |
getNonSyn_vc | 20.735 | 0.145 | 23.702 | |
getPhyloTree | 37.299 | 0.317 | 40.295 | |
getPhyloTreePatient | 37.825 | 0.314 | 41.866 | |
getPhyloTreeRef | 37.732 | 0.557 | 40.684 | |
getPhyloTreeTsbLabel | 38.420 | 0.779 | 45.789 | |
getSampleInfo | 21.014 | 0.324 | 25.207 | |
getTree | 37.964 | 0.286 | 43.196 | |
getTreeMethod | 38.263 | 0.283 | 43.392 | |
mathScore | 21.871 | 0.142 | 24.841 | |
mutCluster | 27.691 | 1.385 | 34.363 | |
mutHeatmap | 35.863 | 0.503 | 42.359 | |
mutTrunkBranch | 28.038 | 0.460 | 33.204 | |
plotCNA | 6.189 | 0.073 | 7.256 | |
plotMutProfile | 27.031 | 0.237 | 31.480 | |
plotMutSigProfile | 37.753 | 0.475 | 43.478 | |
plotPhyloTree | 24.892 | 0.189 | 28.908 | |
readMaf | 21.091 | 0.182 | 25.343 | |
readSegment | 0.997 | 0.013 | 1.149 | |
runMesKit | 0.000 | 0.001 | 0.001 | |
subMaf | 20.959 | 0.167 | 24.818 | |
testNeutral | 26.423 | 0.355 | 32.977 | |
triMatrix | 25.757 | 0.347 | 32.928 | |