Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:37:03 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1167/2233 | 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 | |||||||||
palomino4 | 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: 1.15.0 |
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: 2024-05-30 03:24:53 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 03:51:46 -0400 (Thu, 30 May 2024) |
EllapsedTime: 1612.8 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 4.4.0 Patched (2024-04-24 r86482) * 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 ‘1.15.0’ * 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 calFst 41.819 0.625 48.170 getTreeMethod 39.187 0.337 45.346 getPhyloTreeRef 38.929 0.430 44.460 getMutBranches 38.115 0.776 43.878 getPhyloTreePatient 38.539 0.287 44.456 getBinaryMatrix 38.283 0.518 45.549 getBranchType 38.367 0.317 46.205 getPhyloTree 38.387 0.268 43.718 getCCFMatrix 38.048 0.581 43.918 getBootstrapValue 38.114 0.370 45.838 getTree 38.086 0.285 43.484 getPhyloTreeTsbLabel 37.235 0.270 42.130 plotMutSigProfile 36.804 0.372 41.779 cna2gene 34.103 1.608 41.546 mutHeatmap 35.014 0.412 38.964 compareCCF 30.857 3.394 41.449 calNeiDist 31.852 0.301 36.834 compareTree 29.889 0.418 36.899 mutCluster 28.212 1.344 33.636 calJSI 29.120 0.319 33.665 fitSignatures 28.243 0.607 34.890 mutTrunkBranch 27.599 0.352 30.657 ccfAUC 27.485 0.269 31.801 plotMutProfile 26.838 0.188 30.178 plotPhyloTree 26.661 0.248 30.498 triMatrix 25.325 0.325 31.811 testNeutral 25.226 0.201 31.310 classifyMut 23.810 1.327 28.829 mathScore 21.947 0.206 25.683 readMaf 21.521 0.153 24.535 getNonSyn_vc 20.969 0.139 23.969 getSampleInfo 20.746 0.221 23.707 subMaf 20.785 0.147 25.257 getMafPatient 20.679 0.152 23.874 getMafRef 20.685 0.129 23.582 getMafData 20.575 0.138 23.738 plotCNA 6.368 0.093 7.139 * 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 | 41.819 | 0.625 | 48.170 | |
calJSI | 29.120 | 0.319 | 33.665 | |
calNeiDist | 31.852 | 0.301 | 36.834 | |
ccfAUC | 27.485 | 0.269 | 31.801 | |
classifyMut | 23.810 | 1.327 | 28.829 | |
cna2gene | 34.103 | 1.608 | 41.546 | |
compareCCF | 30.857 | 3.394 | 41.449 | |
compareTree | 29.889 | 0.418 | 36.899 | |
fitSignatures | 28.243 | 0.607 | 34.890 | |
getBinaryMatrix | 38.283 | 0.518 | 45.549 | |
getBootstrapValue | 38.114 | 0.370 | 45.838 | |
getBranchType | 38.367 | 0.317 | 46.205 | |
getCCFMatrix | 38.048 | 0.581 | 43.918 | |
getMafData | 20.575 | 0.138 | 23.738 | |
getMafPatient | 20.679 | 0.152 | 23.874 | |
getMafRef | 20.685 | 0.129 | 23.582 | |
getMutBranches | 38.115 | 0.776 | 43.878 | |
getNonSyn_vc | 20.969 | 0.139 | 23.969 | |
getPhyloTree | 38.387 | 0.268 | 43.718 | |
getPhyloTreePatient | 38.539 | 0.287 | 44.456 | |
getPhyloTreeRef | 38.929 | 0.430 | 44.460 | |
getPhyloTreeTsbLabel | 37.235 | 0.270 | 42.130 | |
getSampleInfo | 20.746 | 0.221 | 23.707 | |
getTree | 38.086 | 0.285 | 43.484 | |
getTreeMethod | 39.187 | 0.337 | 45.346 | |
mathScore | 21.947 | 0.206 | 25.683 | |
mutCluster | 28.212 | 1.344 | 33.636 | |
mutHeatmap | 35.014 | 0.412 | 38.964 | |
mutTrunkBranch | 27.599 | 0.352 | 30.657 | |
plotCNA | 6.368 | 0.093 | 7.139 | |
plotMutProfile | 26.838 | 0.188 | 30.178 | |
plotMutSigProfile | 36.804 | 0.372 | 41.779 | |
plotPhyloTree | 26.661 | 0.248 | 30.498 | |
readMaf | 21.521 | 0.153 | 24.535 | |
readSegment | 1.072 | 0.024 | 1.258 | |
runMesKit | 0.001 | 0.000 | 0.000 | |
subMaf | 20.785 | 0.147 | 25.257 | |
testNeutral | 25.226 | 0.201 | 31.310 | |
triMatrix | 25.325 | 0.325 | 31.811 | |