Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:38 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the MesKit package: - 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: 2024-05-06 22:48:01 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 22:50:52 -0400 (Mon, 06 May 2024) |
EllapsedTime: 170.9 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-mac-arm64/meat/MesKit.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * 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-mac-arm64/meat/MesKit.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 6.0Mb 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 cluster Cytoband Cytoband_pos End_Position gene_id gene_pos genes Hugo_Symbol i.End_Position i.Start_Position is.match org.Hs.eg.db Original overlap_width Patient_ID Reconstructed seg_id seqnames Start_Position Tumor_Sample_Barcode V 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 8.211 0.211 8.432 * 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-mac-arm64/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-arm64/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 | 4.469 | 0.058 | 4.538 | |
calJSI | 2.747 | 0.034 | 2.781 | |
calNeiDist | 3.100 | 0.028 | 3.129 | |
ccfAUC | 2.874 | 0.038 | 2.913 | |
classifyMut | 2.306 | 0.130 | 2.457 | |
cna2gene | 8.211 | 0.211 | 8.432 | |
compareCCF | 3.308 | 0.324 | 3.655 | |
compareTree | 3.083 | 0.067 | 3.150 | |
fitSignatures | 2.805 | 0.102 | 2.909 | |
getBinaryMatrix | 4.046 | 0.185 | 4.244 | |
getBootstrapValue | 4.032 | 0.114 | 4.147 | |
getBranchType | 4.459 | 0.190 | 4.653 | |
getCCFMatrix | 3.839 | 0.154 | 3.995 | |
getMafData | 1.902 | 0.059 | 1.961 | |
getMafPatient | 1.833 | 0.013 | 1.845 | |
getMafRef | 1.948 | 0.011 | 1.960 | |
getMutBranches | 3.951 | 0.126 | 4.076 | |
getNonSyn_vc | 1.990 | 0.010 | 1.999 | |
getPhyloTree | 4.000 | 0.176 | 4.175 | |
getPhyloTreePatient | 3.851 | 0.157 | 4.008 | |
getPhyloTreeRef | 3.953 | 0.109 | 4.061 | |
getPhyloTreeTsbLabel | 3.849 | 0.125 | 3.975 | |
getSampleInfo | 1.904 | 0.014 | 1.919 | |
getTree | 3.885 | 0.167 | 4.051 | |
getTreeMethod | 3.892 | 0.134 | 4.027 | |
mathScore | 2.393 | 0.018 | 2.411 | |
mutCluster | 2.535 | 0.117 | 2.652 | |
mutHeatmap | 3.340 | 0.038 | 3.380 | |
mutTrunkBranch | 2.615 | 0.083 | 2.699 | |
plotCNA | 0.816 | 0.011 | 0.827 | |
plotMutProfile | 2.478 | 0.023 | 2.501 | |
plotMutSigProfile | 3.677 | 0.076 | 3.756 | |
plotPhyloTree | 2.508 | 0.034 | 2.542 | |
readMaf | 2.067 | 0.014 | 2.081 | |
readSegment | 0.139 | 0.011 | 0.149 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 2.135 | 0.051 | 2.186 | |
testNeutral | 2.693 | 0.022 | 2.718 | |
triMatrix | 2.700 | 0.072 | 2.774 | |