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This page was generated on 2024-03-28 11:32:24 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 1192/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.12.0 (landing page) Mengni Liu
| kjohnson1 | macOS 13.6.1 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: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2024-03-27 18:17:52 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 18:26:52 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 539.9 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MesKit.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.12.0’ * 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-3.18-bioc-mac-arm64/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 R 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 22.970 0.943 23.999 calFst 14.845 0.192 15.282 getBranchType 14.021 0.318 14.358 getTreeMethod 13.426 0.363 13.799 getBinaryMatrix 13.154 0.510 13.678 getPhyloTreeTsbLabel 13.211 0.307 13.551 getPhyloTree 13.229 0.268 13.535 getPhyloTreeRef 13.140 0.302 13.462 getPhyloTreePatient 13.081 0.359 13.453 getTree 12.953 0.364 13.389 getBootstrapValue 12.866 0.334 13.218 getMutBranches 12.661 0.474 13.173 getCCFMatrix 12.276 0.313 13.186 plotMutSigProfile 11.422 0.208 11.634 compareCCF 10.338 0.944 11.330 calNeiDist 10.856 0.096 11.027 mutHeatmap 10.639 0.145 10.815 calJSI 10.260 0.093 10.460 compareTree 9.479 0.154 9.634 ccfAUC 8.888 0.127 9.044 fitSignatures 8.749 0.247 9.015 mutTrunkBranch 8.366 0.246 8.629 mutCluster 8.072 0.418 8.503 triMatrix 8.210 0.175 8.528 testNeutral 8.158 0.061 8.231 plotPhyloTree 7.757 0.099 7.869 plotMutProfile 7.641 0.051 7.733 mathScore 7.422 0.084 7.509 classifyMut 6.709 0.389 7.117 subMaf 6.398 0.104 6.505 getSampleInfo 6.305 0.040 6.365 getNonSyn_vc 6.285 0.042 6.375 readMaf 6.260 0.052 6.356 getMafRef 5.991 0.040 6.070 getMafData 5.486 0.121 5.703 getMafPatient 5.043 0.040 5.110 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-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 | 14.845 | 0.192 | 15.282 | |
calJSI | 10.260 | 0.093 | 10.460 | |
calNeiDist | 10.856 | 0.096 | 11.027 | |
ccfAUC | 8.888 | 0.127 | 9.044 | |
classifyMut | 6.709 | 0.389 | 7.117 | |
cna2gene | 22.970 | 0.943 | 23.999 | |
compareCCF | 10.338 | 0.944 | 11.330 | |
compareTree | 9.479 | 0.154 | 9.634 | |
fitSignatures | 8.749 | 0.247 | 9.015 | |
getBinaryMatrix | 13.154 | 0.510 | 13.678 | |
getBootstrapValue | 12.866 | 0.334 | 13.218 | |
getBranchType | 14.021 | 0.318 | 14.358 | |
getCCFMatrix | 12.276 | 0.313 | 13.186 | |
getMafData | 5.486 | 0.121 | 5.703 | |
getMafPatient | 5.043 | 0.040 | 5.110 | |
getMafRef | 5.991 | 0.040 | 6.070 | |
getMutBranches | 12.661 | 0.474 | 13.173 | |
getNonSyn_vc | 6.285 | 0.042 | 6.375 | |
getPhyloTree | 13.229 | 0.268 | 13.535 | |
getPhyloTreePatient | 13.081 | 0.359 | 13.453 | |
getPhyloTreeRef | 13.140 | 0.302 | 13.462 | |
getPhyloTreeTsbLabel | 13.211 | 0.307 | 13.551 | |
getSampleInfo | 6.305 | 0.040 | 6.365 | |
getTree | 12.953 | 0.364 | 13.389 | |
getTreeMethod | 13.426 | 0.363 | 13.799 | |
mathScore | 7.422 | 0.084 | 7.509 | |
mutCluster | 8.072 | 0.418 | 8.503 | |
mutHeatmap | 10.639 | 0.145 | 10.815 | |
mutTrunkBranch | 8.366 | 0.246 | 8.629 | |
plotCNA | 2.530 | 0.078 | 2.613 | |
plotMutProfile | 7.641 | 0.051 | 7.733 | |
plotMutSigProfile | 11.422 | 0.208 | 11.634 | |
plotPhyloTree | 7.757 | 0.099 | 7.869 | |
readMaf | 6.260 | 0.052 | 6.356 | |
readSegment | 0.432 | 0.008 | 0.440 | |
runMesKit | 0.000 | 0.000 | 0.001 | |
subMaf | 6.398 | 0.104 | 6.505 | |
testNeutral | 8.158 | 0.061 | 8.231 | |
triMatrix | 8.210 | 0.175 | 8.528 | |