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This page was generated on 2024-05-20 11:32:14 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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
| kjohnson1 | macOS 13.6.6 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: 1.15.0 |
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: 2024-05-19 18:14:53 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 18:23:29 -0400 (Sun, 19 May 2024) |
EllapsedTime: 517.0 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-mac-arm64/meat/MesKit.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.15.0’ * 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-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 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 cna2gene 22.058 0.716 22.886 calFst 14.166 0.193 14.434 getTreeMethod 13.620 0.356 13.980 getMutBranches 13.003 0.542 13.685 getPhyloTreeTsbLabel 12.953 0.449 13.403 getTree 12.940 0.369 13.314 getPhyloTreeRef 12.831 0.393 13.226 getPhyloTree 12.757 0.337 13.106 getBinaryMatrix 12.666 0.367 13.068 getBranchType 12.452 0.485 12.943 getCCFMatrix 12.500 0.437 12.937 getPhyloTreePatient 12.238 0.286 12.538 getBootstrapValue 12.088 0.343 12.432 plotMutSigProfile 11.457 0.233 11.703 mutHeatmap 10.863 0.282 11.151 compareCCF 10.411 0.665 11.085 calNeiDist 10.102 0.115 10.301 calJSI 9.442 0.081 9.525 compareTree 8.832 0.214 9.052 ccfAUC 8.781 0.103 8.981 fitSignatures 8.473 0.246 8.720 triMatrix 8.414 0.212 8.628 mutCluster 8.057 0.436 8.527 mutTrunkBranch 8.236 0.214 8.456 testNeutral 7.991 0.061 8.054 plotMutProfile 7.828 0.069 7.897 plotPhyloTree 7.694 0.076 7.782 classifyMut 7.159 0.357 7.574 readMaf 6.529 0.128 6.657 subMaf 6.269 0.052 6.324 getMafRef 6.245 0.041 6.450 getSampleInfo 6.147 0.054 6.202 getNonSyn_vc 5.959 0.139 6.132 getMafPatient 6.028 0.051 6.080 getMafData 5.899 0.040 5.943 mathScore 5.630 0.034 5.724 * 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-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 | 14.166 | 0.193 | 14.434 | |
calJSI | 9.442 | 0.081 | 9.525 | |
calNeiDist | 10.102 | 0.115 | 10.301 | |
ccfAUC | 8.781 | 0.103 | 8.981 | |
classifyMut | 7.159 | 0.357 | 7.574 | |
cna2gene | 22.058 | 0.716 | 22.886 | |
compareCCF | 10.411 | 0.665 | 11.085 | |
compareTree | 8.832 | 0.214 | 9.052 | |
fitSignatures | 8.473 | 0.246 | 8.720 | |
getBinaryMatrix | 12.666 | 0.367 | 13.068 | |
getBootstrapValue | 12.088 | 0.343 | 12.432 | |
getBranchType | 12.452 | 0.485 | 12.943 | |
getCCFMatrix | 12.500 | 0.437 | 12.937 | |
getMafData | 5.899 | 0.040 | 5.943 | |
getMafPatient | 6.028 | 0.051 | 6.080 | |
getMafRef | 6.245 | 0.041 | 6.450 | |
getMutBranches | 13.003 | 0.542 | 13.685 | |
getNonSyn_vc | 5.959 | 0.139 | 6.132 | |
getPhyloTree | 12.757 | 0.337 | 13.106 | |
getPhyloTreePatient | 12.238 | 0.286 | 12.538 | |
getPhyloTreeRef | 12.831 | 0.393 | 13.226 | |
getPhyloTreeTsbLabel | 12.953 | 0.449 | 13.403 | |
getSampleInfo | 6.147 | 0.054 | 6.202 | |
getTree | 12.940 | 0.369 | 13.314 | |
getTreeMethod | 13.620 | 0.356 | 13.980 | |
mathScore | 5.630 | 0.034 | 5.724 | |
mutCluster | 8.057 | 0.436 | 8.527 | |
mutHeatmap | 10.863 | 0.282 | 11.151 | |
mutTrunkBranch | 8.236 | 0.214 | 8.456 | |
plotCNA | 2.551 | 0.089 | 2.642 | |
plotMutProfile | 7.828 | 0.069 | 7.897 | |
plotMutSigProfile | 11.457 | 0.233 | 11.703 | |
plotPhyloTree | 7.694 | 0.076 | 7.782 | |
readMaf | 6.529 | 0.128 | 6.657 | |
readSegment | 0.422 | 0.020 | 0.442 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 6.269 | 0.052 | 6.324 | |
testNeutral | 7.991 | 0.061 | 8.054 | |
triMatrix | 8.414 | 0.212 | 8.628 | |