Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:40 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 1207/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.17.0 (landing page) Mengni Liu
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | |||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.17.0 |
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_1.17.0.tar.gz |
StartedAt: 2025-03-16 20:06:59 -0400 (Sun, 16 Mar 2025) |
EndedAt: 2025-03-16 20:09:54 -0400 (Sun, 16 Mar 2025) |
EllapsedTime: 175.1 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_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’ * using R Under development (unstable) (2025-03-02 r87868) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.17.0’ * 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-3.21-bioc/meat/MesKit.Rcheck/00install.out’ for details. * checking installed package size ... INFO 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 8.714 0.298 8.066 getMutBranches 5.033 0.239 4.874 calFst 5.034 0.098 4.688 * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘MesKit’ ... ** this is package ‘MesKit’ version ‘1.17.0’ ** 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 | 5.034 | 0.098 | 4.688 | |
calJSI | 3.282 | 0.066 | 2.938 | |
calNeiDist | 3.547 | 0.073 | 3.214 | |
ccfAUC | 3.381 | 0.095 | 3.075 | |
classifyMut | 2.691 | 0.148 | 2.422 | |
cna2gene | 8.714 | 0.298 | 8.066 | |
compareCCF | 3.429 | 0.341 | 3.395 | |
compareTree | 3.768 | 0.108 | 3.288 | |
fitSignatures | 3.728 | 0.148 | 3.462 | |
getBinaryMatrix | 4.308 | 0.210 | 4.120 | |
getBootstrapValue | 4.292 | 0.184 | 4.093 | |
getBranchType | 4.399 | 0.222 | 4.221 | |
getCCFMatrix | 4.433 | 0.232 | 4.256 | |
getMafData | 2.216 | 0.041 | 2.057 | |
getMafPatient | 2.241 | 0.036 | 2.075 | |
getMafRef | 2.227 | 0.040 | 2.062 | |
getMutBranches | 5.033 | 0.239 | 4.874 | |
getNonSyn_vc | 2.105 | 0.040 | 1.946 | |
getPhyloTree | 4.306 | 0.209 | 4.128 | |
getPhyloTreePatient | 4.353 | 0.167 | 4.111 | |
getPhyloTreeRef | 4.406 | 0.206 | 4.196 | |
getPhyloTreeTsbLabel | 4.475 | 0.221 | 4.290 | |
getSampleInfo | 2.201 | 0.042 | 2.028 | |
getTree | 4.555 | 0.196 | 4.504 | |
getTreeMethod | 4.609 | 0.192 | 4.500 | |
mathScore | 2.413 | 0.036 | 2.278 | |
mutCluster | 3.216 | 0.196 | 3.128 | |
mutHeatmap | 4.328 | 0.083 | 4.078 | |
mutTrunkBranch | 2.942 | 0.101 | 2.655 | |
plotCNA | 1.453 | 0.080 | 0.966 | |
plotMutProfile | 3.021 | 0.059 | 2.732 | |
plotMutSigProfile | 4.132 | 0.124 | 3.975 | |
plotPhyloTree | 2.981 | 0.071 | 2.754 | |
readMaf | 2.339 | 0.045 | 2.197 | |
readSegment | 0.260 | 0.021 | 0.156 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 2.397 | 0.057 | 2.364 | |
testNeutral | 3.084 | 0.058 | 2.755 | |
triMatrix | 3.110 | 0.114 | 2.819 | |