Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1189/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.17.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
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 22.03 LTS-SP1) / 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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.17.0.tar.gz |
StartedAt: 2024-12-23 23:35:05 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:44:54 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 588.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00install.out’ for details. * checking installed package size ... OK * 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 loading without being on the library search path ... 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 20.242 0.645 20.700 calFst 14.915 0.318 15.189 getPhyloTreeRef 15.008 0.110 15.055 getPhyloTreePatient 14.313 0.003 14.264 getPhyloTree 13.701 0.057 13.701 getMutBranches 13.640 0.107 13.695 getBranchType 13.447 0.053 13.452 compareCCF 12.287 1.158 13.397 getCCFMatrix 13.335 0.056 13.345 getBootstrapValue 13.122 0.066 13.123 getBinaryMatrix 12.999 0.099 13.038 getTree 13.036 0.053 13.039 plotMutSigProfile 12.757 0.171 12.891 getPhyloTreeTsbLabel 12.754 0.069 12.760 getTreeMethod 12.736 0.024 12.716 mutHeatmap 11.892 0.068 11.913 calNeiDist 11.035 0.172 11.157 calJSI 10.489 0.077 10.525 compareTree 10.050 0.088 10.094 triMatrix 9.800 0.251 10.011 mutTrunkBranch 9.586 0.171 9.720 testNeutral 9.564 0.075 9.585 ccfAUC 9.347 0.121 9.408 mutCluster 8.981 0.311 9.236 fitSignatures 8.866 0.222 9.049 plotMutProfile 8.594 0.006 8.551 plotPhyloTree 8.530 0.024 8.516 classifyMut 7.679 0.445 8.063 subMaf 7.492 0.043 7.494 readMaf 7.266 0.015 7.218 getMafRef 7.118 0.002 7.086 getNonSyn_vc 7.105 0.005 7.072 getMafData 7.044 0.018 7.029 getMafPatient 7.039 0.003 7.012 mathScore 6.879 0.014 6.844 getSampleInfo 6.692 0.023 6.684 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 | 14.915 | 0.318 | 15.189 | |
calJSI | 10.489 | 0.077 | 10.525 | |
calNeiDist | 11.035 | 0.172 | 11.157 | |
ccfAUC | 9.347 | 0.121 | 9.408 | |
classifyMut | 7.679 | 0.445 | 8.063 | |
cna2gene | 20.242 | 0.645 | 20.700 | |
compareCCF | 12.287 | 1.158 | 13.397 | |
compareTree | 10.050 | 0.088 | 10.094 | |
fitSignatures | 8.866 | 0.222 | 9.049 | |
getBinaryMatrix | 12.999 | 0.099 | 13.038 | |
getBootstrapValue | 13.122 | 0.066 | 13.123 | |
getBranchType | 13.447 | 0.053 | 13.452 | |
getCCFMatrix | 13.335 | 0.056 | 13.345 | |
getMafData | 7.044 | 0.018 | 7.029 | |
getMafPatient | 7.039 | 0.003 | 7.012 | |
getMafRef | 7.118 | 0.002 | 7.086 | |
getMutBranches | 13.640 | 0.107 | 13.695 | |
getNonSyn_vc | 7.105 | 0.005 | 7.072 | |
getPhyloTree | 13.701 | 0.057 | 13.701 | |
getPhyloTreePatient | 14.313 | 0.003 | 14.264 | |
getPhyloTreeRef | 15.008 | 0.110 | 15.055 | |
getPhyloTreeTsbLabel | 12.754 | 0.069 | 12.760 | |
getSampleInfo | 6.692 | 0.023 | 6.684 | |
getTree | 13.036 | 0.053 | 13.039 | |
getTreeMethod | 12.736 | 0.024 | 12.716 | |
mathScore | 6.879 | 0.014 | 6.844 | |
mutCluster | 8.981 | 0.311 | 9.236 | |
mutHeatmap | 11.892 | 0.068 | 11.913 | |
mutTrunkBranch | 9.586 | 0.171 | 9.720 | |
plotCNA | 2.813 | 0.005 | 2.721 | |
plotMutProfile | 8.594 | 0.006 | 8.551 | |
plotMutSigProfile | 12.757 | 0.171 | 12.891 | |
plotPhyloTree | 8.530 | 0.024 | 8.516 | |
readMaf | 7.266 | 0.015 | 7.218 | |
readSegment | 0.469 | 0.004 | 0.413 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 7.492 | 0.043 | 7.494 | |
testNeutral | 9.564 | 0.075 | 9.585 | |
triMatrix | 9.800 | 0.251 | 10.011 | |