Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-15 11:46 -0400 (Thu, 15 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1181/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.15.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MesKit |
Version: 1.15.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MesKit_1.15.0.tar.gz |
StartedAt: 2024-08-15 06:28:03 -0000 (Thu, 15 Aug 2024) |
EndedAt: 2024-08-15 06:40:51 -0000 (Thu, 15 Aug 2024) |
EllapsedTime: 768.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MesKit_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 ‘/home/biocbuild/bbs-3.20-bioc/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 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 24.320 0.371 24.706 calFst 24.268 0.268 24.608 getTreeMethod 22.064 0.503 22.594 getPhyloTreeTsbLabel 21.004 0.871 21.896 getBinaryMatrix 21.457 0.287 21.773 getTree 20.817 0.556 21.395 getPhyloTreePatient 20.859 0.064 20.955 getPhyloTreeRef 20.816 0.067 20.917 getCCFMatrix 20.725 0.028 20.787 getMutBranches 20.608 0.108 20.749 getBranchType 20.613 0.076 20.721 getBootstrapValue 20.467 0.140 20.640 getPhyloTree 20.251 0.100 20.381 plotMutSigProfile 19.134 0.204 19.372 mutHeatmap 17.970 0.236 18.236 calNeiDist 16.930 0.119 17.068 compareCCF 16.424 0.260 16.705 compareTree 16.211 0.036 16.279 calJSI 15.863 0.096 15.974 ccfAUC 14.949 0.100 15.063 fitSignatures 14.509 0.115 14.665 mutTrunkBranch 14.247 0.183 14.458 mutCluster 13.846 0.231 14.094 testNeutral 13.870 0.064 13.948 triMatrix 13.691 0.152 13.861 plotMutProfile 13.492 0.059 13.567 plotPhyloTree 13.311 0.079 13.406 classifyMut 12.688 0.164 12.862 getSampleInfo 11.361 0.539 11.913 getMafRef 11.051 0.080 11.149 getNonSyn_vc 11.051 0.039 11.109 mathScore 10.875 0.147 11.029 readMaf 10.906 0.080 10.989 getMafPatient 10.924 0.004 10.945 subMaf 10.728 0.092 10.819 getMafData 10.774 0.035 10.825 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 | 24.268 | 0.268 | 24.608 | |
calJSI | 15.863 | 0.096 | 15.974 | |
calNeiDist | 16.930 | 0.119 | 17.068 | |
ccfAUC | 14.949 | 0.100 | 15.063 | |
classifyMut | 12.688 | 0.164 | 12.862 | |
cna2gene | 24.320 | 0.371 | 24.706 | |
compareCCF | 16.424 | 0.260 | 16.705 | |
compareTree | 16.211 | 0.036 | 16.279 | |
fitSignatures | 14.509 | 0.115 | 14.665 | |
getBinaryMatrix | 21.457 | 0.287 | 21.773 | |
getBootstrapValue | 20.467 | 0.140 | 20.640 | |
getBranchType | 20.613 | 0.076 | 20.721 | |
getCCFMatrix | 20.725 | 0.028 | 20.787 | |
getMafData | 10.774 | 0.035 | 10.825 | |
getMafPatient | 10.924 | 0.004 | 10.945 | |
getMafRef | 11.051 | 0.080 | 11.149 | |
getMutBranches | 20.608 | 0.108 | 20.749 | |
getNonSyn_vc | 11.051 | 0.039 | 11.109 | |
getPhyloTree | 20.251 | 0.100 | 20.381 | |
getPhyloTreePatient | 20.859 | 0.064 | 20.955 | |
getPhyloTreeRef | 20.816 | 0.067 | 20.917 | |
getPhyloTreeTsbLabel | 21.004 | 0.871 | 21.896 | |
getSampleInfo | 11.361 | 0.539 | 11.913 | |
getTree | 20.817 | 0.556 | 21.395 | |
getTreeMethod | 22.064 | 0.503 | 22.594 | |
mathScore | 10.875 | 0.147 | 11.029 | |
mutCluster | 13.846 | 0.231 | 14.094 | |
mutHeatmap | 17.970 | 0.236 | 18.236 | |
mutTrunkBranch | 14.247 | 0.183 | 14.458 | |
plotCNA | 3.674 | 0.028 | 3.690 | |
plotMutProfile | 13.492 | 0.059 | 13.567 | |
plotMutSigProfile | 19.134 | 0.204 | 19.372 | |
plotPhyloTree | 13.311 | 0.079 | 13.406 | |
readMaf | 10.906 | 0.080 | 10.989 | |
readSegment | 0.562 | 0.004 | 0.558 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 10.728 | 0.092 | 10.819 | |
testNeutral | 13.870 | 0.064 | 13.948 | |
triMatrix | 13.691 | 0.152 | 13.861 | |