Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:44 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.14.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.14.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings MesKit_1.14.0.tar.gz |
StartedAt: 2024-05-04 09:12:03 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 09:24:59 -0000 (Sat, 04 May 2024) |
EllapsedTime: 775.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings MesKit_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MesKit.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 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 ‘1.14.0’ * 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-3.19-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 23.863 0.503 24.380 calFst 23.492 0.686 24.269 getCCFMatrix 22.356 0.327 22.710 getBootstrapValue 21.792 0.319 22.138 getBranchType 21.755 0.184 21.974 getBinaryMatrix 21.484 0.412 21.921 getPhyloTreePatient 20.758 0.132 20.915 getTree 20.729 0.056 20.807 getPhyloTreeTsbLabel 20.665 0.100 20.786 getTreeMethod 20.716 0.044 20.783 getMutBranches 20.607 0.136 20.775 getPhyloTree 20.544 0.188 20.765 getPhyloTreeRef 20.630 0.095 20.752 plotMutSigProfile 19.991 0.216 20.232 mutHeatmap 17.939 0.068 18.023 calNeiDist 16.968 0.195 17.190 compareCCF 16.689 0.235 16.944 compareTree 16.420 0.312 16.752 calJSI 15.857 0.295 16.174 fitSignatures 14.871 0.666 15.560 ccfAUC 14.395 0.144 14.555 mutTrunkBranch 14.371 0.139 14.526 mutCluster 14.054 0.072 14.140 plotMutProfile 13.713 0.072 13.794 triMatrix 13.450 0.084 13.548 testNeutral 13.408 0.075 13.497 classifyMut 12.614 0.207 12.839 plotPhyloTree 12.765 0.056 12.838 mathScore 11.293 0.072 11.374 getMafRef 11.037 0.144 11.196 subMaf 11.016 0.068 11.096 getSampleInfo 10.994 0.088 11.095 getMafData 10.959 0.080 11.053 getNonSyn_vc 10.747 0.095 10.853 getMafPatient 10.722 0.064 10.798 readMaf 10.650 0.028 10.679 * 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-3.19-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 | 23.492 | 0.686 | 24.269 | |
calJSI | 15.857 | 0.295 | 16.174 | |
calNeiDist | 16.968 | 0.195 | 17.190 | |
ccfAUC | 14.395 | 0.144 | 14.555 | |
classifyMut | 12.614 | 0.207 | 12.839 | |
cna2gene | 23.863 | 0.503 | 24.380 | |
compareCCF | 16.689 | 0.235 | 16.944 | |
compareTree | 16.420 | 0.312 | 16.752 | |
fitSignatures | 14.871 | 0.666 | 15.560 | |
getBinaryMatrix | 21.484 | 0.412 | 21.921 | |
getBootstrapValue | 21.792 | 0.319 | 22.138 | |
getBranchType | 21.755 | 0.184 | 21.974 | |
getCCFMatrix | 22.356 | 0.327 | 22.710 | |
getMafData | 10.959 | 0.080 | 11.053 | |
getMafPatient | 10.722 | 0.064 | 10.798 | |
getMafRef | 11.037 | 0.144 | 11.196 | |
getMutBranches | 20.607 | 0.136 | 20.775 | |
getNonSyn_vc | 10.747 | 0.095 | 10.853 | |
getPhyloTree | 20.544 | 0.188 | 20.765 | |
getPhyloTreePatient | 20.758 | 0.132 | 20.915 | |
getPhyloTreeRef | 20.630 | 0.095 | 20.752 | |
getPhyloTreeTsbLabel | 20.665 | 0.100 | 20.786 | |
getSampleInfo | 10.994 | 0.088 | 11.095 | |
getTree | 20.729 | 0.056 | 20.807 | |
getTreeMethod | 20.716 | 0.044 | 20.783 | |
mathScore | 11.293 | 0.072 | 11.374 | |
mutCluster | 14.054 | 0.072 | 14.140 | |
mutHeatmap | 17.939 | 0.068 | 18.023 | |
mutTrunkBranch | 14.371 | 0.139 | 14.526 | |
plotCNA | 3.705 | 0.020 | 3.712 | |
plotMutProfile | 13.713 | 0.072 | 13.794 | |
plotMutSigProfile | 19.991 | 0.216 | 20.232 | |
plotPhyloTree | 12.765 | 0.056 | 12.838 | |
readMaf | 10.650 | 0.028 | 10.679 | |
readSegment | 0.583 | 0.008 | 0.591 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 11.016 | 0.068 | 11.096 | |
testNeutral | 13.408 | 0.075 | 13.497 | |
triMatrix | 13.450 | 0.084 | 13.548 | |