Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
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 1205/2309 | 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 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: /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: 2025-03-13 23:34:22 -0400 (Thu, 13 Mar 2025) |
EndedAt: 2025-03-13 23:43:56 -0400 (Thu, 13 Mar 2025) |
EllapsedTime: 573.8 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) (2025-02-19 r87757) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 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 17.694 0.691 18.216 calFst 14.718 0.364 15.036 getTree 13.711 0.049 13.709 getTreeMethod 13.671 0.028 13.645 getPhyloTreeTsbLabel 13.058 0.093 13.103 getCCFMatrix 12.965 0.093 13.002 getPhyloTreeRef 12.816 0.089 12.857 getBranchType 12.821 0.077 12.851 getBinaryMatrix 12.630 0.183 12.761 getPhyloTreePatient 12.765 0.034 12.752 getBootstrapValue 12.683 0.079 12.708 getPhyloTree 12.701 0.052 12.696 getMutBranches 12.564 0.123 12.644 mutHeatmap 12.095 0.093 12.126 plotMutSigProfile 11.939 0.148 12.025 compareCCF 10.629 1.020 11.599 mutTrunkBranch 10.541 0.334 10.830 calNeiDist 10.670 0.045 10.665 calJSI 9.899 0.116 9.974 compareTree 9.929 0.077 9.960 mutCluster 9.150 0.314 9.425 ccfAUC 9.146 0.048 9.142 fitSignatures 8.743 0.200 8.904 triMatrix 8.726 0.210 8.885 plotPhyloTree 8.806 0.031 8.773 testNeutral 8.744 0.053 8.743 classifyMut 8.071 0.439 8.458 plotMutProfile 8.305 0.004 8.244 getMafData 8.079 0.086 8.132 readMaf 7.155 0.042 7.128 mathScore 7.121 0.023 7.082 getSampleInfo 7.028 0.073 7.060 subMaf 6.763 0.054 6.763 getMafPatient 6.647 0.001 6.615 getMafRef 6.585 0.001 6.558 getNonSyn_vc 6.547 0.003 6.522 * 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’ ... ** 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 | 14.718 | 0.364 | 15.036 | |
calJSI | 9.899 | 0.116 | 9.974 | |
calNeiDist | 10.670 | 0.045 | 10.665 | |
ccfAUC | 9.146 | 0.048 | 9.142 | |
classifyMut | 8.071 | 0.439 | 8.458 | |
cna2gene | 17.694 | 0.691 | 18.216 | |
compareCCF | 10.629 | 1.020 | 11.599 | |
compareTree | 9.929 | 0.077 | 9.960 | |
fitSignatures | 8.743 | 0.200 | 8.904 | |
getBinaryMatrix | 12.630 | 0.183 | 12.761 | |
getBootstrapValue | 12.683 | 0.079 | 12.708 | |
getBranchType | 12.821 | 0.077 | 12.851 | |
getCCFMatrix | 12.965 | 0.093 | 13.002 | |
getMafData | 8.079 | 0.086 | 8.132 | |
getMafPatient | 6.647 | 0.001 | 6.615 | |
getMafRef | 6.585 | 0.001 | 6.558 | |
getMutBranches | 12.564 | 0.123 | 12.644 | |
getNonSyn_vc | 6.547 | 0.003 | 6.522 | |
getPhyloTree | 12.701 | 0.052 | 12.696 | |
getPhyloTreePatient | 12.765 | 0.034 | 12.752 | |
getPhyloTreeRef | 12.816 | 0.089 | 12.857 | |
getPhyloTreeTsbLabel | 13.058 | 0.093 | 13.103 | |
getSampleInfo | 7.028 | 0.073 | 7.060 | |
getTree | 13.711 | 0.049 | 13.709 | |
getTreeMethod | 13.671 | 0.028 | 13.645 | |
mathScore | 7.121 | 0.023 | 7.082 | |
mutCluster | 9.150 | 0.314 | 9.425 | |
mutHeatmap | 12.095 | 0.093 | 12.126 | |
mutTrunkBranch | 10.541 | 0.334 | 10.830 | |
plotCNA | 2.895 | 0.009 | 2.772 | |
plotMutProfile | 8.305 | 0.004 | 8.244 | |
plotMutSigProfile | 11.939 | 0.148 | 12.025 | |
plotPhyloTree | 8.806 | 0.031 | 8.773 | |
readMaf | 7.155 | 0.042 | 7.128 | |
readSegment | 0.517 | 0.005 | 0.437 | |
runMesKit | 0.001 | 0.000 | 0.000 | |
subMaf | 6.763 | 0.054 | 6.763 | |
testNeutral | 8.744 | 0.053 | 8.743 | |
triMatrix | 8.726 | 0.210 | 8.885 | |