Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MesKit_1.14.0.tar.gz |
StartedAt: 2024-07-22 02:00:41 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 02:10:40 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 599.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MesKit_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MesKit.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 ... 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 21.481 0.777 22.083 calFst 15.462 0.288 15.701 getTree 14.140 0.024 14.111 getTreeMethod 13.859 0.032 13.840 getBootstrapValue 13.436 0.100 13.474 getBranchType 13.412 0.032 13.393 getCCFMatrix 13.297 0.092 13.340 getBinaryMatrix 13.040 0.165 13.161 compareCCF 12.050 1.015 13.018 getPhyloTreeRef 12.929 0.124 13.003 getMutBranches 12.669 0.312 12.929 getPhyloTreeTsbLabel 12.823 0.056 12.829 getPhyloTreePatient 12.817 0.060 12.826 getPhyloTree 12.700 0.084 12.734 mutHeatmap 12.558 0.064 12.561 plotMutSigProfile 11.733 0.172 11.855 calNeiDist 11.037 0.112 11.093 ccfAUC 10.323 0.176 10.443 calJSI 10.174 0.132 10.252 compareTree 9.762 0.088 9.806 mutCluster 9.510 0.328 9.796 mutTrunkBranch 9.496 0.236 9.676 plotMutProfile 9.591 0.092 9.633 fitSignatures 8.960 0.216 9.139 triMatrix 8.664 0.140 8.766 testNeutral 8.651 0.072 8.664 classifyMut 7.918 0.480 8.344 plotPhyloTree 8.033 0.028 8.025 getMafRef 7.900 0.140 8.005 getMafData 7.134 0.024 7.127 mathScore 7.080 0.032 7.061 getMafPatient 7.023 0.032 7.022 readMaf 6.880 0.076 6.898 subMaf 6.756 0.044 6.764 getSampleInfo 6.604 0.048 6.619 getNonSyn_vc 6.571 0.000 6.538 * 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-3.19-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 | 15.462 | 0.288 | 15.701 | |
calJSI | 10.174 | 0.132 | 10.252 | |
calNeiDist | 11.037 | 0.112 | 11.093 | |
ccfAUC | 10.323 | 0.176 | 10.443 | |
classifyMut | 7.918 | 0.480 | 8.344 | |
cna2gene | 21.481 | 0.777 | 22.083 | |
compareCCF | 12.050 | 1.015 | 13.018 | |
compareTree | 9.762 | 0.088 | 9.806 | |
fitSignatures | 8.960 | 0.216 | 9.139 | |
getBinaryMatrix | 13.040 | 0.165 | 13.161 | |
getBootstrapValue | 13.436 | 0.100 | 13.474 | |
getBranchType | 13.412 | 0.032 | 13.393 | |
getCCFMatrix | 13.297 | 0.092 | 13.340 | |
getMafData | 7.134 | 0.024 | 7.127 | |
getMafPatient | 7.023 | 0.032 | 7.022 | |
getMafRef | 7.900 | 0.140 | 8.005 | |
getMutBranches | 12.669 | 0.312 | 12.929 | |
getNonSyn_vc | 6.571 | 0.000 | 6.538 | |
getPhyloTree | 12.700 | 0.084 | 12.734 | |
getPhyloTreePatient | 12.817 | 0.060 | 12.826 | |
getPhyloTreeRef | 12.929 | 0.124 | 13.003 | |
getPhyloTreeTsbLabel | 12.823 | 0.056 | 12.829 | |
getSampleInfo | 6.604 | 0.048 | 6.619 | |
getTree | 14.140 | 0.024 | 14.111 | |
getTreeMethod | 13.859 | 0.032 | 13.840 | |
mathScore | 7.080 | 0.032 | 7.061 | |
mutCluster | 9.510 | 0.328 | 9.796 | |
mutHeatmap | 12.558 | 0.064 | 12.561 | |
mutTrunkBranch | 9.496 | 0.236 | 9.676 | |
plotCNA | 2.974 | 0.016 | 2.817 | |
plotMutProfile | 9.591 | 0.092 | 9.633 | |
plotMutSigProfile | 11.733 | 0.172 | 11.855 | |
plotPhyloTree | 8.033 | 0.028 | 8.025 | |
readMaf | 6.880 | 0.076 | 6.898 | |
readSegment | 0.460 | 0.000 | 0.404 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 6.756 | 0.044 | 6.764 | |
testNeutral | 8.651 | 0.072 | 8.664 | |
triMatrix | 8.664 | 0.140 | 8.766 | |