Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:44 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the MesKit package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1124/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.9.0 (landing page) Mengni Liu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: MesKit |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MesKit_1.9.0.tar.gz |
StartedAt: 2023-02-28 07:29:54 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 07:59:55 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1801.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MesKit_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.9.0’ * 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-3.17-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 R 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 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 calFst 108.940 0.636 109.593 getMutBranches 56.962 0.356 57.303 getBootstrapValue 56.688 0.416 57.089 getPhyloTreeTsbLabel 56.098 0.368 56.452 getBinaryMatrix 55.635 0.296 55.917 getPhyloTreeRef 55.705 0.224 55.915 getTreeMethod 55.559 0.284 55.828 getPhyloTreePatient 55.512 0.252 55.748 getTree 55.426 0.302 55.713 getCCFMatrix 55.415 0.254 55.655 getPhyloTree 55.347 0.216 55.548 getBranchType 54.779 0.209 54.973 calJSI 39.397 0.120 39.501 compareCCF 38.228 0.636 38.848 plotMutSigProfile 37.761 0.248 38.000 compareTree 36.511 0.164 36.667 mutHeatmap 36.187 0.204 36.377 calNeiDist 36.118 0.072 36.176 mutTrunkBranch 33.128 0.200 33.319 fitSignatures 33.123 0.132 33.249 plotPhyloTree 32.670 0.112 32.773 triMatrix 32.376 0.184 32.551 ccfAUC 32.352 0.076 32.413 mutCluster 31.832 0.216 32.038 testNeutral 31.687 0.212 31.888 classifyMut 30.374 0.284 30.644 plotMutProfile 29.882 0.136 30.003 readMaf 28.412 0.100 28.496 subMaf 28.421 0.084 28.490 mathScore 27.921 0.104 28.009 getMafRef 27.880 0.088 27.960 getMafData 27.835 0.111 27.937 getMafPatient 27.735 0.148 27.875 getSampleInfo 27.703 0.077 27.772 getNonSyn_vc 27.514 0.088 27.594 cna2gene 23.139 0.536 23.637 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MesKit.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 108.940 | 0.636 | 109.593 | |
calJSI | 39.397 | 0.120 | 39.501 | |
calNeiDist | 36.118 | 0.072 | 36.176 | |
ccfAUC | 32.352 | 0.076 | 32.413 | |
classifyMut | 30.374 | 0.284 | 30.644 | |
cna2gene | 23.139 | 0.536 | 23.637 | |
compareCCF | 38.228 | 0.636 | 38.848 | |
compareTree | 36.511 | 0.164 | 36.667 | |
fitSignatures | 33.123 | 0.132 | 33.249 | |
getBinaryMatrix | 55.635 | 0.296 | 55.917 | |
getBootstrapValue | 56.688 | 0.416 | 57.089 | |
getBranchType | 54.779 | 0.209 | 54.973 | |
getCCFMatrix | 55.415 | 0.254 | 55.655 | |
getMafData | 27.835 | 0.111 | 27.937 | |
getMafPatient | 27.735 | 0.148 | 27.875 | |
getMafRef | 27.880 | 0.088 | 27.960 | |
getMutBranches | 56.962 | 0.356 | 57.303 | |
getNonSyn_vc | 27.514 | 0.088 | 27.594 | |
getPhyloTree | 55.347 | 0.216 | 55.548 | |
getPhyloTreePatient | 55.512 | 0.252 | 55.748 | |
getPhyloTreeRef | 55.705 | 0.224 | 55.915 | |
getPhyloTreeTsbLabel | 56.098 | 0.368 | 56.452 | |
getSampleInfo | 27.703 | 0.077 | 27.772 | |
getTree | 55.426 | 0.302 | 55.713 | |
getTreeMethod | 55.559 | 0.284 | 55.828 | |
mathScore | 27.921 | 0.104 | 28.009 | |
mutCluster | 31.832 | 0.216 | 32.038 | |
mutHeatmap | 36.187 | 0.204 | 36.377 | |
mutTrunkBranch | 33.128 | 0.200 | 33.319 | |
plotCNA | 4.199 | 0.012 | 4.192 | |
plotMutProfile | 29.882 | 0.136 | 30.003 | |
plotMutSigProfile | 37.761 | 0.248 | 38.000 | |
plotPhyloTree | 32.670 | 0.112 | 32.773 | |
readMaf | 28.412 | 0.100 | 28.496 | |
readSegment | 0.636 | 0.028 | 0.656 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 28.421 | 0.084 | 28.490 | |
testNeutral | 31.687 | 0.212 | 31.888 | |
triMatrix | 32.376 | 0.184 | 32.551 | |