Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-23 01:34:09 -0000 (Thu, 23 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
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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 1122/2164 | 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: 2023-02-22 07:41:11 -0000 (Wed, 22 Feb 2023) |
EndedAt: 2023-02-22 08:10:53 -0000 (Wed, 22 Feb 2023) |
EllapsedTime: 1782.5 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 106.304 0.751 107.075 getBootstrapValue 55.646 0.283 55.916 getMutBranches 55.450 0.456 55.893 getPhyloTreeTsbLabel 54.878 0.332 55.199 getPhyloTreeRef 54.638 0.248 54.873 getPhyloTreePatient 54.092 0.308 54.386 getCCFMatrix 54.055 0.268 54.310 getTree 53.865 0.268 54.120 getPhyloTree 53.837 0.264 54.088 getBinaryMatrix 53.585 0.248 53.820 getBranchType 53.253 0.260 53.499 getTreeMethod 53.172 0.280 53.439 calJSI 38.547 0.116 38.648 compareCCF 37.965 0.540 38.491 plotMutSigProfile 37.693 0.284 37.969 compareTree 36.857 0.108 36.958 calNeiDist 35.171 0.060 35.217 mutHeatmap 33.967 0.112 34.066 fitSignatures 32.991 0.124 33.110 mutTrunkBranch 32.241 0.240 32.472 triMatrix 31.745 0.560 32.299 mutCluster 31.789 0.264 32.045 plotPhyloTree 31.892 0.156 32.039 ccfAUC 31.545 0.120 31.650 testNeutral 29.593 1.168 30.752 classifyMut 29.639 0.208 29.833 plotMutProfile 29.603 0.092 29.681 subMaf 28.748 0.220 28.954 readMaf 27.837 0.056 27.878 getMafPatient 27.307 0.044 27.343 getMafRef 27.167 0.092 27.250 mathScore 26.819 0.124 26.928 getNonSyn_vc 26.734 0.148 26.874 getMafData 26.617 0.132 26.740 getSampleInfo 26.264 0.052 26.309 cna2gene 23.045 0.592 23.595 * 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 | 106.304 | 0.751 | 107.075 | |
calJSI | 38.547 | 0.116 | 38.648 | |
calNeiDist | 35.171 | 0.060 | 35.217 | |
ccfAUC | 31.545 | 0.120 | 31.650 | |
classifyMut | 29.639 | 0.208 | 29.833 | |
cna2gene | 23.045 | 0.592 | 23.595 | |
compareCCF | 37.965 | 0.540 | 38.491 | |
compareTree | 36.857 | 0.108 | 36.958 | |
fitSignatures | 32.991 | 0.124 | 33.110 | |
getBinaryMatrix | 53.585 | 0.248 | 53.820 | |
getBootstrapValue | 55.646 | 0.283 | 55.916 | |
getBranchType | 53.253 | 0.260 | 53.499 | |
getCCFMatrix | 54.055 | 0.268 | 54.310 | |
getMafData | 26.617 | 0.132 | 26.740 | |
getMafPatient | 27.307 | 0.044 | 27.343 | |
getMafRef | 27.167 | 0.092 | 27.250 | |
getMutBranches | 55.450 | 0.456 | 55.893 | |
getNonSyn_vc | 26.734 | 0.148 | 26.874 | |
getPhyloTree | 53.837 | 0.264 | 54.088 | |
getPhyloTreePatient | 54.092 | 0.308 | 54.386 | |
getPhyloTreeRef | 54.638 | 0.248 | 54.873 | |
getPhyloTreeTsbLabel | 54.878 | 0.332 | 55.199 | |
getSampleInfo | 26.264 | 0.052 | 26.309 | |
getTree | 53.865 | 0.268 | 54.120 | |
getTreeMethod | 53.172 | 0.280 | 53.439 | |
mathScore | 26.819 | 0.124 | 26.928 | |
mutCluster | 31.789 | 0.264 | 32.045 | |
mutHeatmap | 33.967 | 0.112 | 34.066 | |
mutTrunkBranch | 32.241 | 0.240 | 32.472 | |
plotCNA | 4.195 | 0.028 | 4.204 | |
plotMutProfile | 29.603 | 0.092 | 29.681 | |
plotMutSigProfile | 37.693 | 0.284 | 37.969 | |
plotPhyloTree | 31.892 | 0.156 | 32.039 | |
readMaf | 27.837 | 0.056 | 27.878 | |
readSegment | 0.687 | 0.024 | 0.703 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 28.748 | 0.220 | 28.954 | |
testNeutral | 29.593 | 1.168 | 30.752 | |
triMatrix | 31.745 | 0.560 | 32.299 | |