Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-07 15:40 -0400 (Sat, 07 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 1183/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.15.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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: 1.15.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MesKit_1.15.0.tar.gz |
StartedAt: 2024-09-06 23:11:52 -0400 (Fri, 06 Sep 2024) |
EndedAt: 2024-09-06 23:21:12 -0400 (Fri, 06 Sep 2024) |
EllapsedTime: 560.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MesKit_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-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 ‘1.15.0’ * 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-3.20-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 20.326 0.584 20.756 calFst 14.698 0.388 15.048 getBinaryMatrix 13.541 0.320 13.797 getPhyloTreePatient 13.487 0.076 13.507 getPhyloTreeRef 12.837 0.064 12.855 getPhyloTreeTsbLabel 12.777 0.036 12.746 getTree 12.665 0.056 12.671 getTreeMethod 12.591 0.128 12.673 getBranchType 12.402 0.080 12.425 getCCFMatrix 12.351 0.120 12.408 getBootstrapValue 12.226 0.104 12.265 getPhyloTree 12.232 0.092 12.276 getMutBranches 12.225 0.064 12.246 plotMutSigProfile 11.479 0.100 11.539 mutHeatmap 10.916 0.048 10.896 compareCCF 10.486 0.304 10.729 calNeiDist 10.229 0.120 10.303 calJSI 9.952 0.232 10.138 compareTree 9.564 0.076 9.600 mutCluster 9.417 0.196 9.571 ccfAUC 9.237 0.064 9.249 fitSignatures 8.835 0.060 8.859 mutTrunkBranch 8.592 0.116 8.669 testNeutral 8.247 0.012 8.204 triMatrix 8.131 0.048 8.143 plotMutProfile 7.848 0.060 7.861 plotPhyloTree 7.672 0.064 7.700 classifyMut 7.497 0.148 7.601 getSampleInfo 6.618 0.016 6.604 readMaf 6.614 0.012 6.560 mathScore 6.605 0.016 6.563 getMafRef 6.596 0.008 6.577 subMaf 6.555 0.000 6.520 getMafData 6.530 0.004 6.486 getMafPatient 6.370 0.000 6.340 getNonSyn_vc 6.339 0.016 6.326 * 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 | 14.698 | 0.388 | 15.048 | |
calJSI | 9.952 | 0.232 | 10.138 | |
calNeiDist | 10.229 | 0.120 | 10.303 | |
ccfAUC | 9.237 | 0.064 | 9.249 | |
classifyMut | 7.497 | 0.148 | 7.601 | |
cna2gene | 20.326 | 0.584 | 20.756 | |
compareCCF | 10.486 | 0.304 | 10.729 | |
compareTree | 9.564 | 0.076 | 9.600 | |
fitSignatures | 8.835 | 0.060 | 8.859 | |
getBinaryMatrix | 13.541 | 0.320 | 13.797 | |
getBootstrapValue | 12.226 | 0.104 | 12.265 | |
getBranchType | 12.402 | 0.080 | 12.425 | |
getCCFMatrix | 12.351 | 0.120 | 12.408 | |
getMafData | 6.530 | 0.004 | 6.486 | |
getMafPatient | 6.37 | 0.00 | 6.34 | |
getMafRef | 6.596 | 0.008 | 6.577 | |
getMutBranches | 12.225 | 0.064 | 12.246 | |
getNonSyn_vc | 6.339 | 0.016 | 6.326 | |
getPhyloTree | 12.232 | 0.092 | 12.276 | |
getPhyloTreePatient | 13.487 | 0.076 | 13.507 | |
getPhyloTreeRef | 12.837 | 0.064 | 12.855 | |
getPhyloTreeTsbLabel | 12.777 | 0.036 | 12.746 | |
getSampleInfo | 6.618 | 0.016 | 6.604 | |
getTree | 12.665 | 0.056 | 12.671 | |
getTreeMethod | 12.591 | 0.128 | 12.673 | |
mathScore | 6.605 | 0.016 | 6.563 | |
mutCluster | 9.417 | 0.196 | 9.571 | |
mutHeatmap | 10.916 | 0.048 | 10.896 | |
mutTrunkBranch | 8.592 | 0.116 | 8.669 | |
plotCNA | 2.584 | 0.012 | 2.500 | |
plotMutProfile | 7.848 | 0.060 | 7.861 | |
plotMutSigProfile | 11.479 | 0.100 | 11.539 | |
plotPhyloTree | 7.672 | 0.064 | 7.700 | |
readMaf | 6.614 | 0.012 | 6.560 | |
readSegment | 0.433 | 0.004 | 0.383 | |
runMesKit | 0 | 0 | 0 | |
subMaf | 6.555 | 0.000 | 6.520 | |
testNeutral | 8.247 | 0.012 | 8.204 | |
triMatrix | 8.131 | 0.048 | 8.143 | |