############################################################################## ############################################################################## ### ### 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 21.259 0.516 21.616 calFst 15.165 0.440 15.567 getCCFMatrix 13.757 0.244 13.953 getTreeMethod 13.128 0.588 13.651 getBranchType 13.648 0.032 13.632 getBinaryMatrix 13.520 0.072 13.543 getTree 13.204 0.088 13.228 getBootstrapValue 13.169 0.040 13.162 getPhyloTreeRef 13.014 0.056 13.010 getPhyloTree 12.925 0.112 12.983 getPhyloTreeTsbLabel 13.012 0.017 12.965 getPhyloTreePatient 12.754 0.056 12.762 getMutBranches 12.554 0.079 12.584 plotMutSigProfile 11.652 0.156 11.754 mutHeatmap 10.785 0.300 11.023 calNeiDist 10.455 0.108 10.512 compareTree 10.152 0.155 10.264 mutCluster 9.664 0.504 10.125 compareCCF 9.627 0.392 9.971 calJSI 9.585 0.136 9.675 ccfAUC 9.217 0.116 9.287 fitSignatures 9.246 0.076 9.286 mutTrunkBranch 8.579 0.212 8.748 testNeutral 8.464 0.132 8.541 plotMutProfile 8.238 0.108 8.285 triMatrix 8.228 0.112 8.306 plotPhyloTree 8.115 0.124 8.197 classifyMut 7.567 0.192 7.713 mathScore 7.031 0.459 7.438 getSampleInfo 6.884 0.019 6.875 getNonSyn_vc 6.708 0.036 6.697 readMaf 6.683 0.016 6.616 subMaf 6.561 0.036 6.547 getMafRef 6.508 0.016 6.492 getMafPatient 6.448 0.004 6.420 getMafData 6.308 0.004 6.282 * 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.