############################################################################## ############################################################################## ### ### 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/site-library --timings MesKit_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.10.0’ * 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 ... 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 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 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 18.745 0.792 19.396 calFst 16.144 0.268 16.367 getBootstrapValue 15.732 0.204 15.887 getTreeMethod 15.532 0.240 15.726 getPhyloTreeRef 15.327 0.116 15.396 getPhyloTreeTsbLabel 15.271 0.072 15.287 getTree 15.197 0.092 15.240 getPhyloTree 15.168 0.048 15.166 getPhyloTreePatient 14.956 0.123 15.033 getBinaryMatrix 14.573 0.164 14.676 getMutBranches 14.377 0.212 14.539 getCCFMatrix 14.218 0.128 14.295 getBranchType 13.759 0.052 13.749 compareCCF 11.943 1.040 12.934 plotMutSigProfile 12.313 0.160 12.442 calJSI 12.310 0.112 12.367 calNeiDist 12.111 0.124 12.187 mutHeatmap 11.458 0.056 11.467 compareTree 10.361 0.212 10.523 mutTrunkBranch 9.264 0.152 9.378 mutCluster 9.049 0.304 9.314 fitSignatures 9.123 0.212 9.303 ccfAUC 9.040 0.100 9.096 triMatrix 8.629 0.172 8.757 plotPhyloTree 8.510 0.060 8.519 plotMutProfile 8.412 0.052 8.418 testNeutral 8.405 0.012 8.360 classifyMut 7.774 0.508 8.239 getSampleInfo 7.188 0.016 7.159 getNonSyn_vc 7.100 0.012 7.084 readMaf 6.808 0.008 6.724 getMafData 6.731 0.044 6.743 subMaf 6.677 0.044 6.687 getMafPatient 6.669 0.000 6.641 mathScore 6.589 0.040 6.587 getMafRef 6.553 0.076 6.592 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck/00check.log’ for details.