############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MesKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MesKit_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.4.0’ * 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’ See ‘/Users/biocbuild/bbs-3.14-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 getBinaryMatrix 49.677 0.516 50.237 getPhyloTree 48.025 0.248 48.321 getPhyloTreePatient 47.541 0.266 47.848 getPhyloTreeRef 47.180 0.398 47.615 getBranchType 46.984 0.316 47.332 getMutBranches 46.774 0.489 47.302 getTree 46.849 0.326 47.207 getBootstrapValue 46.608 0.394 47.036 getTreeMethod 46.459 0.215 46.709 getCCFMatrix 45.761 0.500 46.291 getPhyloTreeTsbLabel 45.600 0.239 45.876 calFst 26.842 0.214 27.093 cna2gene 25.266 0.852 26.145 compareCCF 22.637 1.635 24.322 calJSI 23.007 0.089 23.113 plotMutSigProfile 20.968 0.171 21.166 compareTree 20.513 0.354 20.882 calNeiDist 17.595 0.085 17.701 mutTrunkBranch 16.888 0.144 17.052 fitSignatures 16.590 0.246 16.850 mutHeatmap 16.484 0.068 16.562 triMatrix 15.330 0.173 15.517 plotPhyloTree 14.020 0.117 14.157 mutCluster 12.805 0.756 13.581 ccfAUC 12.756 0.085 12.894 plotMutProfile 12.172 0.045 12.229 testNeutral 10.848 0.041 10.899 classifyMut 10.604 0.057 10.675 mathScore 9.060 0.071 9.141 subMaf 8.972 0.036 9.012 getMafData 8.875 0.039 8.917 readMaf 8.662 0.034 8.700 getSampleInfo 8.572 0.033 8.610 getMafPatient 8.454 0.030 8.493 getMafRef 8.343 0.022 8.370 getNonSyn_vc 8.287 0.019 8.311 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00check.log’ for details.