############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MesKit_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 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 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 6.2Mb 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getPhyloTree 26.47 0.13 26.58 getCCFMatrix 26.12 0.11 26.22 getPhyloTreePatient 26.04 0.09 26.12 getMutBranches 25.64 0.25 25.89 getBranchType 25.63 0.18 25.81 getBootstrapValue 24.65 0.03 24.67 getBinaryMatrix 24.38 0.29 24.66 getPhyloTreeTsbLabel 24.55 0.06 24.59 getPhyloTreeRef 24.39 0.03 24.43 getTree 24.28 0.12 24.39 getTreeMethod 24.15 0.14 24.28 cna2gene 18.10 0.66 18.89 calFst 13.42 0.40 14.51 triMatrix 12.52 0.09 12.61 compareCCF 11.39 1.10 12.50 calJSI 12.47 0.01 12.47 compareTree 10.73 0.61 11.33 plotMutSigProfile 11.16 0.12 11.28 mutHeatmap 9.58 0.02 9.59 calNeiDist 9.32 0.05 9.35 mutTrunkBranch 8.45 0.15 8.60 fitSignatures 7.83 0.39 8.23 plotPhyloTree 8.06 0.03 8.08 mutCluster 7.43 0.06 7.48 plotMutProfile 7.17 0.05 7.22 ccfAUC 6.43 0.00 6.43 testNeutral 5.89 0.02 5.91 getMafData 5.63 0.02 5.63 classifyMut 5.14 0.03 5.17 subMaf 5.12 0.01 5.12 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getPhyloTree 29.37 0.06 29.44 getPhyloTreePatient 28.83 0.16 28.98 getMutBranches 28.07 0.12 28.17 getBootstrapValue 28.03 0.04 28.07 getBinaryMatrix 27.68 0.18 27.84 getCCFMatrix 27.78 0.07 27.85 getBranchType 27.34 0.07 27.40 getPhyloTreeRef 26.23 0.09 26.33 getPhyloTreeTsbLabel 25.43 0.05 25.47 getTree 24.71 0.15 24.85 getTreeMethod 24.15 0.09 24.25 cna2gene 20.78 0.71 21.49 calFst 16.45 0.08 16.53 compareCCF 14.50 0.49 14.95 compareTree 14.29 0.12 14.46 plotMutSigProfile 13.25 0.19 13.46 calJSI 13.39 0.02 13.39 calNeiDist 11.22 0.03 11.25 mutHeatmap 10.37 0.08 10.46 mutTrunkBranch 9.94 0.10 10.03 fitSignatures 9.46 0.14 9.59 triMatrix 9.12 0.19 9.30 plotPhyloTree 8.03 0.01 8.04 mutCluster 7.94 0.01 7.93 ccfAUC 7.64 0.04 7.68 plotMutProfile 6.62 0.03 6.67 testNeutral 6.58 0.05 6.62 classifyMut 5.96 0.04 5.98 * 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 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00check.log' for details.