############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSReg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSReg_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GSReg.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GSReg/DESCRIPTION’ ... OK * this is package ‘GSReg’ version ‘1.39.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘GSReg’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * 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 dependencies in R code ... NOTE Packages in Depends field not imported from: ‘AnnotationDbi’ ‘GenomicFeatures’ ‘Homo.sapiens’ ‘org.Hs.eg.db’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GSReg.DIRAC.Pathways: no visible global function definition for ‘pnorm’ GSReg.DIRAC.mu: no visible global function definition for ‘var’ GSReg.Variance: no visible global function definition for ‘var’ GSReg.Variance: no visible global function definition for ‘pnorm’ GSReg.kendall.tau.distance.Restricted.Sparse.internal: no visible global function definition for ‘as’ GSReg.overlapJunction: no visible binding for global variable ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ GSReg.overlapJunction: no visible binding for global variable ‘org.Hs.eg.db’ GSReg.overlapJunction: no visible global function definition for ‘genes’ GSReg.overlapJunction: no visible global function definition for ‘mapIds’ GSReg.overlapJunction: no visible global function definition for ‘GRanges’ GSReg.overlapJunction: no visible global function definition for ‘Rle’ GSReg.overlapJunction: no visible global function definition for ‘IRanges’ GSReg.overlapJunction: no visible global function definition for ‘findOverlaps’ GSReg.overlapJunction: no visible global function definition for ‘queryHits’ GSReg.overlapJunction: no visible global function definition for ‘subjectHits’ GSReg.overlapJunction : : no visible global function definition for ‘findOverlaps’ GSReg.overlapJunction : : no visible global function definition for ‘Matrix’ GSReg.overlapJunction : : no visible global function definition for ‘queryHits’ GSReg.overlapJunction : : no visible global function definition for ‘subjectHits’ Undefined global functions or variables: GRanges IRanges Matrix Rle TxDb.Hsapiens.UCSC.hg19.knownGene as findOverlaps genes mapIds org.Hs.eg.db pnorm queryHits subjectHits var Consider adding importFrom("methods", "as") importFrom("stats", "pnorm", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) GSReg-package.Rd:20: Lost braces; missing escapes or markup? 20 | {B) Calculate the DIRAC measure and p-value for it based on permutation test;} | ^ checkRd: (-1) GSReg-package.Rd:22: Lost braces; missing escapes or markup? 22 | {C) Calculate for a modified DIRAC method and a fast-efficient p-valuebased on U-Statistic theory;} | ^ checkRd: (-1) GSReg-package.Rd:24: Lost braces; missing escapes or markup? 24 | {D) Alternative Splicing Events in genes from a phenotype to other phenotype using their junction expression;} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘GSReg.kendall.tau.distance.template’ Undocumented data sets: ‘geneExrsGSReg’ ‘junc.RPM.Simulated’ ‘phenotypes’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'GSReg_GeneSets_DIRAC.Rd': GSReg.GeneSets.DIRAC Code: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha = 0, minGeneNum = 5) Docs: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha = 0.05, minGeneNum = 5) Mismatches in argument default values: Name: 'alpha' Code: 0 Docs: 0.05 Codoc mismatches from Rd file 'GSReg_GeneSets_VReg..Rd': GSReg.GeneSets.EVA Code: function(geneexpres, pathways, phenotypes, verbose = T, minGeneNum = 5, distFunc = GSReg.kendall.tau.distance, distparamPathways, ...) Docs: function(geneexpres, pathways, phenotypes, minGeneNum = 5) Argument names in code not in docs: verbose distFunc distparamPathways ... Mismatches in argument names: Position: 4 Code: verbose Docs: minGeneNum * checking Rd \usage sections ... WARNING Objects in \usage without \alias in Rd file 'GSReg_Kendall.Rd': ‘GSReg.kendall.tau.distance.template’ Bad \usage lines found in Rd file 'GSReg_OverlapJunction.Rd': GSReg.overlapJunction <- function(juncExprs, GenestoStudy=NULL, geneexpr=NULL, minmeanloggeneexp= 3, alpha =0, sparse = F, genesCoordinatesTxDB = TxDb.Hsapiens.UCSC.hg19.knownGene, geneIDInTxDB = 'ENTREZID', geneIDOut = 'SYMBOL', org=org.Hs.eg.db, ...) Bad \usage lines found in Rd file 'GSReg_SEVA.Rd': function(juncExprs, phenoVect, verbose=T, sparse =F, ...) Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE The following files look like leftovers/mistakes: ‘Rplots.pdf’ Please remove them from your package. * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/GSReg.Rcheck/00check.log’ for details.