############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings deepSNV_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/deepSNV.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘deepSNV/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘deepSNV’ version ‘1.38.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'parallel', 'IRanges', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'VGAM', 'VariantAnnotation' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘deepSNV’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2 * checking top-level files ... OK * 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 ... NOTE Packages in Depends field not imported from: ‘GenomicRanges’ ‘SummarizedExperiment’ ‘VariantAnnotation’ ‘parallel’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘estimateRho’ ‘logbb’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .deepSNVsingle: no visible global function definition for ‘pchisq’ .estimateDispersion: no visible global function definition for ‘optimize’ .significantSNV: no visible global function definition for ‘p.adjust’ .significantSNV: no visible global function definition for ‘VCF’ .significantSNV: no visible global function definition for ‘GRanges’ .significantSNV: no visible global function definition for ‘IRanges’ .significantSNV: no visible global function definition for ‘DataFrame’ .significantSNV: no visible global function definition for ‘SimpleList’ .significantSNV: no visible global function definition for ‘scanVcfHeader’ .significantSNV: no visible global function definition for ‘metadata’ .significantSNV: no visible global function definition for ‘metadata<-’ bbb: no visible global function definition for ‘na.omit’ betabinLRT: no visible global function definition for ‘pchisq’ betabinLRT: no visible global function definition for ‘p.adjust’ bf2Vcf: no visible global function definition for ‘VCF’ bf2Vcf: no visible global function definition for ‘GRanges’ bf2Vcf: no visible global function definition for ‘IRanges’ bf2Vcf: no visible global function definition for ‘DataFrame’ bf2Vcf: no visible global function definition for ‘scanVcfHeader’ bf2Vcf: no visible global function definition for ‘SimpleList’ bf2Vcf: no visible global function definition for ‘metadata’ bf2Vcf: no visible global function definition for ‘metadata<-’ bf2Vcf: no visible global function definition for ‘meta’ bf2Vcf: no visible global function definition for ‘meta<-’ loadAllData: no visible global function definition for ‘mclapply’ makePrior: no visible global function definition for ‘info’ manhattanPlot: no visible global function definition for ‘legend’ mcChunk: no visible global function definition for ‘mclapply’ mutID: no visible global function definition for ‘seqnames’ p.combine: no visible global function definition for ‘pgamma’ plot.deepSNV: no visible global function definition for ‘legend’ plot.deepSNV: no visible global function definition for ‘par’ plot.deepSNV: no visible global function definition for ‘abline’ qvals2Vcf: no visible global function definition for ‘VCF’ qvals2Vcf: no visible global function definition for ‘GRanges’ qvals2Vcf: no visible global function definition for ‘IRanges’ qvals2Vcf: no visible global function definition for ‘DataFrame’ qvals2Vcf: no visible global function definition for ‘scanVcfHeader’ qvals2Vcf: no visible global function definition for ‘SimpleList’ qvals2Vcf: no visible global function definition for ‘metadata’ qvals2Vcf: no visible global function definition for ‘metadata<-’ qvals2Vcf: no visible global function definition for ‘meta’ qvals2Vcf: no visible global function definition for ‘meta<-’ PCRTest,matrix-matrix: no visible global function definition for ‘pnorm’ estimateDirichlet,matrix: no visible binding for global variable ‘dirichlet’ estimateDirichlet,matrix: no visible global function definition for ‘coefficients’ normalize,matrix-matrix : : no visible global function definition for ‘loess’ overDispersion,matrix-matrix: no visible global function definition for ‘optimize’ overDispersion,matrix-matrix : : no visible global function definition for ‘na.omit’ Undefined global functions or variables: DataFrame GRanges IRanges SimpleList VCF abline coefficients dirichlet info legend loess mclapply meta meta<- metadata metadata<- na.omit optimize p.adjust par pchisq pgamma pnorm scanVcfHeader seqnames Consider adding importFrom("graphics", "abline", "legend", "par") importFrom("stats", "coefficients", "loess", "na.omit", "optimize", "p.adjust", "pchisq", "pgamma", "pnorm") to your NAMESPACE file. * 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 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/deepSNV/libs/deepSNV.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_srand48’, possibly from ‘srand48’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed RCC 7.274 0.398 7.687 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/deepSNV.Rcheck/00check.log’ for details.