############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deepSNV_1.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/deepSNV.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘deepSNV/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘deepSNV’ version ‘1.53.0’ * 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' INFO 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 * 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 ... 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 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 whether startup messages can be suppressed ... 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’ .makeVCFheader: no visible global function definition for ‘splitAsList’ .makeVCFheader: no visible global function definition for ‘DataFrame’ .significantSNV: no visible global function definition for ‘p.adjust’ .significantSNV: no visible global function definition for ‘scanVcfHeader’ .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 ‘VCFHeader’ .significantSNV: no visible global function definition for ‘reference’ .significantSNV: no visible global function definition for ‘header’ 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 ‘scanVcfHeader’ 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 ‘VCFHeader’ bf2Vcf: no visible global function definition for ‘reference’ bf2Vcf: no visible global function definition for ‘header’ bf2Vcf: no visible global function definition for ‘SimpleList’ 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 ‘scanVcfHeader’ 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 ‘VCFHeader’ qvals2Vcf: no visible global function definition for ‘reference’ qvals2Vcf: no visible global function definition for ‘header’ qvals2Vcf: no visible global function definition for ‘SimpleList’ 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 VCFHeader abline coefficients dirichlet header info legend loess mclapply na.omit optimize p.adjust par pchisq pgamma pnorm reference scanVcfHeader seqnames splitAsList 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: bf2Vcf.Rd: VCF, GRanges consensusSequence-methods.Rd: DNAString deepSNV-methods.Rd: GRanges qvals2Vcf.Rd: VCF, GRanges repeatMask-methods.Rd: DNAString summary-methods.Rd: VCF-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... INFO 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/4.5-arm64/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) 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 nor [v]sprintf. 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 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/deepSNV.Rcheck/00check.log’ for details.