############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:h5vc.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings h5vc_2.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/h5vc.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'h5vc/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'h5vc' version '2.41.0' * 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 'h5vc' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' See 'E:/biocbuild/bbs-3.21-bioc/meat/h5vc.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.3.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... INFO installed size is 10.8Mb sub-directories of 1Mb or more: libs 10.4Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE 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 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 .h5dapplyIRanges: no visible binding for global variable 'Sample' binnedAFs : : no visible global function definition for 'hist' callVariantsPaired : : : no visible global function definition for 'binom.test' callVariantsPairedFisher : : : : no visible global function definition for 'fisher.test' callVariantsPairedFisher : : : no visible binding for global variable 'pValue' callVariantsPairedFisher : : : no visible binding for global variable 'BlockID' callVariantsSingle : : : no visible binding for global variable 'Support' callVariantsSingle : : : no visible binding for global variable 'AF' callVariantsSingle : : : no visible binding for global variable 'SupFwd' callVariantsSingle : : : no visible binding for global variable 'SupRev' callVariantsSingle : : : binom.test.safe: no visible global function definition for 'binom.test' callVariantsSingle : : : : no visible global function definition for 'fisher.test' callVariantsSingle : : : no visible binding for global variable 'BlockID' mergeTallyFiles : : no visible binding for global variable 'group' mergeTallyFiles: no visible binding for global variable 'SourceFile' mismatchPlot: no visible binding for global variable 'Sample' plotMutationSpectrum: no visible binding for global variable 'altAllele' plotMutationSpectrum: no visible binding for global variable 'tmp' rerunBatchTallies: no visible binding for global variable 'regID' resizeCohort: no visible binding for global variable 'newSamples' tallyRangesBatch : : no visible binding for global variable 'bamFiles' tallyRangesBatch: no visible binding for global variable 'verbose' Undefined global functions or variables: AF BlockID Sample SourceFile SupFwd SupRev Support altAllele bamFiles binom.test fisher.test group hist newSamples pValue regID tmp verbose Consider adding importFrom("graphics", "hist") importFrom("stats", "binom.test", "fisher.test") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) prepareTallyFile.Rd:30: Lost braces 30 | \code{resizeCohort}{Resizes the datasets to a new number of samples, this is limited by the value of \code{maxsamples} that was provided in the initial call to \code{prepareTallyFile}} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: tallyRanges.Rd: BatchJobs 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 for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/h5vc/libs/x64/h5vc.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed applyTallies 25.30 0.73 45.44 callVariantsFisher 7.92 0.17 8.11 writeToTallyFile 6.25 0.77 7.23 mutationSpectrum 3.91 1.08 5.03 tallyRanges 4.16 0.27 6.13 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' 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: 1 WARNING, 5 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/h5vc.Rcheck/00check.log' for details.