############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:h5vc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings h5vc_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/h5vc.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘h5vc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘h5vc’ version ‘2.28.0’ * 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 for sufficient/correct file permissions ... 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 ‘/Users/biocbuild/bbs-3.14-bioc/meat/h5vc.Rcheck/00install.out’ for details. * checking installed package size ... OK * 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 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 ... 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 ... 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/h5vc/libs/h5vc.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 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 15.187 1.536 15.888 callVariantsFisher 15.996 0.096 16.105 writeToTallyFile 11.079 3.301 13.486 tallyRanges 7.668 2.710 9.472 mismatchPlot 6.524 0.082 6.614 plotMutationSpectrum 5.412 1.000 6.417 binnedAFs 5.613 0.532 6.165 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/h5vc.Rcheck/00check.log’ for details.