############################################################################## ############################################################################## ### ### 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_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/h5vc.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘h5vc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘h5vc’ version ‘2.36.0’ * 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-3.18-bioc/meat/h5vc.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/h5vc/libs/h5vc.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 ‘_sprintf’, possibly from ‘sprintf’ (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 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 14.661 1.555 15.846 writeToTallyFile 7.515 2.198 9.292 callVariantsFisher 8.442 0.277 8.802 tallyRanges 5.166 1.738 6.478 * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/h5vc.Rcheck/00check.log’ for details.