############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantTools_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/VariantTools.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VariantTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantTools’ version ‘1.49.0’ * 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' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘VariantTools’ can be installed ... OK * checking installed package size ... INFO installed size is 6.4Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release (start date: 12 September, 2012) * 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 ... WARNING Missing or unexported object: ‘GenomicRanges::genome’ Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘IRanges:::unlist_as_integer’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE LowerFrequencyInOtherFilter : : no visible binding for global variable ‘control.alt.depth’ LowerFrequencyInOtherFilter : : no visible binding for global variable ‘control.total.depth’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.mean’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.mean.ref’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.var’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.var.ref’ ReadPositionTTestFilter : : no visible global function definition for ‘rawDepth’ StrandFETFilter : : no visible binding for global variable ‘count.plus.ref’ StrandFETFilter : : no visible binding for global variable ‘count.minus.ref’ StrandFETFilter : : no visible binding for global variable ‘count.plus’ StrandFETFilter : : no visible binding for global variable ‘count.minus’ calculateConcordanceMatrix: no visible binding for global variable ‘x’ caseControlFET: no visible binding for global variable ‘control.alt.depth’ caseControlFET: no visible binding for global variable ‘control.total.depth’ variantGR2Vcf: no visible global function definition for ‘variantGRangesIsDeprecated’ variantGR2Vcf: no visible global function definition for ‘makeVRangesFromVariantGRanges’ callVariants,GenomicRanges: no visible global function definition for ‘variantGRangesIsDeprecated’ callVariants,GenomicRanges: no visible global function definition for ‘variantGRangesToVRanges’ Undefined global functions or variables: control.alt.depth control.total.depth count.minus count.minus.ref count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref variantGRangesIsDeprecated variantGRangesToVRanges x * checking Rd files ... WARNING checkRd: (-1) callVariants.Rd:48: Lost braces 48 | \code{...}{Arguments for \code{VariantCallingFilters}, listed below.} | ^ ./man/tallyVariants.Rd: non-ASCII input and no declared encoding problem found in ‘tallyVariants.Rd’ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: tallyVariants.Rd: equisplit 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... NOTE The following directories should probably not be installed: ‘fig’ Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callGenotypes 54.689 12.599 50.001 callSampleSpecificVariants 6.229 2.632 3.259 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘VariantTools_unit_tests.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: 2 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/VariantTools.Rcheck/00check.log’ for details.