############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantFiltering.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantFiltering_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/VariantFiltering.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VariantFiltering/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantFiltering’ version ‘1.39.0’ * 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 ‘VariantFiltering’ can be installed ... WARNING Found the following significant warnings: methods-WeightMatrix.c:88:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security] See ‘/Users/biocbuild/bbs-3.19-bioc/meat/VariantFiltering.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: R 1.1Mb extdata 3.7Mb * 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 ... 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 Unexported objects imported by ':::' calls: 'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs' 'VariantAnnotation:::.consolidateHits' 'VariantAnnotation:::.returnEmpty' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.adjustForStrandSense' '.ancestorsSO' '.findSOIDs' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) VariantFiltering-deprecated.Rd:87: Lost braces 87 | \item{dbSNPpresent(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:88: Lost braces 88 | \item{OMIMpresent(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:89: Lost braces 89 | \item{variantType(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:90: Lost braces 90 | \item{aaChangeType(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:91: Lost braces 91 | \item{variantLocation(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:92: Lost braces 92 | \item{variantConsequence(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:93: Lost braces 93 | \item{naMAF(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:94: Lost braces 94 | \item{MAFpop(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:95: Lost braces 95 | \item{maxMAF(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:96: Lost braces 96 | \item{minPhastCons(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:97: Lost braces 97 | \item{minPhylostratum(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:98: Lost braces 98 | \item{minScore5ss(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:99: Lost braces 99 | \item{minScore3ss(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ checkRd: (-1) VariantFiltering-deprecated.Rd:100: Lost braces 100 | \item{minCUfc(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}} | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed VariantFilteringParam-class 8.435 3.633 12.602 * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/VariantFiltering.Rcheck/00check.log’ for details.