############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hapFabia_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/hapFabia.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hapFabia/DESCRIPTION’ ... OK * this is package ‘hapFabia’ version ‘1.46.0’ * 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 ‘hapFabia’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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: The beginning * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘hapFabia/R/zzz.R’: .onLoad calls: packageStartupMessage("+--------------------------+ # # ## ##### \n", "|#.....#...#.......#.#....#| # # # # # # \n", "|#.....#...#.......#.#....#| ###### # # # # \n", "|#.....#...#...............| # # ###### ##### \n", "|#.....#...#.......#.#....#| # # # # # \n", "|#.....#...#...............| # # # # # \n", "|#.....#...#.......#.#....#| ####### \n", "|..................#.#....#| # ## ##### # ## \n", "|#.....#...#.......#.#....#| # # # # # # # # \n", "|..................#.#....#| ##### # # ##### # # # \n", "|#.....#...#.......#.#....#| # ###### # # # ###### \n", "|#.....#...#.......#.#....#| # # # # # # # # \n", "+--------------------------+ # # # ##### # # # \n") packageStartupMessage("Citation: S. Hochreiter,", "\n", "HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data,", "\n", "Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt1013.", "\n", "BibTex: enter 'toBibtex(citation(\"hapFabia\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/index.html", "\n\n", "hapFabia Package Version ", version, "\n") See section ‘Good practice’ in '?.onAttach'. * checking Rd files ... WARNING checkRd: (5) IBDsegment-class.Rd:439: \item in \value must have non-empty label checkRd: (5) IBDsegment-class.Rd:205-209: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:211-215: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:219-223: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:227-231: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:235-239: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:243-247: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:251-255: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:259-263: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:267-271: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:275-279: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:283-287: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:291-295: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:299-303: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:307-311: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:315-319: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:323-327: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:331-335: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:339-343: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:347-351: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:355-359: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:363-367: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:371-375: \item in \describe must have non-empty label checkRd: (5) IBDsegment-class.Rd:379-383: \item in \describe must have non-empty label checkRd: (-1) IBDsegment-class.Rd:408-409: Lost braces 408 | \item{plot}{\code{signature(x = "IBDsegment", y = "missing")}}{ Plot | ^ checkRd: (-1) IBDsegment-class.Rd:411-413: Lost braces 411 | \item{plotLarger}{\code{signature(x="IBDsegment", filename="character",fact="numeric",addSamp="ANY")}}{ Plot | ^ checkRd: (-1) IBDsegment-class.Rd:416-417: Lost braces 416 | \item{summary}{\code{signature(object = "IBDsegment")}}{ Summary of | ^ checkRd: (5) IBDsegmentList-class.Rd:171: \item in \value must have non-empty label checkRd: (5) IBDsegmentList-class.Rd:92-96: \item in \describe must have non-empty label checkRd: (5) IBDsegmentList-class.Rd:98-102: \item in \describe must have non-empty label checkRd: (5) IBDsegmentList-class.Rd:104-108: \item in \describe must have non-empty label checkRd: (5) IBDsegmentList-class.Rd:111-116: \item in \describe must have non-empty label checkRd: (5) IBDsegmentList-class.Rd:118-123: \item in \describe must have non-empty label checkRd: (-1) IBDsegmentList-class.Rd:145-146: Lost braces 145 | \item{plot}{\code{signature(x = "IBDsegmentList", y = "missing")}}{ | ^ checkRd: (-1) IBDsegmentList-class.Rd:149-151: Lost braces 149 | \item{summary}{\code{signature(object = "IBDsegmentList")}}{ Summary | ^ checkRd: (5) toolsFactorizationClass.Rd:83: \item in \value must have non-empty label checkRd: (5) toolsFactorizationClass.Rd:84: \item in \value must have non-empty label checkRd: (5) toolsFactorizationClass.Rd:85: \item in \value must have non-empty label * 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 shell scripts ... 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 ... OK * 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 * 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 iterateIntervals 5.35 0.787 6.303 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/hapFabia.Rcheck/00check.log’ for details.