############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fabia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fabia_2.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/fabia.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 ‘fabia/DESCRIPTION’ ... OK * this is package ‘fabia’ version ‘2.53.0’ * 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 ‘fabia’ can be installed ... OK * 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 ... 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘fabia/R/zzz.R’: .onLoad calls: packageStartupMessage("+----------------------------+ \n", "|............................| \n", "|............................| \n", "|..............########......| ####### # ###### ### # \n", "|..............########......| # # # # # # # # \n", "|.....####.....########......| # # # # # # # # \n", "|.....####.....########......| ##### # # ###### # # # \n", "|.....####...................| # ####### # # # ####### \n", "|.....####...........###.....| # # # # # # # # \n", "|....................###.....| # # # ###### ### # # \n", "|....................###.....| \n", "|............................| \n", "+----------------------------+ \n") packageStartupMessage("Citation: S. Hochreiter et al.,", "\n", "FABIA: Factor Analysis for Bicluster Acquisition,", "\n", "Bioinformatics 26(12):1520-1527, 2010.", "\n", "BibTex: enter 'toBibtex(citation(\"fabia\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html", "\n\n", "FABIA Package Version ", version, "\n") See section ‘Good practice’ in '?.onAttach'. plot,Factorization-missing: warning in symbols(ll[isel, 1], ll[isel, 2], circle = sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg = colors[2]): partial argument match of 'circle' to 'circles' plot,Factorization-missing: warning in symbols(zz[ii, 1], zz[ii, 2], square = sqs, inches = FALSE, lwd = 3, add = TRUE, fg = colors[2 + iGroup[i]]): partial argument match of 'square' to 'squares' plot,Factorization-missing: no visible global function definition for ‘dev.new’ Undefined global functions or variables: dev.new Consider adding importFrom("grDevices", "dev.new") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (5) Factorization-class.Rd:346: \item in \arguments must have non-empty label checkRd: (5) Factorization-class.Rd:398: \item in \arguments must have non-empty label checkRd: (5) Factorization-class.Rd:401: \item in \arguments must have non-empty label checkRd: (5) Factorization-class.Rd:402: \item in \arguments must have non-empty label checkRd: (5) Factorization-class.Rd:408: \item in \arguments must have non-empty label checkRd: (5) Factorization-class.Rd:409: \item in \arguments must have non-empty label checkRd: (5) Factorization-class.Rd:410: \item in \arguments must have non-empty label checkRd: (-1) Factorization-class.Rd:511: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:512: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:513: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:514: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:529: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:530: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:531: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:532: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:548: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:550: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:552: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:554: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:556: Lost braces in \enumerate; meant \describe ? checkRd: (-1) Factorization-class.Rd:558: Lost braces in \enumerate; meant \describe ? checkRd: (5) Factorization-class.Rd:416: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:417-418: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:419: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:424: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:425: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:426: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:427: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:428: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:429: \item in \value must have non-empty label checkRd: (5) Factorization-class.Rd:167-177: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:179-183: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:185-189: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:191-196: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:198-203: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:205-210: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:212-217: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:219-224: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:226-231: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:233-238: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:240-245: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:247-252: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:254-259: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:261-267: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:269-275: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:277-283: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:285-290: \item in \describe must have non-empty label checkRd: (5) Factorization-class.Rd:292-298: \item in \describe must have non-empty label checkRd: (-1) Factorization-class.Rd:331: Lost braces 331 | \item{plot}{\code{signature(x = "Factorization", y = "missing")}}{ Plot of a matrix factorization result} | ^ checkRd: (-1) Factorization-class.Rd:333: Lost braces 333 | \item{show}{\code{signature(object = "Factorization")}}{ Display statistics of a matrix factorization result} | ^ checkRd: (-1) Factorization-class.Rd:336-337: Lost braces 336 | "numeric")}}{ Display | ^ checkRd: (-1) Factorization-class.Rd:339: Lost braces 339 | \item{summary}{\code{signature(object = "Factorization")}}{ Summary of matrix factorization result} | ^ checkRd: (5) fabi.Rd:66-82: \item in \value must have non-empty label checkRd: (5) fabia.Rd:75-91: \item in \value must have non-empty label checkRd: (5) fabiap.Rd:88-104: \item in \value must have non-empty label checkRd: (5) fabias.Rd:77-93: \item in \value must have non-empty label checkRd: (5) fabiasp.Rd:65-81: \item in \value must have non-empty label checkRd: (5) mfsc.Rd:75-83: \item in \value must have non-empty label checkRd: (5) nmfdiv.Rd:49-55: \item in \value must have non-empty label checkRd: (5) nmfeu.Rd:50-56: \item in \value must have non-empty label checkRd: (5) nmfsc.Rd:76-82: \item in \value must have non-empty label checkRd: (5) readSpfabiaResult.Rd:24-35: \item in \value must have non-empty label checkRd: (5) samplesPerFeature.Rd:46-51: \item in \value must have non-empty label checkRd: (-1) samplesPerFeature.Rd:49-50: Lost braces 49 | \code{nsL} {Vector of feature length containing number of samples | ^ checkRd: (5) spfabia.Rd:113-124: \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 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 include directives in Makefiles ... NOTE Found the following Makefile(s) with an include directive with a pathname using R_HOME: src/Makefile.win Even though not recommended, variable R_HOME may contain spaces. Makefile directives use space as a separator and there is no portable way to quote/escape the space in Make rules and directives. However, one can and should quote pathnames when passed from Makefile to the shell, and this can be done specifically when invoking Make recursively. It is therefore recommended to use the Make '-f' option to include files in directories specified using R_HOME. This option can be specified multiple times to include multiple Makefiles. Note that 'Makeconf' is included automatically into top-level makefile of a package. More information can be found in 'Writing R Extensions'. * checking compiled code ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/fabia/libs/fabia.so’: Found ‘___sprintf_chk’, 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/fabia.Rcheck/00check.log’ for details.