############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:crlmm.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings crlmm_1.65.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/crlmm.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘crlmm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘crlmm’ version ‘1.65.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘crlmm’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘preprocessCore’ 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 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘RUnit’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘splines’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’ 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 .test: no visible global function definition for ‘defineTestSuite’ .test: no visible global function definition for ‘runTestSuite’ .test: no visible global function definition for ‘printTextProtocol’ calculateRBafCNSet : processByChromosome: no visible global function definition for ‘position’ genotypeInf: no visible binding for global variable ‘anno’ krlmm: no visible binding for global variable ‘VGLMparameters’ Undefined global functions or variables: VGLMparameters anno defineTestSuite position printTextProtocol runTestSuite * checking Rd files ... WARNING checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_ checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_ checkRd: (-1) genotype.Illumina.Rd:127: Lost braces 127 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readGenCallOutput.Rd:39: Lost braces 39 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_ checkRd: (-1) readIdatFiles.Rd:68: Lost braces 68 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) snprma.Rd:38: Escaped LaTeX specials: \_ \_ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AssayData-methods.Rd: CNSet-class CNSet-methods.Rd: CNSet-class ListClassConstructors.Rd: BeadStudioSetList-class PredictionRegion-class.Rd: AssayData-class, list_or_ffdf-class batchStatisticAccessors.Rd: batchStatistics celfile-utils.Rd: read.celfile constructInf.Rd: ldPath, ocSamples, ocProbesets, CNSet-class copynumberAccessors.Rd: CNSet-class crlmm.Rd: i2p, snpCall, snpCallProbability genotype.Rd: batch genotypeAffy.Rd: calls, confs genotypeInf.Rd: snpCall, snpCallProbability, annotationPackages preprocessInf.Rd: CNSet-class, A, B, annotationPackages 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crlmm 90.454 2.062 92.537 genotype 73.001 2.075 75.122 snprma 18.450 0.901 19.357 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘crlmm_unit_tests.R’ Running ‘doRUnit.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/crlmm.Rcheck/00check.log’ for details.