############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DECIPHER_3.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘3.5.0’ * 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 ‘DECIPHER’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 13.9Mb sub-directories of 1Mb or more: R 1.4Mb data 7.5Mb extdata 2.8Mb libs 1.6Mb * 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 loading without being on the library search path ... 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 AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’ DesignSignatures: no visible binding for global variable ‘deltaHrules’ FindGenes: no visible binding for global variable ‘deltaHrulesRNA’ FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’ LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’ PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’ Treeline: multiple local function definitions for ‘.NNI’ with different formal arguments Treeline: multiple local function definitions for ‘.minimize’ with different formal arguments Undefined global functions or variables: deltaGrulesRNA deltaHrules deltaHrulesRNA * checking Rd files ... OK * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignSeqs 168.834 0.849 169.698 LearnNonCoding 118.838 4.612 127.099 Treeline 58.317 0.226 58.544 FindNonCoding 55.906 0.450 56.357 ExtractGenes 38.152 0.293 38.447 InferSelection 36.628 0.108 36.737 Genes-class 35.964 0.221 36.186 FindGenes 36.056 0.085 36.143 WriteGenes 33.397 0.365 33.763 BrowseSeqs 25.156 0.059 25.215 DistanceMatrix 23.127 0.115 23.242 InferRecombination 18.916 0.024 18.942 CorrectFrameshifts 16.345 0.046 16.391 StaggerAlignment 12.467 0.074 12.541 AlignTranslation 11.258 0.060 11.317 DetectRepeats 10.888 0.021 10.910 Taxa-class 10.162 0.007 10.169 TrimDNA 10.038 0.088 10.126 IdTaxa 9.584 0.013 9.597 InferDemography 8.332 0.003 8.336 Clusterize 8.270 0.035 8.304 LearnTaxa 6.369 0.550 6.920 AlignPairs 5.376 0.203 5.581 Array2Matrix 5.095 0.023 5.119 DesignArray 5.076 0.032 5.109 ScoreAlignment 5.031 0.021 5.052 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck/00check.log’ for details.