############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DECIPHER_3.5.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘3.5.1’ * 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * 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 233.591 1.172 235.323 LearnNonCoding 119.635 2.045 121.989 Treeline 84.110 0.756 85.265 FindNonCoding 73.290 0.319 73.812 InferSelection 54.904 0.096 55.162 ExtractGenes 45.066 0.850 46.059 FindGenes 43.922 0.601 44.638 Genes-class 43.921 0.112 44.157 WriteGenes 42.267 0.449 42.889 InferRecombination 30.917 0.063 35.961 BrowseSeqs 29.095 0.431 29.610 DistanceMatrix 28.767 0.179 29.027 CorrectFrameshifts 17.913 0.127 18.102 StaggerAlignment 16.762 0.279 17.130 DetectRepeats 16.710 0.088 16.862 AlignTranslation 15.621 0.100 15.769 LearnTaxa 12.508 0.394 12.957 InferDemography 12.349 0.028 12.409 TrimDNA 11.693 0.182 11.932 Taxa-class 11.292 0.123 11.479 IdTaxa 10.410 0.004 10.444 Clusterize 9.767 0.180 9.979 ScoreAlignment 7.063 0.064 7.158 TileSeqs 5.983 0.095 6.113 Array2Matrix 5.308 0.100 5.424 MapCharacters 5.334 0.048 5.409 DesignArray 5.173 0.052 5.240 AlignPairs 5.117 0.080 5.219 * 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 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck/00check.log’ for details.