############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DECIPHER_2.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DECIPHER.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘2.27.0’ * 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’ * checking installed package size ... NOTE installed size is 13.3Mb sub-directories of 1Mb or more: R 1.4Mb data 7.3Mb extdata 2.3Mb libs 1.9Mb * 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 R 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 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 ‘deltaHrulesRNA’ TreeLine: multiple local function definitions for ‘.minimize’ with different formal arguments Undefined global functions or variables: 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 PredictDBN 112.038 0.312 112.415 MapCharacters 90.839 0.247 91.090 FindNonCoding 60.390 0.412 60.984 LearnNonCoding 46.598 3.900 50.501 BrowseSeqs 43.440 0.344 43.866 Genes-class 38.506 0.260 39.234 WriteGenes 37.110 0.180 37.291 ExtractGenes 36.830 0.396 37.227 FindGenes 35.736 0.168 35.904 AlignSeqs 22.767 0.484 23.251 CorrectFrameshifts 16.057 0.120 16.177 StaggerAlignment 12.043 0.092 12.135 Taxa-class 11.675 0.060 11.736 AlignTranslation 11.348 0.124 11.472 IdTaxa 11.337 0.015 11.354 DetectRepeats 9.353 0.040 9.393 TreeLine 8.145 0.076 8.222 LearnTaxa 6.740 0.595 7.337 Clusterize 5.404 0.021 5.425 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ArtOfAlignmentInR.Rnw’... OK ‘ClassifySequences.Rnw’... OK ‘ClusteringSequences.Rnw’... OK ‘DECIPHERing.Rnw’... OK ‘DesignMicroarray.Rnw’... OK ‘DesignPrimers.Rnw’... OK ‘DesignProbes.Rnw’... OK ‘DesignSignatures.Rnw’... OK ‘FindChimeras.Rnw’... OK ‘FindingGenes.Rnw’... OK ‘FindingNonCodingRNAs.Rnw’... OK ‘GrowingTrees.Rnw’... OK ‘RepeatRepeat.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/DECIPHER.Rcheck/00check.log’ for details.