############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SynExtend_1.20.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SynExtend/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SynExtend’ version ‘1.20.2’ * package encoding: UTF-8 * 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 ‘SynExtend’ can be installed ... OK * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘DECIPHER:::.detectCores’ ‘DECIPHER:::.getSubMatrix’ ‘DECIPHER:::.nucleotideSubstitutionMatrix’ 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AAHitScoping.Rd: SearchIndex ApproximateBackground.Rd: translate, FindSynteny BlockByRank.Rd: FindSynteny BlockExpansion.Rd: FindSynteny BlockReconciliation.Rd: FindSynteny, Synteny-class CheckAgainstReport.Rd: readDNAStringSet ClusterByK.Rd: FindSynteny CompetePairs.Rd: FindSynteny DisjointSet.Rd: FindSynteny, Synteny-class EstimRearrScen.Rd: Synteny-class, FindSynteny ExpandDiagonal.Rd: AlignPairs, FindSynteny ExtractBy.Rd: FindSynteny, Synteny-class HitConsensus.Rd: FindSynteny NucleotideOverlap.Rd: FindSynteny, Synteny-class PairSummaries.Rd: FindSynteny, Synteny-class PrepareSeqs.Rd: FindSynteny SelectByK.Rd: FindSynteny SequenceSimilarity.Rd: AlignSeqs, AlignProfiles, AlignTranslation, DistanceMatrix SummarizePairs.Rd: AlignPairs, getGeneticCode, IndexSeqs, SearchIndex, FindSynteny 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 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 usage of KIND in Fortran files ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BuiltInEnsembles 119.436 0.420 120.131 ExampleStreptomycesData 82.569 0.244 83.093 BlockExpansion 79.363 1.301 80.930 SummarizePairs 75.732 0.156 75.977 SelectByK 44.635 0.155 44.871 ExpandDiagonal 44.382 0.152 44.619 gffToDataFrame 12.073 0.012 12.106 predict.EvoWeaver 10.943 0.020 10.978 PairSummaries 5.647 0.004 5.661 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_ExoLabel.R’ 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck/00check.log’ for details.