############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GenomicTuples.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GenomicTuples_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicTuples.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 ‘GenomicTuples/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicTuples’ version ‘1.43.0’ * 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 ‘GenomicTuples’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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: ‘GenomicRanges:::extraColumnSlotNames’ ‘GenomicRanges:::extraColumnSlots’ ‘GenomicRanges:::extraColumnSlotsAsDF’ ‘S4Vectors:::VH_recycle’ ‘S4Vectors:::orderBy’ 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 .GTuples.asIntegerTuples: no visible global function definition for ‘seqnames’ .findEqual.GTuples: no visible global function definition for ‘seqinfo’ .findEqual.GTuples: no visible global function definition for ‘isCircular’ .findEqual.GTuples: no visible global function definition for ‘seqnames’ .findEqual.GTuples: no visible global function definition for ‘seqlengths’ .makeNakedMatFromGTuples: no visible global function definition for ‘seqnames’ .pcompare_GTuples: no visible global function definition for ‘seqlevels<-’ .pcompare_GTuples: no visible global function definition for ‘seqnames’ .unlist_list_of_GTuples: no visible binding for global variable ‘seqinfo’ .unlist_list_of_GTuples: no visible binding for global variable ‘seqnames’ showGTuples: no visible global function definition for ‘seqinfo’ [<-,GTuples: no visible global function definition for ‘seqinfo<-’ [<-,GTuples: no visible global function definition for ‘seqinfo’ as.character,GTuples: no visible global function definition for ‘seqnames’ as.data.frame,GTuples: no visible global function definition for ‘seqnames’ disjoin,GTuples: no visible global function definition for ‘seqlengths’ disjoin,GTuplesList: no visible global function definition for ‘seqlengths’ gaps,GTuples: no visible global function definition for ‘seqlengths’ is.unsorted,GTuples: no visible global function definition for ‘seqnames’ match,GTuples-GTuples: no visible global function definition for ‘seqinfo’ Undefined global functions or variables: isCircular seqinfo seqinfo<- seqlengths seqlevels<- seqnames * checking Rd files ... NOTE checkRd: (-1) intra-tuple-methods.Rd:39-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) intra-tuple-methods.Rd:44-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:84-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:91-97: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:98-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:105-133: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:120-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:124-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:128-131: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:134-136: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:137-141: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'GTuples-class.Rd': ‘[GenomeInfoDb:seqinfo]{seqlevels}’ ‘[GenomeInfoDb]{seqinfo}’ Missing link(s) in Rd file 'GTuplesList-class.Rd': ‘[GenomeInfoDb:seqinfo]{seqlevels}’ ‘[GenomeInfoDb]{seqinfo}’ Missing link(s) in Rd file 'findOverlaps-methods.Rd': ‘seqnames’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: GTuples-class.Rd: GRanges-class, Rle-class, IRanges-class, DataFrame-class, GenomicRanges-class, Vector-class GTuples-comparison.Rd: Hits-class GTuplesList-class.Rd: GRangesList-class, RleList-class, CharacterList-class, SimpleList-class, CompressedIRangesList-class, IntegerRangesList-class, DataFrame-class, Seqinfo, Vector-class, DataFrameList-class findOverlaps-methods.Rd: GenomicRanges-class, GRangesList-class, Hits-class, seqnames, strand, GRanges-class illdefined-methods.Rd: GRanges-class, GRangesList-class intra-tuple-methods.Rd: GRanges-class nearest-methods.Rd: GRanges-class, Hits-class, GRanges, GenomicRanges-class, IPosRanges-class 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9. │ ├─methods (local) c(``) 10. │ └─GenomicTuples (local) c(``) 11. │ └─GenomicTuples (local) .local(x, ...) 12. │ └─GenomicTuples:::.unlist_list_of_GTuples(args, ignore.mcols = ignore.mcols) 13. │ ├─BiocGenerics::do.call(merge, lapply(x, seqinfo)) 14. │ ├─base::do.call(merge, lapply(x, seqinfo)) 15. │ ├─base (local) ``(``) 16. │ └─Seqinfo::merge.Seqinfo(``) 17. │ └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...) 18. │ └─S4Vectors::unname(list(...)) 19. └─base (local) ``(``) [ FAIL 7 | WARN 0 | SKIP 0 | PASS 1062 ] Error: Test failures Execution halted * 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 ERROR, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicTuples.Rcheck/00check.log’ for details.