############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:annmap.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings annmap_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/annmap.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘annmap/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘annmap’ version ‘1.49.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘annmap’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘rjson’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.make.hash’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .get.stats.cache: no visible global function definition for ‘flush.console’ .layout.genes: no visible global function definition for ‘strwidth’ .load.and.parse: no visible global function definition for ‘fromJSON’ .read.databases: no visible global function definition for ‘read.table’ .single.transcript.coords.to.genome: no visible global function definition for ‘tail’ .xmc.connect: no visible global function definition for ‘menu’ .xmcws.connect: no visible global function definition for ‘fromJSON’ .xmcws.connect: no visible global function definition for ‘menu’ annmapAddConnection: no visible global function definition for ‘write.table’ annmapConnect: no visible global function definition for ‘install.packages’ arrayType: no visible global function definition for ‘menu’ convertBamToRle: no visible global function definition for ‘RangedData’ convertBamToRle : : no visible global function definition for ‘Rle’ geneToGeneRegionTrack : generate: no visible global function definition for ‘GeneRegionTrack’ generateBridgeData: no visible global function definition for ‘rainbow’ genomicPlot : : no visible global function definition for ‘rgb’ genomicPlot: no visible global function definition for ‘rgb’ ngsTracePlotter : local.draw: no visible global function definition for ‘runValue’ ngsTracePlotter: no visible global function definition for ‘modifyList’ ngsTraceScale : : no visible global function definition for ‘runValue’ seqnameMapping: no visible global function definition for ‘seqlevels<-’ seqnameMapping: no visible global function definition for ‘seqlevels’ Undefined global functions or variables: GeneRegionTrack RangedData Rle flush.console fromJSON install.packages menu modifyList rainbow read.table rgb runValue seqlevels seqlevels<- strwidth tail write.table Consider adding importFrom("grDevices", "rainbow", "rgb") importFrom("graphics", "strwidth") importFrom("utils", "flush.console", "install.packages", "menu", "modifyList", "read.table", "tail", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) NEWS.Rd:5: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:10: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:11: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:84: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:90: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:100: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:117: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:122: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:127: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:132: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:139: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:140: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:141: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:146: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:151: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:152: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:153: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'annmap.range.Rd': ‘RangedData’ Missing link or links in Rd file 'annmap.utils.Rd': ‘RangedData’ Missing link or links in Rd file 'plot.ngs.Rd': ‘[IRanges]{Rle}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: annmap-package.Rd: GenomicRanges annmap.all.Rd: GRanges annmap.details.Rd: GRanges annmap.range.Rd: GRanges, RangedData annmap.to.Rd: GRanges annmap.utils.Rd: RangedData 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 Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’ OK * 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 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/annmap.Rcheck/00check.log’ for details.