############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:annaffy.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings annaffy_1.78.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/annaffy.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘annaffy/DESCRIPTION’ ... OK * this is package ‘annaffy’ version ‘1.78.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘annaffy’ can be installed ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' call to ‘tcltk’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘Biobase’ ‘BiocManager’ ‘GO.db’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘BiocManager:::available’ 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 File ‘annaffy/R/zzz.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. .aaf.goterm: no visible binding for global variable ‘GOTERM’ aafGO: no visible global function definition for ‘GO_dbfile’ aafTableInt: no visible global function definition for ‘sampleNames’ aafTableInt: no visible global function definition for ‘featureNames’ aafTableInt: no visible global function definition for ‘exprs’ chkPkgs: no visible global function definition for ‘userQuery’ selectorWidget : move: no visible global function definition for ‘tkcurselection’ selectorWidget : move: no visible global function definition for ‘tclvalue’ selectorWidget : move: no visible global function definition for ‘tkget’ selectorWidget : move: no visible global function definition for ‘tkinsert’ selectorWidget : move: no visible global function definition for ‘tkdelete’ selectorWidget : move: no visible global function definition for ‘tkselection.clear’ selectorWidget : ok: no visible global function definition for ‘tkget’ selectorWidget : ok: no visible global function definition for ‘tkdestroy’ selectorWidget: no visible global function definition for ‘tktoplevel’ selectorWidget: no visible global function definition for ‘tkwm.title’ selectorWidget: no visible global function definition for ‘tkwm.resizable’ selectorWidget: no visible global function definition for ‘tkframe’ selectorWidget: no visible global function definition for ‘tklistbox’ selectorWidget : : no visible global function definition for ‘tkset’ selectorWidget: no visible global function definition for ‘tkscrollbar’ selectorWidget : : no visible global function definition for ‘tkyview’ selectorWidget: no visible global function definition for ‘tkgrid’ selectorWidget: no visible global function definition for ‘tklabel’ selectorWidget: no visible global function definition for ‘tkbutton’ selectorWidget: no visible global function definition for ‘tkinsert’ selectorWidget : : no visible global function definition for ‘tkdestroy’ selectorWidget: no visible global function definition for ‘tkbind’ selectorWidget: no visible global function definition for ‘tkwait.window’ saveHTML,aafTable: no visible global function definition for ‘browseURL’ Undefined global functions or variables: GOTERM GO_dbfile browseURL exprs featureNames sampleNames tclvalue tkbind tkbutton tkcurselection tkdelete tkdestroy tkframe tkget tkgrid tkinsert tklabel tklistbox tkscrollbar tkselection.clear tkset tktoplevel tkwait.window tkwm.resizable tkwm.title tkyview userQuery Consider adding importFrom("utils", "browseURL") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) aafTable-class.Rd:89: Escaped LaTeX specials: \$ * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'getURL-methods.Rd': ‘aafUniGene-class’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in ‘vignettes’ ... OK * checking examples ... 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/annaffy.Rcheck/00check.log’ for details.