############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings genefilter_1.86.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/genefilter.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genefilter/DESCRIPTION’ ... OK * this is package ‘genefilter’ version ‘1.86.0’ * 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 ‘genefilter’ can be installed ... WARNING Found the following significant warnings: half_range_mode.cpp:100:60: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] pAUC.c:140:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] See ‘/home/biocbuild/bbs-3.19-bioc/meat/genefilter.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 10.3.1’ * used Fortran compiler: ‘GNU Fortran (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 ... WARNING Vignettes with missing or empty \VignetteIndexEntry: howtogenefinder.Rmd See sections ‘The INDEX file’ and ‘Package subdirectories’ in the ‘Writing R Extensions’ manual. * 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 ‘tkWidgets’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. ':::' call which should be '::': ‘tkWidgets:::formatArg’ 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 eSetFilter : buildGUI: no visible binding for '<<-' assignment to ‘END’ eSetFilter : buildGUI : setFilter: no visible global function definition for ‘tkget’ eSetFilter : buildGUI : setFilter: no visible global function definition for ‘tkcurselection’ eSetFilter : buildGUI : setFilter: no visible global function definition for ‘writeList’ eSetFilter : buildGUI : setFilter: no visible global function definition for ‘tkconfigure’ eSetFilter : buildGUI : cancel: no visible global function definition for ‘tkdestroy’ eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment to ‘END’ eSetFilter : buildGUI : finish: no visible global function definition for ‘tkdestroy’ eSetFilter : buildGUI : viewFilter: no visible global function definition for ‘tkget’ eSetFilter : buildGUI : viewFilter: no visible global function definition for ‘tkcurselection’ eSetFilter : buildGUI : viewFilter: no visible global function definition for ‘tkconfigure’ eSetFilter : buildGUI : viewFilter: no visible global function definition for ‘writeText’ eSetFilter : buildGUI : pickedSel: no visible global function definition for ‘tkconfigure’ eSetFilter : buildGUI : remove: no visible global function definition for ‘tkget’ eSetFilter : buildGUI : remove: no visible global function definition for ‘tkcurselection’ eSetFilter : buildGUI : remove: no visible global function definition for ‘writeList’ eSetFilter : buildGUI : remove: no visible global function definition for ‘tkconfigure’ eSetFilter : buildGUI: no visible global function definition for ‘tktoplevel’ eSetFilter : buildGUI: no visible global function definition for ‘tktitle<-’ eSetFilter : buildGUI: no visible global function definition for ‘tktext’ eSetFilter : buildGUI: no visible global function definition for ‘writeText’ eSetFilter : buildGUI: no visible global function definition for ‘tkconfigure’ eSetFilter : buildGUI: no visible global function definition for ‘tkpack’ eSetFilter : buildGUI: no visible global function definition for ‘tkframe’ eSetFilter : buildGUI: no visible global function definition for ‘tklabel’ eSetFilter : buildGUI: no visible global function definition for ‘makeViewer’ eSetFilter : buildGUI: no visible global function definition for ‘tkbind’ eSetFilter : buildGUI: no visible global function definition for ‘writeList’ eSetFilter : buildGUI: no visible global function definition for ‘tkbutton’ eSetFilter : buildGUI: no visible global function definition for ‘tkwait.window’ eSetFilter : buildGUI: no visible binding for global variable ‘END’ getRdAsText: no visible global function definition for ‘.path.package’ isESet: no visible global function definition for ‘tkmessageBox’ setESetArgs: no visible global function definition for ‘tkdestroy’ setESetArgs : cancel: no visible global function definition for ‘tkdestroy’ setESetArgs : end: no visible global function definition for ‘tkdestroy’ setESetArgs: no visible global function definition for ‘tktoplevel’ setESetArgs: no visible global function definition for ‘tktitle<-’ setESetArgs: no visible global function definition for ‘tkgrid’ setESetArgs: no visible global function definition for ‘tklabel’ setESetArgs: no visible global function definition for ‘tclVar’ setESetArgs: no visible global function definition for ‘tkframe’ setESetArgs: no visible global function definition for ‘makeViewer’ setESetArgs: no visible global function definition for ‘writeText’ setESetArgs: no visible global function definition for ‘tkconfigure’ setESetArgs: no visible global function definition for ‘tkentry’ setESetArgs: no visible global function definition for ‘tkbind’ setESetArgs: no visible global function definition for ‘tkgrid.configure’ setESetArgs: no visible global function definition for ‘tkbutton’ setESetArgs: no visible global function definition for ‘tkpack’ setESetArgs: no visible global function definition for ‘tkwait.window’ setESetArgs: no visible global function definition for ‘tclvalue’ showESet : end: no visible global function definition for ‘tkdestroy’ showESet: no visible global function definition for ‘tktoplevel’ showESet: no visible global function definition for ‘tktitle<-’ showESet: no visible global function definition for ‘tkframe’ showESet: no visible global function definition for ‘makeViewer’ showESet: no visible global function definition for ‘writeList’ showESet: no visible global function definition for ‘tkpack’ showESet: no visible global function definition for ‘tkbutton’ Undefined global functions or variables: .path.package END makeViewer tclVar tclvalue tkbind tkbutton tkconfigure tkcurselection tkdestroy tkentry tkframe tkget tkgrid tkgrid.configure tklabel tkmessageBox tkpack tktext tktitle<- tktoplevel tkwait.window writeList writeText * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/genefilter/libs/genefilter.so’: Found ‘sprintf’, possibly from ‘sprintf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking usage of KIND in Fortran files ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/genefilter.Rcheck/00check.log’ for details.