############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rsbml.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rsbml_2.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/rsbml.Rcheck' * using R version 4.3.1 (2023-06-16 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'rsbml/DESCRIPTION' ... OK * this is package 'rsbml' version '2.58.0' * 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 ... 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 whether package 'rsbml' can be installed ... WARNING Found the following significant warnings: C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] See 'F:/biocbuild/bbs-3.17-bioc/meat/rsbml.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 12.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 12.2.0' * checking installed package size ... NOTE installed size is 19.5Mb sub-directories of 1Mb or more: SBML_odeSolver-1.7.0beta 1.6Mb libs 16.3Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'BiocGenerics' 'utils' A package should be listed in only one of these fields. * checking top-level files ... NOTE Found a 'configure.in' file: 'configure.ac' has long been preferred. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'utils' All declared Imports should be used. Package in Depends field not imported from: 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: 'graph:::listLen' 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 .simulate.SBML: no visible global function definition for 'tail' .simulate.SBML: no visible global function definition for 'new' .simulate.SBML: no visible global function definition for 'is' .simulate.SBML : : no visible global function definition for 'head' .simulate.SBML: no visible global function definition for 'slotNames' .simulate.SBML: no visible binding for global variable 'new' as.ts,SOSResult: no visible global function definition for 'ts' coerce,SBMLProblems-character: no visible binding for global variable 'as' describe,CompartmentGlyph: no visible global function definition for 'callNextMethod' describe,CubicBezier: no visible global function definition for 'callNextMethod' describe,ReactionGlyph: no visible global function definition for 'callNextMethod' describe,SpeciesGlyph: no visible global function definition for 'callNextMethod' describe,SpeciesReference: no visible global function definition for 'callNextMethod' describe,SpeciesReferenceGlyph: no visible global function definition for 'callNextMethod' describe,TextGlyph: no visible global function definition for 'callNextMethod' end<-,LineSegment: no visible binding for global variable 'object' glyphCurve<-,ReactionGlyph: no visible global function definition for 'new' glyphCurve<-,SpeciesReferenceGlyph: no visible global function definition for 'new' kineticLaw<-,Reaction: no visible global function definition for 'new' rsbml_graph,Model: no visible global function definition for 'new' rsbml_problems,SBMLDocument : makeProblems : : no visible binding for global variable 'new' rsbml_problems,SBMLDocument: no visible binding for global variable 'new' show,SBMLProblem: no visible global function definition for 'as' simulate,SBMLDocument: no visible global function definition for 'tail' simulate,SBMLDocument: no visible global function definition for 'new' simulate,SBMLDocument: no visible global function definition for 'is' simulate,SBMLDocument : : no visible global function definition for 'head' simulate,SBMLDocument: no visible global function definition for 'slotNames' simulate,SBMLDocument: no visible binding for global variable 'new' simulate,SOSExperiment: no visible global function definition for 'slotNames' simulate,SOSExperiment : : no visible global function definition for 'slot' Undefined global functions or variables: as callNextMethod head is new object slot slotNames tail ts Consider adding importFrom("methods", "as", "callNextMethod", "is", "new", "slot", "slotNames") importFrom("stats", "ts") importFrom("utils", "head", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) SBML-class.Rd:74: Escaped LaTeX specials: \_ checkRd: (-1) SBML-class.Rd:76: Escaped LaTeX specials: \_ checkRd: (-1) SBML-class.Rd:78: Escaped LaTeX specials: \_ checkRd: (-1) SBML-class.Rd:80: Escaped LaTeX specials: \_ checkRd: (-1) SBML-class.Rd:82: Escaped LaTeX specials: \_ checkRd: (-1) SBMLDocument-class.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) SBMLDocument-class.Rd:36: Escaped LaTeX specials: \_ checkRd: (-1) SBMLDocument-class.Rd:38: Escaped LaTeX specials: \_ checkRd: (-1) SBMLDocument-class.Rd:40: Escaped LaTeX specials: \_ checkRd: (-1) SBMLDocument-class.Rd:42: Escaped LaTeX specials: \_ checkRd: (-1) SBMLDocument-class.Rd:44: Escaped LaTeX specials: \_ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'asMath' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 shell scripts ... 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 include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/rsbml/libs/x64/rsbml.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 8 NOTEs See 'F:/biocbuild/bbs-3.17-bioc/meat/rsbml.Rcheck/00check.log' for details.