CHECK report for rsbml on merida1
This page was generated on 2020-04-15 12:35:15 -0400 (Wed, 15 Apr 2020).
rsbml 2.44.0
Michael Lawrence
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/rsbml |
| Branch: RELEASE_3_10 |
| Last Commit: 6e45be1 |
| Last Changed Date: 2019-10-29 13:07:53 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rsbml.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rsbml_2.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rsbml.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rsbml/DESCRIPTION’ ... OK
* this is package ‘rsbml’ version ‘2.44.0’
* 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 ‘rsbml’ can be installed ... WARNING
Found the following significant warnings:
Warning: multiple methods tables found for ‘type’
Warning: multiple methods tables found for ‘type<-’
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/rsbml.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ... NOTE
Warning: multiple methods tables found for ‘type’
Warning: multiple methods tables found for ‘type<-’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
as.character.SBML as.character.SBMLDocument
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 ... OK
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
‘/Users/biocbuild/bbs-3.10-bioc/meat/rsbml.Rcheck/00check.log’
for details.
Installation output
rsbml.Rcheck/00install.out
Tests output
Example timings
rsbml.Rcheck/rsbml-Ex.timings