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This page was generated on 2021-08-02 15:05:27 -0400 (Mon, 02 Aug 2021).

CHECK results for rsbml on tokay2

To the developers/maintainers of the rsbml package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rsbml.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1635/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.50.0  (landing page)
Michael Lawrence
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/rsbml
Branch: RELEASE_3_13
Last Commit: 84b2f61
Last Changed Date: 2021-05-19 11:39:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: rsbml
Version: 2.50.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rsbml.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rsbml_2.50.0.tar.gz
StartedAt: 2021-08-02 05:07:36 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 05:11:41 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 245.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rsbml.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rsbml.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rsbml_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '2.50.0'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 25.2Mb
  sub-directories of 1Mb or more:
    SBML_odeSolver-1.7.0beta   1.6Mb
    libs                      20.9Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/i386/bzip2.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/x64/rsbml.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/i386/iconv.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/x64/rsbml.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/i386/libxml2.dll':
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/x64/rsbml.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/i386/rsbml.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rsbml/libs/x64/rsbml.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
SBML-class 0.35   0.05   16.75
** running examples for arch 'x64' ... 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: 1 WARNING, 8 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.Rcheck/00check.log'
for details.



Installation output

rsbml.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/rsbml_2.50.0.tar.gz && rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rsbml.buildbin-libdir rsbml_2.50.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL rsbml_2.50.0.zip && rm rsbml_2.50.0.tar.gz rsbml_2.50.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  442k  100  442k    0     0  2554k      0 --:--:-- --:--:-- --:--:-- 2573k

install for i386

* installing *source* package 'rsbml' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c StringMap.c -o StringMap.o
In file included from C:/libsbml/i386/include/sbml/common/common.h:111,
                 from StringMap.c:52:
C:/libsbml/i386/include/sbml/util/util.h:343:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
   int finite (double d);
       ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c check.c -o check.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c doc.c -o doc.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c dom.c -o dom.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graph.c -o graph.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c layoutWrappers.cpp -o layoutWrappers.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mathml.c -o mathml.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o rsbml.dll tmp.def StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -LC:/libsbml/i386/bin -lsbml -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
mkdir -p C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/i386
cp C:/libsbml/i386/bin/*.dll C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs//i386
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rsbml'
    finding HTML links ... done
    AlgebraicRule-class                     html  
    AssignmentRule-class                    html  
REDIRECT:topic	 type<-,AssignmentRule-method -> AssignmentRule-class.html [ FAIL ]
REDIRECT:topic	 type<- -> AssignmentRule-class.html [ FAIL ]
REDIRECT:topic	 variable<-,AssignmentRule-method -> AssignmentRule-class.html [ FAIL ]
    BoundingBox-class                       html  
REDIRECT:topic	 position<-,BoundingBox-method -> BoundingBox-class.html [ FAIL ]
REDIRECT:topic	 position<- -> BoundingBox-class.html [ FAIL ]
REDIRECT:topic	 id<-,BoundingBox-method -> BoundingBox-class.html [ FAIL ]
REDIRECT:topic	 dimensions<-,BoundingBox-method -> BoundingBox-class.html [ FAIL ]
    CVTerm-class                            html  
REDIRECT:topic	 biologicalQualifierType<- -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 modelQualifierType<- -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 qualifierType<- -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 resources<- -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 biologicalQualifierType<-,CVTerm-method -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 modelQualifierType<-,CVTerm-method -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 qualifierType<-,CVTerm-method -> CVTerm-class.html [ FAIL ]
REDIRECT:topic	 resources<-,CVTerm-method -> CVTerm-class.html [ FAIL ]
    Compartment-class                       html  
REDIRECT:topic	 outside<-,Compartment-method -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 outside<- -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 size<-,Compartment-method -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 size<- -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 spatialDimensions<-,Compartment-method -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 spatialDimensions<- -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 id<-,Compartment-method -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 name<-,Compartment-method -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 constant<-,Compartment-method -> Compartment-class.html [ FAIL ]
REDIRECT:topic	 units<-,Compartment-method -> Compartment-class.html [ FAIL ]
    CompartmentGlyph-class                  html  
REDIRECT:topic	 compartment<-,CompartmentGlyph-method -> CompartmentGlyph-class.html [ FAIL ]
    CompartmentType-class                   html  
REDIRECT:topic	 id<-,CompartmentType-method -> CompartmentType-class.html [ FAIL ]
REDIRECT:topic	 name<-,CompartmentType-method -> CompartmentType-class.html [ FAIL ]
    CompartmentVolumeRule-class             html  
REDIRECT:topic	 compartment<-,CompartmentVolumeRule-method -> CompartmentVolumeRule-class.html [ FAIL ]
    Constraint-class                        html  
REDIRECT:topic	 math<-,Constraint-method -> Constraint-class.html [ FAIL ]
REDIRECT:topic	 msg<-,Constraint-method -> Constraint-class.html [ FAIL ]
REDIRECT:topic	 msg<- -> Constraint-class.html [ FAIL ]
    CubicBezier-class                       html  
REDIRECT:topic	 basePoint1<-,CubicBezier-method -> CubicBezier-class.html [ FAIL ]
REDIRECT:topic	 basePoint1<- -> CubicBezier-class.html [ FAIL ]
REDIRECT:topic	 basePoint2<-,CubicBezier-method -> CubicBezier-class.html [ FAIL ]
REDIRECT:topic	 basePoint2<- -> CubicBezier-class.html [ FAIL ]
    Curve-class                             html  
REDIRECT:topic	 curveSegments<-,Curve-method -> Curve-class.html [ FAIL ]
REDIRECT:topic	 curveSegments<- -> Curve-class.html [ FAIL ]
    Delay-class                             html  
REDIRECT:topic	 math<-,Delay-method -> Delay-class.html [ FAIL ]
    Describable-class                       html  
    Dimensions-class                        html  
REDIRECT:topic	 depth<-,Dimensions-method -> Dimensions-class.html [ FAIL ]
REDIRECT:topic	 depth<- -> Dimensions-class.html [ FAIL ]
REDIRECT:topic	 height<-,Dimensions-method -> Dimensions-class.html [ FAIL ]
REDIRECT:topic	 height<- -> Dimensions-class.html [ FAIL ]
REDIRECT:topic	 width<-,Dimensions-method -> Dimensions-class.html [ FAIL ]
REDIRECT:topic	 width<- -> Dimensions-class.html [ FAIL ]
    Event-class                             html  
REDIRECT:topic	 eventDelay<-,Event-method -> Event-class.html [ FAIL ]
REDIRECT:topic	 eventDelay<- -> Event-class.html [ FAIL ]
REDIRECT:topic	 eventAssignments<-,Event-method -> Event-class.html [ FAIL ]
REDIRECT:topic	 eventAssignments<- -> Event-class.html [ FAIL ]
REDIRECT:topic	 trigger<-,Event-method -> Event-class.html [ FAIL ]
REDIRECT:topic	 trigger<- -> Event-class.html [ FAIL ]
REDIRECT:topic	 id<-,Event-method -> Event-class.html [ FAIL ]
REDIRECT:topic	 name<-,Event-method -> Event-class.html [ FAIL ]
REDIRECT:topic	 timeUnits<-,Event-method -> Event-class.html [ FAIL ]
    EventAssignment-class                   html  
REDIRECT:topic	 variable<-,EventAssignment-method -> EventAssignment-class.html [ FAIL ]
REDIRECT:topic	 math<-,EventAssignment-method -> EventAssignment-class.html [ FAIL ]
    Experiment-class                        html  
REDIRECT:topic	 design<- -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 design<-,Experiment-method -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 protocol<- -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 protocol<-,Experiment-method -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 reactions<-,Experiment-method -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 result<-,Experiment-method -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 result<- -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 subject<-,Experiment-method -> Experiment-class.html [ FAIL ]
REDIRECT:topic	 subject<- -> Experiment-class.html [ FAIL ]
    FunctionDefinition-class                html  
REDIRECT:topic	 id<-,FunctionDefinition-method -> FunctionDefinition-class.html [ FAIL ]
REDIRECT:topic	 name<-,FunctionDefinition-method -> FunctionDefinition-class.html [ FAIL ]
REDIRECT:topic	 math<-,FunctionDefinition-method -> FunctionDefinition-class.html [ FAIL ]
    GraphicalObject-class                   html  
REDIRECT:topic	 boundingBox<-,GraphicalObject-method -> GraphicalObject-class.html [ FAIL ]
REDIRECT:topic	 boundingBox<- -> GraphicalObject-class.html [ FAIL ]
REDIRECT:topic	 id<-,GraphicalObject-method -> GraphicalObject-class.html [ FAIL ]
    InitialAssignment-class                 html  
REDIRECT:topic	 symbol<- -> InitialAssignment-class.html [ FAIL ]
REDIRECT:topic	 math<-,InitialAssignment-method -> InitialAssignment-class.html [ FAIL ]
REDIRECT:topic	 symbol<-,InitialAssignment-method -> InitialAssignment-class.html [ FAIL ]
    KineticLaw-class                        html  
REDIRECT:topic	 math<-,KineticLaw-method -> KineticLaw-class.html [ FAIL ]
REDIRECT:topic	 math<- -> KineticLaw-class.html [ FAIL ]
REDIRECT:topic	 substanceUnits<-,KineticLaw-method -> KineticLaw-class.html [ FAIL ]
REDIRECT:topic	 substanceUnits<- -> KineticLaw-class.html [ FAIL ]
REDIRECT:topic	 timeUnits<-,KineticLaw-method -> KineticLaw-class.html [ FAIL ]
REDIRECT:topic	 timeUnits<- -> KineticLaw-class.html [ FAIL ]
REDIRECT:topic	 parameters<-,KineticLaw-method -> KineticLaw-class.html [ FAIL ]
    Layout-class                            html  
REDIRECT:topic	 additionalGraphicalObjects<-,Layout-method -> Layout-class.html [ FAIL ]
REDIRECT:topic	 additionalGraphicalObjects<- -> Layout-class.html [ FAIL ]
REDIRECT:topic	 compartmentGlyphs<-,Layout-method -> Layout-class.html [ FAIL ]
REDIRECT:topic	 compartmentGlyphs<- -> Layout-class.html [ FAIL ]
REDIRECT:topic	 dimensions<-,Layout-method -> Layout-class.html [ FAIL ]
REDIRECT:topic	 dimensions<- -> Layout-class.html [ FAIL ]
REDIRECT:topic	 reactionGlyphs<-,Layout-method -> Layout-class.html [ FAIL ]
REDIRECT:topic	 reactionGlyphs<- -> Layout-class.html [ FAIL ]
REDIRECT:topic	 speciesGlyphs<-,Layout-method -> Layout-class.html [ FAIL ]
REDIRECT:topic	 speciesGlyphs<- -> Layout-class.html [ FAIL ]
REDIRECT:topic	 textGlyphs<-,Layout-method -> Layout-class.html [ FAIL ]
REDIRECT:topic	 textGlyphs<- -> Layout-class.html [ FAIL ]
REDIRECT:topic	 id<-,Layout-method -> Layout-class.html [ FAIL ]
    LineSegment-class                       html  
REDIRECT:topic	 end<-,LineSegment-method -> LineSegment-class.html [ FAIL ]
REDIRECT:topic	 end<- -> LineSegment-class.html [ FAIL ]
REDIRECT:topic	 start<-,LineSegment-method -> LineSegment-class.html [ FAIL ]
REDIRECT:topic	 start<- -> LineSegment-class.html [ FAIL ]
    Model-class                             html  
REDIRECT:topic	 compartments<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 compartments<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 events<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 events<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 functionDefinitions<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 functionDefinitions<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 layouts<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 layouts<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 parameters<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 parameters<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 reactions<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 reactions<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 rules<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 rules<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 unitDefinitions<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 unitDefinitions<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 compartmentTypes<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 constraints<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 initialAssignments<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 speciesTypes<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 id<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 name<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 species<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 speciesTypes<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 compartmentTypes<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 constraints<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 initialAssignments<-,Model-method -> Model-class.html [ FAIL ]
REDIRECT:topic	 modelHistory<- -> Model-class.html [ FAIL ]
REDIRECT:topic	 modelHistory<-,Model-method -> Model-class.html [ FAIL ]
    ModelCreator-class                      html  
REDIRECT:topic	 email<- -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 email<-,ModelCreator-method -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 familyName<- -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 familyName<-,ModelCreator-method -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 givenName<- -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 givenName<-,ModelCreator-method -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 organization<- -> ModelCreator-class.html [ FAIL ]
REDIRECT:topic	 organization<-,ModelCreator-method -> ModelCreator-class.html [ FAIL ]
    ModelHistory-class                      html  
REDIRECT:topic	 createdDate<- -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 creators<- -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 modifiedDate<- -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 createdDate<-,ModelHistory,character-method -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 createdDate<-,ModelHistory,POSIXt-method -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 creators<-,ModelHistory-method -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 modifiedDate<-,ModelHistory-method -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 modifiedDate<-,ModelHistory,character-method -> ModelHistory-class.html [ FAIL ]
REDIRECT:topic	 modifiedDate<-,ModelHistory,POSIXt-method -> ModelHistory-class.html [ FAIL ]
    ModifierSpeciesReference-class          html  
    Parameter-class                         html  
REDIRECT:topic	 value<-,Parameter-method -> Parameter-class.html [ FAIL ]
REDIRECT:topic	 value<- -> Parameter-class.html [ FAIL ]
REDIRECT:topic	 id<-,Parameter-method -> Parameter-class.html [ FAIL ]
REDIRECT:topic	 name<-,Parameter-method -> Parameter-class.html [ FAIL ]
REDIRECT:topic	 units<-,Parameter-method -> Parameter-class.html [ FAIL ]
REDIRECT:topic	 constant<-,Parameter-method -> Parameter-class.html [ FAIL ]
    ParameterRule-class                     html  
REDIRECT:topic	 units<-,ParameterRule-method -> ParameterRule-class.html [ FAIL ]
REDIRECT:topic	 name<-,ParameterRule-method -> ParameterRule-class.html [ FAIL ]
REDIRECT:topic	 variable<-,ParameterRule-method -> ParameterRule-class.html [ FAIL ]
REDIRECT:topic	 math<-,ParameterRule-method -> ParameterRule-class.html [ FAIL ]
REDIRECT:topic	 type<-,ParameterRule-method -> ParameterRule-class.html [ FAIL ]
    Point-class                             html  
REDIRECT:topic	 x<-,Point-method -> Point-class.html [ FAIL ]
REDIRECT:topic	 x<- -> Point-class.html [ FAIL ]
REDIRECT:topic	 y<-,Point-method -> Point-class.html [ FAIL ]
REDIRECT:topic	 y<- -> Point-class.html [ FAIL ]
REDIRECT:topic	 z<-,Point-method -> Point-class.html [ FAIL ]
REDIRECT:topic	 z<- -> Point-class.html [ FAIL ]
    RateRule-class                          html  
REDIRECT:topic	 variable<-,RateRule-method -> RateRule-class.html [ FAIL ]
REDIRECT:topic	 variable<- -> RateRule-class.html [ FAIL ]
    Reaction-class                          html  
REDIRECT:topic	 fast<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 fast<- -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 kineticLaw<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 kineticLaw<- -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 modifiers<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 modifiers<- -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 products<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 products<- -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 reactants<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 reactants<- -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 reversible<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 reversible<- -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 id<-,Reaction-method -> Reaction-class.html [ FAIL ]
REDIRECT:topic	 name<-,Reaction-method -> Reaction-class.html [ FAIL ]
    ReactionGlyph-class                     html  
REDIRECT:topic	 glyphCurve<-,ReactionGlyph-method -> ReactionGlyph-class.html [ FAIL ]
REDIRECT:topic	 glyphCurve<- -> ReactionGlyph-class.html [ FAIL ]
REDIRECT:topic	 reaction<-,ReactionGlyph-method -> ReactionGlyph-class.html [ FAIL ]
REDIRECT:topic	 reaction<- -> ReactionGlyph-class.html [ FAIL ]
REDIRECT:topic	 speciesReferenceGlyphs<-,ReactionGlyph-method -> ReactionGlyph-class.html [ FAIL ]
REDIRECT:topic	 speciesReferenceGlyphs<- -> ReactionGlyph-class.html [ FAIL ]
    Rule-class                              html  
REDIRECT:topic	 math<-,Rule-method -> Rule-class.html [ FAIL ]
    SBML-class                              html  
REDIRECT:topic	 level<-,SBML-method -> SBML-class.html [ FAIL ]
REDIRECT:topic	 level<- -> SBML-class.html [ FAIL ]
REDIRECT:topic	 model<-,SBML-method -> SBML-class.html [ FAIL ]
REDIRECT:topic	 model<- -> SBML-class.html [ FAIL ]
REDIRECT:topic	 ver<-,SBML-method -> SBML-class.html [ FAIL ]
REDIRECT:topic	 ver<- -> SBML-class.html [ FAIL ]
    SBMLDocument-class                      html  
    SBMLProblem-class                       html  
    SBMLProblems-class                      html  
    SBase-class                             html  
REDIRECT:topic	 annotation<-,SBase-method -> SBase-class.html [ FAIL ]
REDIRECT:topic	 annotation<- -> SBase-class.html [ FAIL ]
REDIRECT:topic	 metaId<-,SBase-method -> SBase-class.html [ FAIL ]
REDIRECT:topic	 metaId<- -> SBase-class.html [ FAIL ]
REDIRECT:topic	 notes<-,SBase-method -> SBase-class.html [ FAIL ]
REDIRECT:topic	 notes<- -> SBase-class.html [ FAIL ]
REDIRECT:topic	 cvTerms<- -> SBase-class.html [ FAIL ]
REDIRECT:topic	 cvTerms<-,SBase-method -> SBase-class.html [ FAIL ]
REDIRECT:topic	 sboTerm<- -> SBase-class.html [ FAIL ]
REDIRECT:topic	 sboTerm<-,SBase-method -> SBase-class.html [ FAIL ]
    SOSDesign-class                         html  
REDIRECT:topic	 reactions<-,SOSDesign-method -> SOSDesign-class.html [ FAIL ]
    SOSExperiment-class                     html  
    SOSProtocol-class                       html  
    SOSResult-class                         html  
    SOSSubject-class                        html  
    SimpleSpeciesReference-class            html  
REDIRECT:topic	 id<-,SimpleSpeciesReference-method -> SimpleSpeciesReference-class.html [ FAIL ]
REDIRECT:topic	 species<-,SimpleSpeciesReference-method -> SimpleSpeciesReference-class.html [ FAIL ]
    Species-class                           html  
REDIRECT:topic	 boundaryCondition<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 boundaryCondition<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 charge<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 charge<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 compartment<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 compartment<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 constant<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 constant<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 hasOnlySubstanceUnits<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 hasOnlySubstanceUnits<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 initialAmount<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 initialAmount<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 initialConcentration<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 initialConcentration<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 spatialSizeUnits<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 spatialSizeUnits<- -> Species-class.html [ FAIL ]
REDIRECT:topic	 substanceUnits<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 id<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 name<-,Species-method -> Species-class.html [ FAIL ]
REDIRECT:topic	 units<-,Species-method -> Species-class.html [ FAIL ]
    SpeciesConcentrationRule-class          html  
REDIRECT:topic	 species<-,SpeciesConcentrationRule-method -> SpeciesConcentrationRule-class.html [ FAIL ]
    SpeciesGlyph-class                      html  
REDIRECT:topic	 species<-,SpeciesGlyph-method -> SpeciesGlyph-class.html [ FAIL ]
REDIRECT:topic	 species<- -> SpeciesGlyph-class.html [ FAIL ]
    SpeciesReference-class                  html  
REDIRECT:topic	 stoichiometry<-,SpeciesReference-method -> SpeciesReference-class.html [ FAIL ]
REDIRECT:topic	 stoichiometry<- -> SpeciesReference-class.html [ FAIL ]
REDIRECT:topic	 stoichiometryMath<-,SpeciesReference-method -> SpeciesReference-class.html [ FAIL ]
REDIRECT:topic	 stoichiometryMath<- -> SpeciesReference-class.html [ FAIL ]
    SpeciesReferenceGlyph-class             html  
REDIRECT:topic	 role<-,SpeciesReferenceGlyph-method -> SpeciesReferenceGlyph-class.html [ FAIL ]
REDIRECT:topic	 role<- -> SpeciesReferenceGlyph-class.html [ FAIL ]
REDIRECT:topic	 speciesGlyph<-,SpeciesReferenceGlyph-method -> SpeciesReferenceGlyph-class.html [ FAIL ]
REDIRECT:topic	 speciesGlyph<- -> SpeciesReferenceGlyph-class.html [ FAIL ]
REDIRECT:topic	 speciesReference<-,SpeciesReferenceGlyph-method -> SpeciesReferenceGlyph-class.html [ FAIL ]
REDIRECT:topic	 speciesReference<- -> SpeciesReferenceGlyph-class.html [ FAIL ]
REDIRECT:topic	 glyphCurve<-,SpeciesReferenceGlyph-method -> SpeciesReferenceGlyph-class.html [ FAIL ]
    SpeciesType-class                       html  
REDIRECT:topic	 id<-,SpeciesType-method -> SpeciesType-class.html [ FAIL ]
REDIRECT:topic	 name<-,SpeciesType-method -> SpeciesType-class.html [ FAIL ]
    StoichiometryMath-class                 html  
REDIRECT:topic	 math<-,StoichiometryMath-method -> StoichiometryMath-class.html [ FAIL ]
    TextGlyph-class                         html  
REDIRECT:topic	 graphicalObject<-,TextGlyph-method -> TextGlyph-class.html [ FAIL ]
REDIRECT:topic	 graphicalObject<- -> TextGlyph-class.html [ FAIL ]
REDIRECT:topic	 originOfText<-,TextGlyph-method -> TextGlyph-class.html [ FAIL ]
REDIRECT:topic	 originOfText<- -> TextGlyph-class.html [ FAIL ]
REDIRECT:topic	 text<-,TextGlyph-method -> TextGlyph-class.html [ FAIL ]
REDIRECT:topic	 text<- -> TextGlyph-class.html [ FAIL ]
    Trigger-class                           html  
REDIRECT:topic	 math<-,Trigger-method -> Trigger-class.html [ FAIL ]
    Unit-class                              html  
REDIRECT:topic	 exponent<-,Unit-method -> Unit-class.html [ FAIL ]
REDIRECT:topic	 exponent<- -> Unit-class.html [ FAIL ]
REDIRECT:topic	 kind<-,Unit-method -> Unit-class.html [ FAIL ]
REDIRECT:topic	 kind<- -> Unit-class.html [ FAIL ]
REDIRECT:topic	 multiplier<-,Unit-method -> Unit-class.html [ FAIL ]
REDIRECT:topic	 multiplier<- -> Unit-class.html [ FAIL ]
REDIRECT:topic	 offset<-,Unit-method -> Unit-class.html [ FAIL ]
REDIRECT:topic	 offset<- -> Unit-class.html [ FAIL ]
REDIRECT:topic	 unitScale<-,Unit-method -> Unit-class.html [ FAIL ]
REDIRECT:topic	 unitScale<- -> Unit-class.html [ FAIL ]
    UnitDefinition-class                    html  
REDIRECT:topic	 id<-,UnitDefinition-method -> UnitDefinition-class.html [ FAIL ]
REDIRECT:topic	 id<- -> UnitDefinition-class.html [ FAIL ]
REDIRECT:topic	 name<-,UnitDefinition-method -> UnitDefinition-class.html [ FAIL ]
REDIRECT:topic	 name<- -> UnitDefinition-class.html [ FAIL ]
REDIRECT:topic	 units<-,UnitDefinition-method -> UnitDefinition-class.html [ FAIL ]
REDIRECT:topic	 units<- -> UnitDefinition-class.html [ FAIL ]
    math                                    html  
    read                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'rsbml' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c StringMap.c -o StringMap.o
In file included from C:/libsbml/x64/include/sbml/common/common.h:111,
                 from StringMap.c:52:
C:/libsbml/x64/include/sbml/util/util.h:343:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
   int finite (double d);
       ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c check.c -o check.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c doc.c -o doc.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c dom.c -o dom.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graph.c -o graph.o
graph.c: In function 'rsbml_build_graph':
graph.c:55:57: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
     StringMap_put(id_map, CHAR(STRING_ELT(r_nodes, i)), (void *)i);
                                                         ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c layoutWrappers.cpp -o layoutWrappers.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mathml.c -o mathml.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.13-/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o rsbml.dll tmp.def StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -LC:/libsbml/x64/bin -lsbml -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
mkdir -p C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//x64
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rsbml' as rsbml_2.50.0.zip
* DONE (rsbml)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'rsbml' successfully unpacked and MD5 sums checked

Tests output


Example timings

rsbml.Rcheck/examples_i386/rsbml-Ex.timings

nameusersystemelapsed
SBML-class 0.35 0.0516.75
SBMLDocument-class0.400.000.41
read0.30.00.3

rsbml.Rcheck/examples_x64/rsbml-Ex.timings

nameusersystemelapsed
SBML-class0.310.020.84
SBMLDocument-class0.350.000.36
read0.270.000.27