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INSTALL report for rsbml on tokay2

This page was generated on 2020-10-17 11:57:42 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rsbml PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1540/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.46.0
Michael Lawrence
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rsbml
Branch: RELEASE_3_11
Last Commit: bc64b06
Last Changed Date: 2020-04-28 18:33:15 -0400 (Tue, 28 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64 ...NOT SUPPORTED...

Summary

Package: rsbml
Version: 2.46.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/rsbml_2.46.0.tar.gz && rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rsbml.buildbin-libdir rsbml_2.46.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL rsbml_2.46.0.zip && rm rsbml_2.46.0.tar.gz rsbml_2.46.0.zip
StartedAt: 2020-10-16 18:16:29 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:20:01 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 211.4 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/rsbml_2.46.0.tar.gz && rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rsbml.buildbin-libdir rsbml_2.46.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL rsbml_2.46.0.zip && rm rsbml_2.46.0.tar.gz rsbml_2.46.0.zip
###
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100  442k  100  442k    0     0  7914k      0 --:--:-- --:--:-- --:--:-- 8843k

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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/bin/i386 -lR
mkdir -p C:/Users/biocbuild/bbs-3.11-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/i386
cp C:/libsbml/i386/bin/*.dll C:/Users/biocbuild/bbs-3.11-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs//i386
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'type' in package 'rsbml'
Creating a new generic function for 'type<-' in package 'rsbml'
** help
*** installing help indices
  converting help for package 'rsbml'
    finding HTML links ... done
    AlgebraicRule-class                     html  
    AssignmentRule-class                    html  
    BoundingBox-class                       html  
    CVTerm-class                            html  
    Compartment-class                       html  
    CompartmentGlyph-class                  html  
    CompartmentType-class                   html  
    CompartmentVolumeRule-class             html  
    Constraint-class                        html  
    CubicBezier-class                       html  
    Curve-class                             html  
    Delay-class                             html  
    Describable-class                       html  
    Dimensions-class                        html  
    Event-class                             html  
    EventAssignment-class                   html  
    Experiment-class                        html  
    FunctionDefinition-class                html  
    GraphicalObject-class                   html  
    InitialAssignment-class                 html  
    KineticLaw-class                        html  
    Layout-class                            html  
    LineSegment-class                       html  
    Model-class                             html  
    ModelCreator-class                      html  
    ModelHistory-class                      html  
    ModifierSpeciesReference-class          html  
    Parameter-class                         html  
    ParameterRule-class                     html  
    Point-class                             html  
    RateRule-class                          html  
    Reaction-class                          html  
    ReactionGlyph-class                     html  
    Rule-class                              html  
    SBML-class                              html  
    SBMLDocument-class                      html  
    SBMLProblem-class                       html  
    SBMLProblems-class                      html  
    SBase-class                             html  
    SOSDesign-class                         html  
    SOSExperiment-class                     html  
    SOSProtocol-class                       html  
    SOSResult-class                         html  
    SOSSubject-class                        html  
    SimpleSpeciesReference-class            html  
    Species-class                           html  
    SpeciesConcentrationRule-class          html  
    SpeciesGlyph-class                      html  
    SpeciesReference-class                  html  
    SpeciesReferenceGlyph-class             html  
    SpeciesType-class                       html  
    StoichiometryMath-class                 html  
    TextGlyph-class                         html  
    Trigger-class                           html  
    Unit-class                              html  
    UnitDefinition-class                    html  
    math                                    html  
    read                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for 'type'
Warning: multiple methods tables found for 'type<-'
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for 'type'
Warning: multiple methods tables found for 'type<-'
** 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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/bin/x64 -lR
mkdir -p C:/Users/biocbuild/bbs-3.11-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll C:/Users/biocbuild/bbs-3.11-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//x64
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
** testing if installed package can be loaded
Warning: multiple methods tables found for 'type'
Warning: multiple methods tables found for 'type<-'
* MD5 sums
packaged installation of 'rsbml' as rsbml_2.46.0.zip
* DONE (rsbml)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'rsbml' successfully unpacked and MD5 sums checked