Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:08:33 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for rsbml on riesling1


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 1668/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.53.0  (landing page)
Michael Lawrence
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/rsbml
git_branch: master
git_last_commit: 91a9078
git_last_commit_date: 2021-10-26 11:51:36 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: rsbml
Version: 2.53.0
Command: rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir rsbml_2.53.0.tar.gz
StartedAt: 2022-03-17 21:35:40 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 21:37:25 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 104.2 seconds
RetCode: 0
Status:   OK  
PackageFile: rsbml_2.53.0.zip
PackageFileSize: 7.06 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir rsbml_2.53.0.tar.gz
###
##############################################################################
##############################################################################


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

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


** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c StringMap.c -o StringMap.o
In file included from C:/libsbml/x64/include/sbml/common/common.h:117,
                 from StringMap.c:52:
C:/libsbml/x64/include/sbml/util/util.h:369:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
   int finite (double d);
       ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c check.c -o check.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c doc.c -o doc.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dom.c -o dom.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c io.c -o io.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c layoutWrappers.cpp -o layoutWrappers.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c mathml.c -o mathml.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -ID:/biocbuild/bbs-3.15-bioc/R/include -DLIBSBML3    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
mkdir -p D:/biocbuild/bbs-3.15-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll D:/biocbuild/bbs-3.15-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs//x64
installing to D:/biocbuild/bbs-3.15-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/x64
** 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  
    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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'rsbml' as rsbml_2.53.0.zip
* DONE (rsbml)