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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
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 1540/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rsbml 2.46.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | ...NOT SUPPORTED... | ||||||||||
| 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 |
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### Running command:
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### 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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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