Michael Lawrence
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/rsbml |
| Branch: RELEASE_3_6 |
| Last Commit: b9f662d |
| Last Changed Date: 2017-10-30 12:39:21 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:18:58 -0400 (Thu, 12 Apr 2018).
| Package 1217/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rsbml 2.36.0 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: rsbml |
| Version: 2.36.0 |
| Command: rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/rsbml_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir --merge-multiarch rsbml_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL rsbml_2.36.0.zip && rm rsbml_2.36.0.tar.gz rsbml_2.36.0.zip |
| StartedAt: 2018-04-11 18:16:30 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:22:38 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 367.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/rsbml_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir --merge-multiarch rsbml_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL rsbml_2.36.0.zip && rm rsbml_2.36.0.tar.gz rsbml_2.36.0.zip
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install for i386
* installing *source* package 'rsbml' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c StringMap.c -o StringMap.o
In file included from C:/libsbml/i386/include/sbml/common/common.h:111:0,
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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c check.c -o check.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c doc.c -o doc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c dom.c -o dom.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -mtune=generic -c layoutWrappers.cpp -o layoutWrappers.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c mathml.c -o mathml.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/i386/include -IC:/libsbml/i386/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c simulate.c -o simulate.o
C:/Rtools/mingw_32/bin/g++ -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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
mkdir -p C:/Users/biocbuild/bbs-3.6-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/i386
cp C:/libsbml/i386/bin/*.dll C:/Users/biocbuild/bbs-3.6-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//i386
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/i386
** R
** inst
** preparing 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
In R CMD INSTALL
install for x64
* installing *source* package 'rsbml' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c StringMap.c -o StringMap.o
In file included from C:/libsbml/x64/include/sbml/common/common.h:111:0,
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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c check.c -o check.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c doc.c -o doc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c dom.c -o dom.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -mtune=generic -c layoutWrappers.cpp -o layoutWrappers.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c mathml.c -o mathml.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c simulate.c -o simulate.o
C:/Rtools/mingw_64/bin/g++ -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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
mkdir -p C:/Users/biocbuild/bbs-3.6-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll C:/Users/biocbuild/bbs-3.6-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//x64
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rsbml' as rsbml_2.36.0.zip
* DONE (rsbml)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'rsbml' successfully unpacked and MD5 sums checked
In R CMD INSTALL