| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:48 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the rsbml package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1715/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rsbml 2.57.0 (landing page) Michael Lawrence
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: rsbml |
| Version: 2.57.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rsbml |
| StartedAt: 2022-12-28 15:30:34 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 15:31:31 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 57.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rsbml
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'rsbml' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/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: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]
369 | int finite (double d);
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check.c -o check.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c doc.c -o doc.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dom.c -o dom.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/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]
55 | StringMap_put(id_map, CHAR(STRING_ELT(r_nodes, i)), (void *)i);
| ^
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c layoutWrappers.cpp -o layoutWrappers.o
In file included from C:/libsbml/x64/include/sbml/FunctionDefinition.h:136,
from C:/libsbml/x64/include/sbml/SBMLTransforms.h:52,
from C:/libsbml/x64/include/sbml/SBMLDocument.h:302,
from C:/libsbml/x64/include/sbml/SBMLTypes.h:43,
from rsbml.h:1,
from layoutWrappers.cpp:1:
C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
111 | struct IdEq : public std::unary_function<SBase*, bool>
| ^~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
from C:/libsbml/x64/include/sbml/util/util.h:49,
from C:/libsbml/x64/include/sbml/xml/XMLError.h:344,
from C:/libsbml/x64/include/sbml/SBMLError.h:461,
from C:/libsbml/x64/include/sbml/SBMLDocument.h:299:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mathml.c -o mathml.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulate.c -o simulate.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
mkdir -p F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs//x64
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (rsbml)