rsbml 2.32.0
Michael Lawrence
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/rsbml | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | 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 http://172.29.0.3/BBS/3.4/bioc/src/contrib/rsbml_2.32.0.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir --merge-multiarch rsbml_2.32.0.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL rsbml_2.32.0.zip && rm rsbml_2.32.0.tar.gz rsbml_2.32.0.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˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -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˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c check.c -o check.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c doc.c -o doc.o
doc.c: In function 'rsbml_build_doc_simple_species_reference':
doc.c:453:8: warning: unused variable 'tmp' [-Wunused-variable]
SEXP tmp = GET_SLOT(r_simple_species_reference, install("species"));
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dom.c -o dom.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c graph.c -o graph.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -mtune=core2 -c layoutWrappers.cpp -o layoutWrappers.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mathml.c -o mathml.o
mathml.c: In function 'rmathml_SEXP':
mathml.c:56:12: warning: unused variable 'closure' [-Wunused-variable]
SEXP closure, pargs;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -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˜1.4-B/R/bin/i386 -lR
mkdir -p C:/Users/biocbuild/bbs-3.4-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/i386
cp C:/libsbml/i386/bin/*.dll C:/Users/biocbuild/bbs-3.4-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//i386
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
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˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -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˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c check.c -o check.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c doc.c -o doc.o
doc.c: In function 'rsbml_build_doc_simple_species_reference':
doc.c:453:8: warning: unused variable 'tmp' [-Wunused-variable]
SEXP tmp = GET_SLOT(r_simple_species_reference, install("species"));
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dom.c -o dom.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c graph.c -o graph.o
graph.c: In function 'rsbml_build_graph':
graph.c:57:57: 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˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -mtune=core2 -c layoutWrappers.cpp -o layoutWrappers.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mathml.c -o mathml.o
mathml.c: In function 'rmathml_SEXP':
mathml.c:56:12: warning: unused variable 'closure' [-Wunused-variable]
SEXP closure, pargs;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-B/R/include -DLIBSBML3 -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -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˜1.4-B/R/bin/x64 -lR
mkdir -p C:/Users/biocbuild/bbs-3.4-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll C:/Users/biocbuild/bbs-3.4-bioc/meat/rsbml.buildbin-libdir/rsbml/libs//x64
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/rsbml.buildbin-libdir/rsbml/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rsbml' as rsbml_2.32.0.zip
* DONE (rsbml)
* installing to library 'C:/Users/biocbuild/bbs-3.4-bioc/R/library'
package 'rsbml' successfully unpacked and MD5 sums checked