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Package 438/516HostnameOS / ArchBUILDCHECKBUILD BIN
rsbml 2.12.0
Michael Lawrence
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/rsbml
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  ERROR  skipped  skipped 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: rsbml
Version: 2.12.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch rsbml_2.12.0.tar.gz
StartedAt: 2012-01-09 05:29:46 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 05:30:47 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 60.8 seconds
RetCode: 0
Status:  OK  
CheckDir: rsbml.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/rsbml.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'rsbml' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs                       5.0Mb
    SBML_odeSolver-1.7.0beta   1.6Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

rsbml.Rcheck/00install.out:

* installing *source* package 'rsbml' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c StringMap.c -o StringMap.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/common.h:28,
                 from StringMap.c:52:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c check.c -o check.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from check.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from check.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c doc.c -o doc.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from doc.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from doc.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c dom.c -o dom.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from dom.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from dom.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from graph.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from graph.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from init.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from init.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from io.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from io.c:1:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c mathml.c -o mathml.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-config.h:62,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/common/sbmlfwd.h:35,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:28,
                 from rsbml.h:4,
                 from mathml.c:3:
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:56:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61:0: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70:0: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294:0,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLError.h:580,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLDocument.h:237,
                 from C:/libSBML-3.3.2-expat/win32/include/sbml/SBMLTypes.h:30,
                 from rsbml.h:4,
                 from mathml.c:3:
C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLExtern.h:65:0: warning: ignoring #pragma warning 
mathml.c: In function 'rmathml_SEXP':
mathml.c:56:12: warning: unused variable 'closure'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g -D_R_=1 -DUSE_R=1 -IC:/libSBML-3.3.2-expat/win32/include -IC:/libSBML-3.3.2-expat/win32/include/expat -IE:/biocbld/BBS-2˜1.9-B/R/include -DLIBSBML3         -O3 -Wall  -std=gnu99 -mtune=core2 -c simulate.c -o simulate.o
gcc -shared -s -static-libgcc -o rsbml.dll tmp.def StringMap.o check.o doc.o dom.o graph.o init.o io.o mathml.o simulate.o -LC:/libSBML-3.3.2-expat/win32/bin -lsbml -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/rsbml.Rcheck/rsbml/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'quick-start.Rnw' 
** testing if installed package can be loaded

* DONE (rsbml)

rsbml.Rcheck/rsbml-Ex.timings:

nameusersystemelapsed
SBML-class0.250.000.35
SBMLDocument-class0.520.000.51
read0.360.000.36