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Package 296/354HostnameOS / ArchBUILDCHECKBUILD BIN
rsbml 2.5.0
Michael Lawrence
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rsbml
Last Changed Rev: 42686 / Revision: 43434
Last Changed Date: 2009-10-27 16:45:24 -0700 (Tue, 27 Oct 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: rsbml
Version: 2.5.0
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes rsbml_2.5.0.tar.gz
StartedAt: 2009-12-07 18:22:27 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 18:23:39 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 71.8 seconds
RetCode: 0
Status: WARNINGS
CheckDir: rsbml.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/rsbml.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '2.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rsbml' can be installed ... OK
* 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 name space can be loaded with stated dependencies ... WARNING
Loading required package: methods
Error in paste(normalizePath(file.path(libname, pkgname, "libs")), file.path(Sys.getenv("R_HOME"),  : 
  could not find function "normalizePath"
Error: .onLoad failed in 'loadNamespace' for 'rsbml'
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.6-bioc/meat/rsbml.Rcheck/00check.log
for details

rsbml.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'rsbml' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c StringMap.c -o StringMap.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c check.c -o check.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c doc.c -o doc.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c dom.c -o dom.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c graph.c -o graph.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c init.c -o init.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c io.c -o io.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c mathml.c -o mathml.o
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/common/libsbml-version.h:28,
                 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: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:61: warning: ignoring #pragma warning 
C:/libSBML-3.3.2-expat/win32/include/sbml/common/extern.h:70: warning: ignoring #pragma warning 
In file included from C:/libSBML-3.3.2-expat/win32/include/sbml/xml/XMLError.h:294,
                 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: warning: ignoring #pragma warning 
mathml.c: In function 'rmathml_SEXP':
mathml.c:56: warning: unused variable 'closure'
gcc -I"e:/biocbld/bbs-2.6-bioc/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-2.6-bioc/R/include -DLIBSBML3       -O3 -Wall  -std=gnu99 -c simulate.c -o simulate.o
gcc -shared -s -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-2.6-bioc/R/bin -lR
  ... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (rsbml)