rsbml 2.2.1
Michael Lawrence
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/rsbml | | Last Changed Rev: 39231 / Revision: 42512 | | Last Changed Date: 2009-04-29 15:36:12 -0700 (Wed, 29 Apr 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 |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/rsbml.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '2.2.1'
* 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 ... 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'
Error: package/namespace load failed for 'rsbml'
Execution halted
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... WARNING
Error: package/namespace load failed for 'rsbml'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", package),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 files against version 2 parser ... 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 were 3 warnings, see
E:/biocbld/bbs-2.4-bioc/meat/rsbml.Rcheck/00check.log
for details
* Installing *source* package 'rsbml' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-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-2.4-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'rsbml'
Formats: text html latex example chm
AlgebraicRule-class text html latex chm
AssignmentRule-class text html latex chm
BoundingBox-class text html latex chm
CVTerm-class text html latex chm
Compartment-class text html latex chm
CompartmentGlyph-class text html latex chm
CompartmentType-class text html latex chm
CompartmentVolumeRule-class text html latex chm
Constraint-class text html latex chm
CubicBezier-class text html latex chm
Curve-class text html latex chm
Delay-class text html latex chm
Describable-class text html latex chm
Dimensions-class text html latex chm
Event-class text html latex chm
EventAssignment-class text html latex chm
Experiment-class text html latex chm
FunctionDefinition-class text html latex chm
GraphicalObject-class text html latex chm
InitialAssignment-class text html latex chm
KineticLaw-class text html latex chm
Layout-class text html latex chm
LineSegment-class text html latex chm
Model-class text html latex chm
ModelCreator-class text html latex chm
ModelHistory-class text html latex chm
ModifierSpeciesReference-class text html latex chm
Parameter-class text html latex chm
ParameterRule-class text html latex chm
Point-class text html latex chm
RateRule-class text html latex chm
Reaction-class text html latex chm
ReactionGlyph-class text html latex chm
Rule-class text html latex chm
SBML-class text html latex example chm
SBMLDocument-class text html latex example chm
SBMLProblem-class text html latex chm
SBMLProblems-class text html latex chm
SBase-class text html latex chm
SOSDesign-class text html latex chm
SOSExperiment-class text html latex chm
SOSProtocol-class text html latex chm
SOSResult-class text html latex chm
SOSSubject-class text html latex chm
SimpleSpeciesReference-class text html latex chm
Species-class text html latex chm
SpeciesConcentrationRule-class text html latex chm
SpeciesGlyph-class text html latex chm
SpeciesReference-class text html latex chm
SpeciesReferenceGlyph-class text html latex chm
SpeciesType-class text html latex chm
StoichiometryMath-class text html latex chm
TextGlyph-class text html latex chm
Trigger-class text html latex chm
Unit-class text html latex chm
UnitDefinition-class text html latex chm
math text html latex chm
read text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\RSBML~1.RCH\00_PKG~1\rsbml\chm\rsbml.chm
Compile time: 0 minutes, 1 second
59 Topics
1,014 Local links
52 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\RSBML~1.RCH\00_PKG~1\rsbml\chm\rsbml.chm, 85,326 bytes
Compression decreased file by 361,187 bytes.
** building package indices ...
** MD5 sums
* DONE (rsbml)