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Bioconductor Changlog.
Tue, 13 Oct 2009
rsbml
Fix errors in man pages.
rsbml
- Fix configuration issues with SOSlib (not finding libsbml).
- Add "describe" method for generating short character descriptions of
objects in the DOM. The 'show' method cats this to the console.
- Remove a bunch of generated files that should not have been in svn.
- Fix handling of MathML and(), xor(), etc (only for libsbml 3.2.0)
rsbml
Crude hack to get SBML ODE solver to look in lib64 for sundials libraries.
rsbml
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
rsbml
removed quotes from do.call
rsbml
Do not use any extern declarations for the StringMap stuff.
rsbml
Disable graphviz and grace support in SBML ODE Solver.
Try again to disable arithmetic compiler on the Mac.
Disable arithmetic compiler on WIN32 and DARWIN.
Regenerated configure with new macros.
Synchronize with latest CVS snapshot of SBML ODE Solver.
Delete the .deps subdirectory of examples in SBML_odeSolver.
Removing support for Windows.
No longer attempt to set edgemode slot in the graph object (was
causing a seg fault on Windows).
Add -DLIBSBML3 to PKG_CPPFLAGS for Windows (so we always require
libsbml 3.0 or higher on Windows).
rsbml
supported again on wellington
rsbml
Rework checking. All documents are checked after reading, so the 'check'
argument is removed. It is replaced with 'quiet' which indicates whether
the errors/warnings should be emitted. rsbml_check now has a 'verbose =
FALSE' argument, which indicates whether libsbml 'info' and 'warning'
messages are output to console (via message()). Libsbml errors now
become R warnings and libsbml fatals now become R errors.
Also fix some bugs in parsing libsbml3 constructs like the model
history. Thought I had fixed these before, not sure what happened.
rsbml
Add curto purine metabolism model. Remove sample3-layout.xml, as it does
not seem useful.
Simulation support via SOSLib integration.
Complete support for (SBML subset of) MathML to R expressions.
Object-oriented error reporting mechanism.
This is the first beta of rsbml 2.0.
rsbml
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
rsbml
Removed prohibition on Mac OS X support since the Mac OS X machine now has libsbml installed in the i386 architecture.
rsbml
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
rsbml
Remove these two temporary files from the repository.
Missing updates.
SOSLib support now only built by default if prequisites are met. If explicitly requested and prequisites fail, we generate an error. Explicit disabling is also supported.
Give informative error when simulate() is called on a build without SOSLib support.
Fix rsbml_graph so that it does not use the deprecated edgemode slot.
rsbml
Add NAMESPACE, bump version.
Add convenience rsbml_check method on SBML DOM.
Doc cleanup for new Rd parser.
Store logicals as logicals, not integers.
Fix minor issue in MathML handling.
rsbml
Fix vignette for API changes.
Update documentation for API changes in the rsbml_read and rsbml_check.
commented out the sixth chunk in the vignette so at least it builds
rsbml
Adding support for windows.
Import symbols from 'stats' package to avoid masking.
rsbml
Add wrappers for simulate. Other tweaks and fixes.
modified one test
Don't initialize eventDelay to NULL in Event. Remove legacy signal
constructor method to fix vignette.
Tweak configure script, fix error throwing, update vignette.
Bump version to get this in the repository.
rsbml
Bumping version.
rsbml
Support for libsbml 3.0. Documentation forthcoming.
rsbml
Rip out 'odeSolver' and 'examples' from SOS lib build to simplify things.
rsbml
Remove stray debugging command (which somehow broke linking too).
rsbml
Add some missing files for libsbml 3.0.
rsbml
Some tweaks to the configure script (SOSLib integration). Introduce SOSLIB_CONFIGURE_ARGS to pass arguments to the SOSLib configure script.
Since there is no recent release of SOSLib, we are bundling the source
with rsbml and building it during configure time. This is still somewhat
limited, in that it only supports libsbml compiled with libxml2 as the
XML backend (the default on Linux and OS X) and it also assumes SUNDIALS
is installed in the /usr prefix. Will add an option to override that.
Fix MathML output (actually set the names of the nodes). Thought it was working before, but had a bug in my tests.
Add rsbml_graph method for dom object, for convenience. Will soon rewrite rsbml_graph in R for better maintainability.
Fix vignette for change to rsbml_read signature.
Add real support for R -> MathML translation. Add 'dom' argument to rsbml_read for convenience.
rsbml
Import/export SBase fields for Models. Also avoid conflict with R macro
SET_ATTR (changed to SET_XML_ATTR).
Add missing documentation. Also make Model inherit from SBase and add
convenience methods for setting dates using POSIXt objects.