| NEWS | R Documentation |
Maintainer change.
Changes to be able to build package without libSBML FBC and Groups
plugins. In that case, FBC-constraints and groups in the SBML model will
be ignored. Added functions isAvailableFBCPlugin and
isAvailableGroupsPlugin.
Corrections for CRAN, where && or || encountered arguments of length > 1.
Fix for CRAN issue: 'config' variable 'CPP' is deprecated.
Fix for CRAN issue: too many states (abstraction error?).
Fix for CRAN issue, where a terminating nul character may be written
past the end of the destination in function exportSBML.
Fix for CRAN issue, where example file modified user's home filespace.
Added support for the groups plugin of SBML. Now the subSys
(sub system) is read and written from/to the groups plugin. This is necessary
for some newer models.
Removed bug when trying to write models with NA in, e.g. met_attr.
sybilSBML now supports writing of SBML files.
The new FBC additional package for SBML is now fully integrated.
Urls in NEWS file are now in default style.
gprRules-Slot in modelorg has changed. Thus
readSBMLmod had to be updated.
gprRules-Slot in modelorg has changed. Thus
readSBMLmod had to be updated.
Changed Maintainer.
function openSBMLfile does a normalizePath on its
argument fname
added file CITATION
a minor bugfix in file ‘configure.ac’
function readSBMLmod returns an error if the input file does
not contain a – or contains an empty – listOfReactions,
listOfSpecies or listOfCompartments section.
function getSBMLCompartList() returns also the compartment
names, if given
fixed a bug in file ‘configure.ac’ which occurs when
pkg-config is not used
some improvements in ‘Makevars.win’ suggested by Brian D. Ripley and Uwe Ligges
removed glpkAPI from Suggests in the ‘DESCRIPTION’ file
some small changes in package vignette
some changes in ‘Makevars.win’, so that precompiled libSBML binaries will be packed (for WIndows)
added glpkAPI to Suggests in the ‘DESCRIPTION’ file
changed argument checkrsbml to validateSBML in
function readSBMLmod() and set its default value to
FALSE
added new function validateSBMLdocument()
installation of sybilSBML requires libSBML version 5.6.0 or higher, rsbml is no longer required
added functions
versionLibSBML(),
openSBMLfile(),
closeSBMLfile(),
getSBMLmodel(),
delSBMLmodel(),
getSBMLlevel(),
getSBMLversion(),
validateSBMLdocument(),
getSBMLerrors(),
getSBMLmodId(),
getSBMLmodName(),
getSBMLnumCompart(),
getSBMLnumSpecies(),
getSBMLnumReactions(),
getSBMLunitDefinitionsList(),
getSBMLCompartList(),
getSBMLSpeciesList() and
getSBMLReactionsList()
as low-level interface funcitons to the C-API of libSBML
added classes sbmlPtr and sbmlError
removed old file ‘NEWS.Rd’ from top level directory
updated package vignette
slot rhs of class modelorg is not set
file ‘NEWS’ is now in ‘inst/NEWS.Rd’
removed arguments verboseMode, loglevel, logfile
and logfileEnc from function readSBMLmod; use function
sink instead
fixed a bug in .uglyHack: tries no longer to fix SBMLWarnings,
which is not necessary
.uglyHack uses tempfile() to generate corrected
SBML files
fixed a bug in readSBMLmod(): slot subSys was not of
correct data type in rare cases
better SBML id formatting in readSBMLmod()
compatible with sybil version 0.5.12: replaced SparseM with Matrix
some additions to .uglyHack()
fixed a small bug in readSBMLmod(), when parsing sub systems
fixed a small bug in readSBMLmod() concerning the detection of
gpr rules
fixed a bug in readSBMLmod(): genes from reactions which
are excluded from the model are not read
very minor adjustments in readSBMLmod()
readSBMLmod() will continue reading the model,
if rsbml produces warnings. Check warnings in the log file;
arguments loglevel and logfile in readSBMLmod()
updated documentation
added boolean arguments remMet, contrMet,
singletonMet and deadEndmet to readSBMLmod(),
the two boolen arguments remSingleMet and
constrSingleMet are removed, see help("readSBMLmod")
for details
some small changes according to codetools
slots met_single and react_single of class
modelorg are initialized with NA, not FALSE
new arguments for readSBMLmod():
mergeMet, balanceReact, remUnusedMetReact,
remSingleMet, constrSingleMet and tol.
See help("readSBMLmod") for details
a warning is produced, if a metabolite is used only once in S
readSBMLmod() removes unused metabolites and reactions
(rows and lines without any non-zero entries)
readSBMLmod() merges and balances metabolites as in
readTSVmod() from sybil
fixed a bug in readSBMLmod() concerning the number of
metabolite names and metabolite compartments
added NAMESPACE
new boolean parameter bndCnd in readSBMLmod():
If set to TRUE, external metabolites are those,
having the SBML tag boundaryCondition set to TRUE.
If set to FALSE, external metabolites are recogized via
extMetFlag
usage of class sybilLog in readSBMLmod() with four new
parameters. See help("readSBMLmod") for details.
fixed a bug in readSBMLmod():
if an external metabolite id is removed and it occcurs in
a reaction, that particular reaction is read correctly.
new boolean parameter ignoreNoAn in readSBMLmod():
if set to TRUE, any notes and annotation fields in the
listOfReactions in an SBML file are ignored
(default: TRUE).
unused metabolites having no non-zero entry in S, are removed from S
and the metabolites list in instances of class modelorg
updated documentation
added compatibility to sybil version >= 0.4.1:
slot subSys is now of class matrix
fixed a bug in readSBMLmod(): metablite id's differing
only in the number of consecutive '_' are now recogized
as different metabolite id's.
readSBMLmod() can now read the Yeast model in the file
‘Sc_iND750_GlcMM.xml’ from the Palsson group.
If the SBML file contains reactions with metabolites used as reactands and products at the same time, the stoichiometric coefficient for those metabolites is the sum of reactand and product.
fixed some regular expressions when parsing metabolite names and id's
added argument extMetFlag which is used to identify external
metabolites
reads subsystem information also from annotations
initial public release