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libSBML "5.10.0" |
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make uninstall
behaviorlibsbml.so
, libsbml.dylib
or
libsbml.dll
, depending on your operating system). If a user's
environment includes an old version of this library file, and it is picked
up at run-time instead of the correct library version, linking may fail
with mysterious errors about undefined symbols. Users and developers are
cautioned to make sure that their installations have matched versions of
libSBML components and are free of older versions that may be picked up
inadvertently.
"/unix/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found"
.)
The solution is to preload the system stdc++ library before invoking
MATLAB. You can accomplish this by setting the Linux environment variable
LD_PRELOAD
to the path of the system's libstdc++
library file. This will take the form of the following:
export LD_PRELOAD=/path/to/system/libstdc++for sh-based shells such as Bash, or
setenv LD_PRELOAD /path/to/system/libstdc++for csh-based shells.
free()
function call to free memory allocated and returned by libSBML.
Without the ability to use free()
to free the string returned
by libSBML, the calling application will leak memory. An example
of typical code where one would want to free the returned by libSBML
is the following:
char * formula = SBML_formulaToString(astNode); /* ... do some work with formula here ... */ free(formula);
To cope with this issue, beginning with version 4.2, libSBML provides a
special function for this situation: util_free()
.
In the C-like, text-based, formula expression syntax supported by libSBML
and used in SBML Level 1, four constants are reserved words:
true
, false
, exponentiale
and
pi
. Most of them will not easily lead to a name collision,
but unfortunately, the character sequence pi
is also
sometimes used as a species identifier by biological modelers (e.g., to use
"Pi" to represent a phosphate ion). If the string "pi
" or
"Pi
" appears in a text string passed to a libSBML method that
interprets formulas, it will be interpreted as the mathematical constant
π (pi). For example, the expression 2 * Pi will yield
<math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <cn type="integer"> 2 </cn> <pi/> </apply> </math>
This problem exists for all four of the constants mentioned above, but is most commonly encountered in the context of "pi". Currently, the only ways to avoid this problem are either to avoid using the strings "pi" and "Pi" in this context, or to avoid using the text-string expressions altogether and instead use ASTs. All libSBML methods that accept text-string mathematical formulas have variants that accept ASTs instead.
The different parsers supported by libSBML (Xerces, Expat, libxml2) behave slightly differently when reading files, and the differences are difficult for libSBML to hide. The following are the differences of which we are currently aware:
n:attribute
, where n
is a namespace prefix
that is not defined, will be silently ignored. As a result, libSBML cannot
catch and report this error when libSBML has been configured with this
version of libxml2. We know of no workaround at this time if you are using
a system with libxml2 2.6.16, except to compile your own copy of libxml2 or
use another parser library. (Incredibly enough, libxml 2.6.16 built from
original sources on a Mac does report the error. The only
explanation is that that Apple is shipping a modified version of libxml
2.6.16 in versions of the operating system up through 10.5.8.)
<notes>
and
<annotation>
elements).xmlns=" "
, with
a space character). Versions of libxml prior 2.7.7 will report this as an
invalid or undefined XML namespace, but in fact a namespace URI containing
a single space is valid (albeit not a very useful one). This highlights
another issue: different versions of the underlying XML parsers may behave
differently in the face of unusual (though not necessarily illegal) inputs.
checking for Expat version >= 1.95.8...
*** The Expat header file (version 2.1.0) does not match
*** the Expat library found (version 2.0.1).
. However if the gnumake
./configure, make & make install is used to build the Expat library the
header mismatch is avoided.
string
. Unfortunately,
given the way that all three XML parser libraries (libxml2, Expat, and
Xerces) work, it is impossible for libSBML to ever report this error
directly. The kinds of SBML input that would lead to a failure of this
validation rule cause the XML parsers to report overly general errors of
the "XML content not well formed" variety, and libSBML cannot determine the
true root cause. As a result, libSBML cannot detect when rule #10312 is
breached.
make uninstall
behavior The libSBML make uninstall
command on Linux, Mac OS, Cygwin,
and Solaris only knows about the features most recently configured
into libSBML. If you run configure
, then make
install
, then run configure
again with different
options, and finally try make uninstall
, the result will be to
attempt removing the files implied by the most recent run of
configure
, not the files installed by the
original make install
.
setLevelAndVersion()
on the class
SBMLDocument
performs conversion between versions and levels
of SBML (to the extent possible within technical and practical limits).
However, conversion to/from SBML Level 1 Version 1 is not
supported.
SBMLError
and XMLError
will be set to either
0
or the value of the maximum unsigned long integer
representable on the platform where libSBML is running. The probability
that a true line or column number in a real-life SBML model would
equal this value is vanishingly small; thus, if an application encounters
these values in an XMLError object, it can assume no valid line/column
number could be provided by libSBML in that situation.
libsbml_wrap.cpp
in the respective language binding's
subdirectory (e.g., src/bindings/java
), sometimes in
combination with other files, depending on the language in question. If you
obtained your copy of libSBML as a distribution archive (e.g., from SourceForge), this
file will already be present in the distribution. If, instead, you obtained
your copy of libSBML from the SVN source tree, you will need to have SWIG
available on your system in order to regenerate the
libsbml_wrap.cpp
file. In both cases, all things should work
fine.
If you modify the libSBML source files yourself (and in
particular, files upon which the SWIG binding code depends), the makefile
rules should always automatically cause the appropriate
libsbml_wrap.cpp
files to be recreated. However,
sometimes the makefile rules do not regenerate the wrapper files
when they should. This happens very rarely, and under conditions that the
libSBML developers have had a very hard time reproducing consistently. In
some versions of libSBML, it seemed to happen slightly more often under
cygwin.
When a version skew occurs with the language binding wrapper files, either the compilation phase or the link phase will fail, often with cryptic and mysterious errors about missing methods. Often it is possible to guess that the language bindings are the problem from the error messages.
The solution is to delete the libsbml_wrap.cpp
file(s),
and when the Java interface is involved, also delete the
src/bindings/java/java-files
subdirectory. Re-running make
will regenerate the files and (if the problem was indeed due to the SWIG
binding files being out of date) compilation/linking will work.
We emphasize that this problem should not affect normal users of libSBML, only the libSBML developers and those are are venturing into developing new features in libSBML.
libsbml_wrap.cpp
in the respective language binding's
subdirectory (e.g., src/bindings/java
).
In some cases, the libsbml_wrap.cpp
file produced by SWIG
will cause compilers to issue warnings during compilation. The following is
an example from the Ruby language bindings compiled on Mac OS X
10.9 using plain make
:
libsbml_wrap.cpp:4802:13: warning: unused variable 'r' [-Wunused-variable] VALUE r = Qnil; ^ libsbml_wrap.cpp:4957:9: warning: unused variable 'type' [-Wunused-variable] VALUE type = TYPE(obj); ^
The warnings are about harmless issues. Unfortunately, there is very little that libSBML can do about these warnings, since they come from code auto-generated by SWIG.
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