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ccb
sybilSBML
Commits
1cd91bdf
Commit
1cd91bdf
authored
Mar 25, 2020
by
Mayo Roettger
Browse files
Fixed function exportSBML for possible overflow in buffer
parent
ac7da9a1
Changes
6
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DESCRIPTION
View file @
1cd91bdf
Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
Version: 3.1.
0
Date: 2020-03-2
3
Version: 3.1.
1
Date: 2020-03-2
5
Authors@R: c(person("Mayo", "Roettger", role = "cre", email = "mayo.roettger@hhu.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut", "ctb")),
person(c("C.", "Jonathan"), "Fritzemeier", role = "ctb", email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
...
...
@@ -17,7 +17,7 @@ License: GPL-3 | file LICENSE
LazyLoad: yes
Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R
uglyHack.R readSBMLmod.R zzz.R
Packaged: 2020-03-2
3
1
2:00
:00 UTC; mayo
Packaged: 2020-03-2
5
1
0:38
:00 UTC; mayo
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut, ctb],
C. Jonathan Fritzemeier [ctb],
...
...
configure
View file @
1cd91bdf
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for sybilSBML 3.1.
0
.
# Generated by GNU Autoconf 2.69 for sybilSBML 3.1.
1
.
#
# Report bugs to <mayo.roettger@hhu.de>.
#
...
...
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME
=
'sybilSBML'
PACKAGE_TARNAME
=
'sybilsbml'
PACKAGE_VERSION
=
'3.1.
0
'
PACKAGE_STRING
=
'sybilSBML 3.1.
0
'
PACKAGE_VERSION
=
'3.1.
1
'
PACKAGE_STRING
=
'sybilSBML 3.1.
1
'
PACKAGE_BUGREPORT
=
'mayo.roettger@hhu.de'
PACKAGE_URL
=
''
...
...
@@ -1243,7 +1243,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat
<<
_ACEOF
\`
configure' configures sybilSBML 3.1.
0
to adapt to many kinds of systems.
\`
configure' configures sybilSBML 3.1.
1
to adapt to many kinds of systems.
Usage:
$0
[OPTION]... [VAR=VALUE]...
...
...
@@ -1305,7 +1305,7 @@ fi
if
test
-n
"
$ac_init_help
"
;
then
case
$ac_init_help
in
short
|
recursive
)
echo
"Configuration of sybilSBML 3.1.
0
:"
;;
short
|
recursive
)
echo
"Configuration of sybilSBML 3.1.
1
:"
;;
esac
cat
<<
\
_ACEOF
...
...
@@ -1392,7 +1392,7 @@ fi
test
-n
"
$ac_init_help
"
&&
exit
$ac_status
if
$ac_init_version
;
then
cat
<<
\
_ACEOF
sybilSBML configure 3.1.
0
sybilSBML configure 3.1.
1
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
...
...
@@ -1761,7 +1761,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by sybilSBML
$as_me
3.1.
0
, which was
It was created by sybilSBML
$as_me
3.1.
1
, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0
$@
...
...
@@ -4254,7 +4254,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by sybilSBML
$as_me
3.1.
0
, which was
This file was extended by sybilSBML
$as_me
3.1.
1
, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
$CONFIG_FILES
...
...
@@ -4316,7 +4316,7 @@ _ACEOF
cat
>>
$CONFIG_STATUS
<<
_ACEOF
|| ac_write_fail=1
ac_cs_config="`
$as_echo
"
$ac_configure_args
" | sed 's/^ //; s/[
\\
""
\`\$
]/
\\\\
&/g'`"
ac_cs_version="
\\
sybilSBML config.status 3.1.
0
sybilSBML config.status 3.1.
1
configured by
$0
, generated by GNU Autoconf 2.69,
with options
\\
"
\$
ac_cs_config
\\
"
...
...
configure.ac
View file @
1cd91bdf
AC_INIT([sybilSBML], [3.1.
0
], [mayo.roettger@hhu.de])
AC_INIT([sybilSBML], [3.1.
1
], [mayo.roettger@hhu.de])
dnl # --------------------------------------------------------------------
dnl # template config.h.in
...
...
inst/NEWS.Rd
View file @
1cd91bdf
...
...
@@ -6,7 +6,7 @@
\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
% ---------------------------------------------------------------------------- %
\section{Changes in version 3.0.4 - 3.1.
0
2020-03-2
3
}{
\section{Changes in version 3.0.4 - 3.1.
1
2020-03-2
4
}{
\itemize{
\item Maintainer change.
\item Changes to be able to build package without libSBML FBC and Groups
...
...
@@ -16,6 +16,8 @@
\item Corrections for CRAN, where && or || encountered arguments of length > 1.
\item Fix for CRAN issue: 'config' variable 'CPP' is deprecated.
\item Fix for CRAN issue: too many states (abstraction error?).
\item Fix for CRAN issue, where a terminating nul character may be written
past the end of the destination in function \code{exportSBML}.
}
}
...
...
man/writeSBML.Rd
View file @
1cd91bdf
...
...
@@ -116,6 +116,7 @@
file <- file.path(dir, "ecoli_core_model.xml")
mod <- readSBMLmod(file, bndCond = FALSE)
writeSBML(mod,level=3,version=1,fbcLevel=2)
unlink("export.xml") # remove created example file
}
\keyword{ IO }
...
...
src/sybilSBML.c
View file @
1cd91bdf
...
...
@@ -2319,7 +2319,7 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
const
double
*
lower_bnd
=
REAL
(
lowbnd
);
const
double
*
upper_bnd
=
REAL
(
uppbnd
);
char
buf
[
2
1
];
//
changed from 20 to 21 to avoid buffer overflow
char
buf
[
2
4
];
//
11 + 10 + 1 (signed, even if not used here) + nul = 23 (24 to be absolutely safe)
// FBC1 FLUXBOUNDS
sprintf
(
buf
,
"LOWER_BOUND%d"
,
i
);
if
(
INTEGER
(
obj_coef
)[
i
]
!=
1
)
...
...
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