Fixed function exportSBML for possible overflow in buffer

DESCRIPTION

 Package: sybilSBML
 Type: Package
 Title: SBML Integration in Package 'Sybil'
-Version: 3.1.0
-Date: 2020-03-23
+Version: 3.1.1
+Date: 2020-03-25
 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: 2020-03-23 12:00:00 UTC; mayo
+Packaged: 2020-03-25 10:38:00 UTC; mayo
 Author: Mayo Roettger [cre],
   Gabriel Gelius-Dietrich [aut, ctb],
   C. Jonathan Fritzemeier [ctb],

configure

 #! /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

-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

@@ -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 2020-03-23}{
+\section{Changes in version 3.0.4 - 3.1.1 2020-03-24}{
   \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

@@ -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

@@ -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[21]; // changed from 20 to 21 to avoid buffer overflow
+      char buf[24]; // 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)