diff --git a/DESCRIPTION b/DESCRIPTION index 57f3938d67973197b589b77164f52b1b92f3d344..0acff548773dcda1c18d1d558f15486fdcee5646 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ 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], diff --git a/configure b/configure index 6c660c64991c4b1c19d3d5ea69f266c6119a46fc..72fb6f148f0b9cfa80349c37b9de2f8910403ee0 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /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\\" diff --git a/configure.ac b/configure.ac index f589d1c3777aa261e1a8fe517190a5c3f63bb88a..b105b8d29b647e58058fd59abb88a70e86a6bb26 100644 --- a/configure.ac +++ b/configure.ac @@ -1,4 +1,4 @@ -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 diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index eeeea6a5d96713d02f4b3ac83587710a3cbf0ec5..8bb4a15b8b47e1753e1557ca882e27056503e94c 100644 --- a/inst/NEWS.Rd +++ b/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}. } } diff --git a/man/writeSBML.Rd b/man/writeSBML.Rd index 268d20fcc5ad578c881ee429c5810e4e760a5d73..68331471eab51983d1058ea580b6751d057856b1 100644 --- a/man/writeSBML.Rd +++ b/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 } diff --git a/src/sybilSBML.c b/src/sybilSBML.c index 1011b2b5ee830251e2591dccb922118e66922e7d..7c847cc002befb8f6ea487a4af7397fcbcfd6a39 100644 --- a/src/sybilSBML.c +++ b/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)