From 88d556670c69b459dae215b7c2ceb36126853ad8 Mon Sep 17 00:00:00 2001
From: Mayo Roettger <mayo.roettger@uni-duesseldorf.de>
Date: Thu, 26 Mar 2020 17:00:04 +0100
Subject: [PATCH] Fix for example file written into user's home filespace
---
DESCRIPTION | 6 +++---
configure | 18 +++++++++---------
configure.ac | 2 +-
inst/NEWS.Rd | 4 +++-
man/writeSBML.Rd | 4 ++--
src/symbols.rds | Bin 2899 -> 2890 bytes
6 files changed, 18 insertions(+), 16 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index f51d6bd..32ceb2f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybilSBML
Type: Package
Title: 'SBML' Integration in Package 'Sybil'
-Version: 3.1.1
-Date: 2020-03-25
+Version: 3.1.2
+Date: 2020-03-26
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: 2020-03-25 10:38:00 UTC; mayo
+Packaged: 2020-03-26 15:45:00 UTC; mayo
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut, ctb],
C. Jonathan Fritzemeier [ctb],
diff --git a/configure b/configure
index 72fb6f1..367f60d 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 3.1.1.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.1.2.
#
# Report bugs to <mayo.roettger@hhu.de>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='sybilSBML'
PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='3.1.1'
-PACKAGE_STRING='sybilSBML 3.1.1'
+PACKAGE_VERSION='3.1.2'
+PACKAGE_STRING='sybilSBML 3.1.2'
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 3.1.1 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.1.2 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 $ac_init_help in
- short | recursive ) echo "Configuration of sybilSBML 3.1.1:";;
+ short | recursive ) echo "Configuration of sybilSBML 3.1.2:";;
esac
cat <<\_ACEOF
@@ -1392,7 +1392,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-sybilSBML configure 3.1.1
+sybilSBML configure 3.1.2
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 3.1.1, which was
+It was created by sybilSBML $as_me 3.1.2, 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 3.1.1, which was
+This file was extended by sybilSBML $as_me 3.1.2, 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 3.1.1
+sybilSBML config.status 3.1.2
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index b105b8d..2de6803 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([sybilSBML], [3.1.1], [mayo.roettger@hhu.de])
+AC_INIT([sybilSBML], [3.1.2], [mayo.roettger@hhu.de])
dnl # --------------------------------------------------------------------
dnl # template config.h.in
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 8bb4a15..fc85384 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 - 3.1.1 2020-03-24}{
+\section{Changes in version 3.0.4 - 3.1.2 2020-03-26}{
\itemize{
\item Maintainer change.
\item Changes to be able to build package without libSBML FBC and Groups
@@ -18,6 +18,8 @@
\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}.
+ \item Fix for CRAN issue, where example file was written into user's home
+ filespace.
}
}
diff --git a/man/writeSBML.Rd b/man/writeSBML.Rd
index 6833147..ec3ef4f 100644
--- a/man/writeSBML.Rd
+++ b/man/writeSBML.Rd
@@ -115,8 +115,8 @@
dir <- system.file(package = "sybilSBML", "extdata")
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
+ # write SBML file to tempdir():
+ writeSBML(mod,level=3,version=1,fbcLevel=2,filename=file.path(tempdir(), "export.xml"))
}
\keyword{ IO }
diff --git a/src/symbols.rds b/src/symbols.rds
index 6c50fca8d9500273b256cbe890ebb2d111bb0c44..ddeee5ade278be28c7cf156abc93ab2abca5c95f 100644
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