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ccb
sybilSBML
Commits
76d49fc0
Commit
76d49fc0
authored
Mar 10, 2020
by
Mayo Roettger
Browse files
Corrections for CRAN issues
parent
3e988bb4
Changes
12
Hide whitespace changes
Inline
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DESCRIPTION
View file @
76d49fc0
Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
Version: 3.0.
7
Date: 20
19-08-02
Version: 3.0.
8
Date: 20
20-03-10
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: 20
19-08-02 15:05:2
0 UTC; mayo
Packaged: 20
20-03-10 09:00:0
0 UTC; mayo
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut, ctb],
C. Jonathan Fritzemeier [ctb],
...
...
R/readSBMLmod.R
View file @
76d49fc0
...
...
@@ -973,16 +973,15 @@ else {
# if there were fbcgprRules or notes with gpr rules,
# create reaction x nGene matrix, with TRUE for respective genes for each reaction
if
(
isTRUE
(
hasNotes
)
||
!
is.null
(
fbcgprRules
)
)
{
if
(
isTRUE
(
hasNotes
)
||
!
is.null
(
fbcgprRules
)
)
{
message
(
"GPR mapping ... "
,
appendLF
=
FALSE
)
# Vector with all gene names != "":
#allGenes <- unique(allGenes)
#allGenesTMP <- unique(allGenes)
allGenesTMP
<-
unique
(
unlist
(
genes
))
temp
<-
nchar
(
allGenesTMP
)
allGenes
<-
allGenesTMP
[
which
(
temp
!=
0
)]
# reaction x nGene matrix initialization with FALSE:
rxnGeneMat
<-
Matrix
::
Matrix
(
FALSE
,
nrow
=
numreact
,
ncol
=
length
(
allGenes
),
...
...
@@ -990,7 +989,7 @@ else {
for
(
i
in
1
:
numreact
)
{
# if genes list element i has only 1 element and that element is not equal ""
if
(
(
length
(
genes
[[
i
]]
==
1
))
&&
(
genes
[[
i
]]
!=
""
)
)
{
if
(
(
length
(
genes
[[
i
]]
==
1
))
&&
all
(
genes
[[
i
]]
!=
""
)
)
{
geneInd
<-
match
(
genes
[[
i
]],
allGenes
)
# find gene in allGenes
# Mark which genes are used in reaction with TRUE
rxnGeneMat
[
i
,
geneInd
]
<-
TRUE
...
...
R/sybilSBML.R
View file @
76d49fc0
...
...
@@ -362,15 +362,15 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
# test if Matrix has no double values
if
(
!
all
(
S
(
morg
)
==
floor
(
S
(
morg
)))
)
warning
(
"Level 1 does not support double values"
)
fbcLevel
=
0
if
(
version
!=
2
)
{
warning
(
"just Level 1 Version 2 will be supported"
)
version
=
2
}
}
else
if
(
level
==
2
)
if
(
version
!=
2
)
{
warning
(
"just Level 1 Version 2 will be supported"
)
version
=
2
}
}
else
if
(
level
==
2
)
{
fbcLevel
=
0
if
(
version
>
5
)
if
(
version
>
5
)
{
warning
(
"Level 2 Version 5 will be supported"
)
version
=
5
...
...
@@ -380,16 +380,19 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
warning
(
"Level 2 Version 1 will be supported"
)
version
=
1
}
}
else
if
(
level
==
3
)
{
if
(
fbcLevel
>
2
)
fbcLevel
=
2
if
(
version
!=
1
)
{
print
(
"Level 3 Version 1 will be supported"
)
version
=
1
}
}
else
{
}
else
if
(
level
==
3
)
{
if
(
fbcLevel
>
2
)
{
print
(
"FBC level 2 will be supported"
)
fbcLevel
=
2
}
if
(
version
!=
1
)
{
print
(
"Level 3 Version 1 will be supported"
)
version
=
1
}
}
else
{
stop
(
" Support just for Level 1,2 and 3 \n"
)
}
...
...
@@ -630,6 +633,7 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
as.integer
(
obj_coef
(
morg
)),
as.character
(
newsubS
),
subSysGroups
,
as.character
(
names
(
subSysGroups
)),
as.character
(
deformatGene
(
gpr
(
morg
))),
as.numeric
(
shrinkMatrix
(
morg
,
j
=
1
:
react_num
(
morg
))),
mod_notes
,
...
...
configure
View file @
76d49fc0
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.
7
.
# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.
8
.
#
# Report bugs to <mayo.roettger@hhu.de>.
#
...
...
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME
=
'sybilSBML'
PACKAGE_TARNAME
=
'sybilsbml'
PACKAGE_VERSION
=
'3.0.
7
'
PACKAGE_STRING
=
'sybilSBML 3.0.
7
'
PACKAGE_VERSION
=
'3.0.
8
'
PACKAGE_STRING
=
'sybilSBML 3.0.
8
'
PACKAGE_BUGREPORT
=
'mayo.roettger@hhu.de'
PACKAGE_URL
=
''
...
...
@@ -1241,7 +1241,7 @@ 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 3.0.
7
to adapt to many kinds of systems.
\`
configure' configures sybilSBML 3.0.
8
to adapt to many kinds of systems.
Usage:
$0
[OPTION]... [VAR=VALUE]...
...
...
@@ -1303,7 +1303,7 @@ fi
if
test
-n
"
$ac_init_help
"
;
then
case
$ac_init_help
in
short
|
recursive
)
echo
"Configuration of sybilSBML 3.0.
7
:"
;;
short
|
recursive
)
echo
"Configuration of sybilSBML 3.0.
8
:"
;;
esac
cat
<<
\
_ACEOF
...
...
@@ -1390,7 +1390,7 @@ fi
test
-n
"
$ac_init_help
"
&&
exit
$ac_status
if
$ac_init_version
;
then
cat
<<
\
_ACEOF
sybilSBML configure 3.0.
7
sybilSBML configure 3.0.
8
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
...
...
@@ -1759,7 +1759,7 @@ 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
3.0.
7
, which was
It was created by sybilSBML
$as_me
3.0.
8
, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0
$@
...
...
@@ -2118,7 +2118,7 @@ if test -z "${R_HOME}"; then
fi
CC
=
`
"
${
R_HOME
}
/bin/R"
CMD config CC
`
CPP
=
`
"
${
R_HOME
}
/bin/R"
CMD config CPP
`
#
CPP=`"${R_HOME}/bin/R" CMD config CPP`
CFLAGS
=
`
"
${
R_HOME
}
/bin/R"
CMD config CFLAGS
`
CPPFLAGS
=
`
"
${
R_HOME
}
/bin/R"
CMD config CPPFLAGS
`
ac_ext
=
c
...
...
@@ -4249,7 +4249,7 @@ cat >>$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
3.0.
7
, which was
This file was extended by sybilSBML
$as_me
3.0.
8
, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
$CONFIG_FILES
...
...
@@ -4311,7 +4311,7 @@ _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 3.0.
7
sybilSBML config.status 3.0.
8
configured by
$0
, generated by GNU Autoconf 2.69,
with options
\\
"
\$
ac_cs_config
\\
"
...
...
configure.ac
View file @
76d49fc0
AC_INIT([sybilSBML], [3.0.
7
], [mayo.roettger@hhu.de])
AC_INIT([sybilSBML], [3.0.
8
], [mayo.roettger@hhu.de])
dnl # --------------------------------------------------------------------
dnl # global (environment) variables
...
...
@@ -21,7 +21,7 @@ fi
dnl # GNU R default settings
CC=`"${R_HOME}/bin/R" CMD config CC`
CPP=`"${R_HOME}/bin/R" CMD config CPP`
#
CPP=`"${R_HOME}/bin/R" CMD config CPP`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
AC_PROG_CC
...
...
inst/NEWS.Rd
View file @
76d49fc0
...
...
@@ -6,15 +6,19 @@
\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
% ---------------------------------------------------------------------------- %
\section{Changes in version 3.0.4 - 3.0.
7
20
19-08-02
}{
\section{Changes in version 3.0.4 - 3.0.
8
20
20-03-10
}{
\itemize{
\item Maintainer change.
\item Changes to be able to build package without libSBML FBC and Groups
plugins. In that case, FBC-constraints and groups in the SBML model will
be ignored. Added functions \code{isAvailableFBCPlugin} and
\code{isAvailableGroupsPlugin}.
\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?).
}
}
% ---------------------------------------------------------------------------- %
\section{Changes in version 3.0.3 2018-01-02}{
\itemize{
...
...
@@ -23,6 +27,7 @@
for some newer models.
}
}
% ---------------------------------------------------------------------------- %
\section{Changes in version 3.0.2 2017-10-24}{
\itemize{
...
...
src/Makevars
deleted
100644 → 0
View file @
3e988bb4
PKG_CFLAGS=
PKG_CPPFLAGS=-I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml
PKG_LIBS= -L/usr/local/lib -L/usr/lib -L/usr/lib64 -lsbml
src/config.h
deleted
100644 → 0
View file @
3e988bb4
/* src/config.h. Generated from config.h.in by configure. */
/* src/config.h.in. Generated from configure.ac by autoheader. */
/* Define to 1 if you have the `FbcReactionPlugin_getLowerFluxBound' function.
*/
#define HAVE_FBCREACTIONPLUGIN_GETLOWERFLUXBOUND 1
/* define if FBC plugin is available */
#define HAVE_FBC_PLUGIN 1
/* Define to 1 if you have the `GeneProductAssociation_setAssociation'
function. */
#define HAVE_GENEPRODUCTASSOCIATION_SETASSOCIATION 1
/* define if Groups plugin is available */
#define HAVE_GROUPS_PLUGIN 1
/* Define to 1 if you have the <inttypes.h> header file. */
#define HAVE_INTTYPES_H 1
/* Define to 1 if you have the `sbml' library (-lsbml). */
#define HAVE_LIBSBML 1
/* Define to 1 if you have the <memory.h> header file. */
#define HAVE_MEMORY_H 1
/* Define to 1 if you have the `SBase_getPlugin' function. */
#define HAVE_SBASE_GETPLUGIN 1
/* Define to 1 if you have the `SBMLExtensionRegistry_getRegisteredPackages'
function. */
#define HAVE_SBMLEXTENSIONREGISTRY_GETREGISTEREDPACKAGES 1
/* Define to 1 if you have the <sbml/packages/fbc/common/FbcExtensionTypes.h>
header file. */
#define HAVE_SBML_PACKAGES_FBC_COMMON_FBCEXTENSIONTYPES_H 1
/* Define to 1 if you have the
<sbml/packages/groups/common/GroupsExtensionTypes.h> header file. */
#define HAVE_SBML_PACKAGES_GROUPS_COMMON_GROUPSEXTENSIONTYPES_H 1
/* Define to 1 if you have the <stdint.h> header file. */
#define HAVE_STDINT_H 1
/* Define to 1 if you have the <stdlib.h> header file. */
#define HAVE_STDLIB_H 1
/* Define to 1 if you have the <strings.h> header file. */
#define HAVE_STRINGS_H 1
/* Define to 1 if you have the <string.h> header file. */
#define HAVE_STRING_H 1
/* Define to 1 if you have the <sys/stat.h> header file. */
#define HAVE_SYS_STAT_H 1
/* Define to 1 if you have the <sys/types.h> header file. */
#define HAVE_SYS_TYPES_H 1
/* Define to 1 if you have the <unistd.h> header file. */
#define HAVE_UNISTD_H 1
/* Define to the address where bug reports for this package should be sent. */
#define PACKAGE_BUGREPORT "mayo.roettger@hhu.de"
/* Define to the full name of this package. */
#define PACKAGE_NAME "sybilSBML"
/* Define to the full name and version of this package. */
#define PACKAGE_STRING "sybilSBML 3.0.6"
/* Define to the one symbol short name of this package. */
#define PACKAGE_TARNAME "sybilsbml"
/* Define to the home page for this package. */
#define PACKAGE_URL ""
/* Define to the version of this package. */
#define PACKAGE_VERSION "3.0.6"
/* Define to 1 if you have the ANSI C header files. */
#define STDC_HEADERS 1
src/init.c
View file @
76d49fc0
...
...
@@ -55,7 +55,7 @@ static const R_CallMethodDef callMethods[] = {
{
"getSBMLCompartList"
,
(
DL_FUNC
)
&
getSBMLCompartList
,
1
},
{
"getSBMLSpeciesList"
,
(
DL_FUNC
)
&
getSBMLSpeciesList
,
1
},
{
"getSBMLReactionsList"
,
(
DL_FUNC
)
&
getSBMLReactionsList
,
1
},
{
"exportSBML"
,
(
DL_FUNC
)
&
exportSBML
,
3
4
},
{
"exportSBML"
,
(
DL_FUNC
)
&
exportSBML
,
3
5
},
{
"getSBMLFbcversion"
,
(
DL_FUNC
)
&
getSBMLFbcversion
,
1
},
{
"isAvailableFbcPlugin"
,
(
DL_FUNC
)
&
isAvailableFbcPlugin
,
0
},
{
"isAvailableGroupsPlugin"
,
(
DL_FUNC
)
&
isAvailableGroupsPlugin
,
0
},
...
...
src/sybilSBML.c
View file @
76d49fc0
...
...
@@ -1682,12 +1682,12 @@ void ParseModtoAnno (SBase_t* comp , char* Mannocopy)
SEXP
exportSBML
(
SEXP
version
,
SEXP
level
,
SEXP
FbcLevel
,
SEXP
filename
,
SEXP
sybil_max
,
SEXP
mod_desc
,
SEXP
mod_name
,
SEXP
mod_compart
,
SEXP
met_id
,
SEXP
met_name
,
SEXP
met_comp
,
SEXP
met_form
,
SEXP
met_charge
,
SEXP
react_id
,
SEXP
react_name
,
SEXP
react_rev
,
SEXP
lowbnd
,
SEXP
uppbnd
,
SEXP
obj_coef
,
SEXP
subSys
,
SEXP
subSysGroups
,
SEXP
gpr
,
SEXP
SMatrix
,
SEXP
mod_notes
,
SEXP
mod_anno
,
SEXP
com_notes
,
SEXP
com_anno
,
SEXP
met_notes
,
SEXP
met_anno
,
SEXP
met_bnd
,
SEXP
react_notes
,
SEXP
react_anno
,
SEXP
ex_react
,
SEXP
allgenes
)
SEXP
exportSBML
(
SEXP
version
,
SEXP
level
,
SEXP
FbcLevel
,
SEXP
filename
,
SEXP
sybil_max
,
SEXP
mod_desc
,
SEXP
mod_name
,
SEXP
mod_compart
,
SEXP
met_id
,
SEXP
met_name
,
SEXP
met_comp
,
SEXP
met_form
,
SEXP
met_charge
,
SEXP
react_id
,
SEXP
react_name
,
SEXP
react_rev
,
SEXP
lowbnd
,
SEXP
uppbnd
,
SEXP
obj_coef
,
SEXP
subSys
,
SEXP
subSysGroups
,
SEXP
subSysGroupsNames
,
SEXP
gpr
,
SEXP
SMatrix
,
SEXP
mod_notes
,
SEXP
mod_anno
,
SEXP
com_notes
,
SEXP
com_anno
,
SEXP
met_notes
,
SEXP
met_anno
,
SEXP
met_bnd
,
SEXP
react_notes
,
SEXP
react_anno
,
SEXP
ex_react
,
SEXP
allgenes
)
{
#if defined(HAVE_FBC_PLUGIN) && defined(HAVE_GROUPS_PLUGIN)
//Var
a
ibles from R
//Vari
a
bles from R
const
char
*
fname
=
CHAR
(
STRING_ELT
(
filename
,
0
));
const
char
*
model_desc
=
CHAR
(
STRING_ELT
(
mod_desc
,
0
));
//unused:
const char* model_desc = CHAR(STRING_ELT(mod_desc, 0));
const
char
*
model_name
=
CHAR
(
STRING_ELT
(
mod_name
,
0
));
int
SBMLlevel
=
INTEGER
(
level
)[
0
];
...
...
@@ -1698,7 +1698,7 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
double
sybilmin
=
sybilmax
*
(
-
1
);
// variable FBC
XMLNamespaces_t
*
fbc
;
//currently unused:
XMLNamespaces_t * fbc;
SBMLNamespaces_t
*
sbmlns
;
FluxBound_t
*
fluxBound
;
Objective_t
*
objective
;
...
...
@@ -1712,13 +1712,13 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
// Variable inital
SBMLDocument_t
*
sbmlDoc
;
SBMLDocument_t
*
sbmlDoc
=
NULL
;
Model_t
*
model
;
XMLNamespaces_t
*
xmlns
;
UnitDefinition_t
*
unitdef
;
Unit_t
*
unit
;
//currently unused:
UnitDefinition_t* unitdef;
//currently unused:
Unit_t* unit;
Species_t
*
sp
;
Reaction_t
*
reaction
;
...
...
@@ -1727,7 +1727,7 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
KineticLaw_t
*
kl
;
Parameter_t
*
para
;
// ASTNode_t* flux;
// ASTNode_t* flux;
ASTNode_t
*
astMath
;
//ASTNode_t* ast;
//char* mathXMLString;
...
...
@@ -2300,6 +2300,7 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
}
// ENDE REACTION
if
(
SBMLfbcversion
==
1
)
{
...
...
@@ -2358,30 +2359,31 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
}
}
/* add subsystem as groups if fbc is >= 2 */
if
(
SBMLfbcversion
>=
2
){
if
(
!
Rf_isNull
(
subSysGroups
)){
GroupsModelPlugin_t
*
groupsPlug
=
NULL
;
GroupsModelPlugin_t
*
groupsPlug
=
NULL
;
groupsPlug
=
(
GroupsModelPlugin_t
*
)
SBase_getPlugin
((
SBase_t
*
)(
model
),
"groups"
);
for
(
int
i
=
0
;
i
<
Rf_length
(
subSysGroups
);
i
++
){
Group_t
*
newGroup
=
GroupsModelPlugin_createGroup
(
groupsPlug
);
Group_setKindAsString
(
newGroup
,
"partonomy"
);
Group_setName
(
newGroup
,
CHAR
(
STRING_ELT
(
Rf_getAttrib
(
subSysGroups
,
R_
Names
Symbol
)
,
i
)));
Group_setName
(
newGroup
,
CHAR
(
STRING_ELT
(
subSysGroupsNames
,
i
)));
SBase_setSBOTerm
((
SBase_t
*
)
newGroup
,
0000633
);
for
(
int
j
=
0
;
j
<
Rf_length
(
VECTOR_ELT
(
subSysGroups
,
i
));
j
++
){
Member_t
*
newMember
=
Member_create
(
SBMLlevel
,
SBMLversion
,
SBMLgroupsversion
);
Member_setIdRef
(
newMember
,
CHAR
(
STRING_ELT
(
VECTOR_ELT
(
subSysGroups
,
i
),
j
)));
Group_addMember
(
newGroup
,
newMember
);
}
//GroupsModelPlugin_addGroup(groupsPlug, newGroup);
}
}
}
// write SBML file
int
result
=
writeSBML
(
sbmlDoc
,
fname
);
SEXP
out
=
R_NilValue
;
...
...
@@ -2390,7 +2392,7 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
#else
SEXP
out
=
Rf_ScalarLogical
(
0
);
/* no success */
#endif
//UNPROTECT(1);
return
out
;
}
...
...
src/sybilSBML.h
View file @
76d49fc0
...
...
@@ -112,7 +112,7 @@ SEXP getSBMLGroupsList(SEXP sbmlmod);
SEXP
getSBMLReactionsList
(
SEXP
sbmlmod
);
/* export Modelorg to SBML*/
SEXP
exportSBML
(
SEXP
version
,
SEXP
level
,
SEXP
FbcLevel
,
SEXP
filename
,
SEXP
sybil_max
,
SEXP
mod_desc
,
SEXP
mod_name
,
SEXP
mod_compart
,
SEXP
met_id
,
SEXP
met_name
,
SEXP
met_comp
,
SEXP
met_form
,
SEXP
met_charge
,
SEXP
react_id
,
SEXP
react_name
,
SEXP
react_rev
,
SEXP
lowbnd
,
SEXP
uppbnd
,
SEXP
obj_coef
,
SEXP
subSys
,
SEXP
subSysGroups
,
SEXP
gpr
,
SEXP
SMatrix
,
SEXP
mod_notes
,
SEXP
mod_anno
,
SEXP
com_notes
,
SEXP
com_anno
,
SEXP
met_notes
,
SEXP
met_anno
,
SEXP
met_bnd
,
SEXP
react_notes
,
SEXP
react_anno
,
SEXP
ex_react
,
SEXP
allgenes
);
SEXP
exportSBML
(
SEXP
version
,
SEXP
level
,
SEXP
FbcLevel
,
SEXP
filename
,
SEXP
sybil_max
,
SEXP
mod_desc
,
SEXP
mod_name
,
SEXP
mod_compart
,
SEXP
met_id
,
SEXP
met_name
,
SEXP
met_comp
,
SEXP
met_form
,
SEXP
met_charge
,
SEXP
react_id
,
SEXP
react_name
,
SEXP
react_rev
,
SEXP
lowbnd
,
SEXP
uppbnd
,
SEXP
obj_coef
,
SEXP
subSys
,
SEXP
subSysGroups
,
SEXP
subSysGroupsNames
,
SEXP
gpr
,
SEXP
SMatrix
,
SEXP
mod_notes
,
SEXP
mod_anno
,
SEXP
com_notes
,
SEXP
com_anno
,
SEXP
met_notes
,
SEXP
met_anno
,
SEXP
met_bnd
,
SEXP
react_notes
,
SEXP
react_anno
,
SEXP
ex_react
,
SEXP
allgenes
);
/* check, if FBC-Plugin is available */
SEXP
isAvailableFbcPlugin
();
...
...
src/symbols.rds
View file @
76d49fc0
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