[BioC] rsbml package installation error

[Stefan Gries]

Dear list,

for several days now I've been experiencing an odd error when trying to 
install the rsbml package (be it using biocLite("rsbml") or a downloaded 
package source via install.packages() ). I mainly find it odd because I 
couldn't find any other mentions of this error occurring in internet 
searches.

First of all: I'm running R 3.0.1 and Bioconductor 2.12 with all base 
packages up to date on Linux Mint 15 (64-bit), with libsbml5, libxml2 
and SUNDIALS (and probably whatever package else is necessary) installed.

I'll post a full installation log here, although I suppose the primarily 
relevant lines are the first two error messages that occur when g++ 
tries to compile the ASTIndexNameNode.cpp file: first, obviously, the 
'class' keyword isn't recognised properly, as the C file's source code 
looks quite all right (although I won't make any guarantees for the 
definitions and includes). Second, the libsbml namespace (as far as I 
know, ASTNode_t is from libsbml, correct me if I'm wrong) seems not to 
be imported correctly, as said type isn't found. Anyhow: any help in 
figuring out how to solve this mess would be gladly appreciated.

 > biocLite("rsbml")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
Installing package(s) 'rsbml'
trying URL 
'http://bioconductor.org/packages/2.12/bioc/src/contrib/rsbml_2.18.0.tar.gz'
Content type 'application/x-gzip' length 629617 bytes (614 Kb)
opened URL
==================================================
downloaded 614 Kb

* installing *source* package ‘rsbml’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... yes
configure: === Begin local SOSLib build ===
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc accepts -fpic... yes
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for autoconf... /usr/bin/autoconf
checking for aclocal... /usr/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for SBML... yes
checking for correct functioning of SBML... yes
checking for SUNDIALS Library headers... yes
checking for SUNDIALS Library... yes
checking correct functioning of SUNDIALS... yes
checking correct functioning of GRACE... yes
checking for isnan in -lm... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/libODES.pc
config.status: creating src/sbmlsolver/config.h
config.status: executing depfiles commands

Build Settings for SBML_odeSolver v1.7.0beta:
----------------------------------
host type = linux
shared lib extension = so
install dir = /tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/local
CC = gcc
CFLAGS = -g -O2 -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990
LDFLAGS =
LIBS = -lm -ldl -lm -lstdc++
SBML Library = yes
CFLAGS = -I/usr/include/libxml2
LDFLAGS =
LIBS = -lz -lbz2 -lsbml -lstdc++ -lm -lxml2
SUNDIALS Library = yes
CFLAGS = -I/usr/local/include
LDFLAGS = -L/usr/local/lib
LIBS = -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial
GRACE = yes
CFLAGS = -Ino/include
LDFLAGS = -Lno/lib
LIBS = -lgrace_np
GRAPHVIZ = no
GRAPHVIZ functionality will NOT be installed!

NOTE:
SOSlib has the following dependencies:
(*) SUNDIALS suite v2.3.0
(*) libSBML v3.0.2 or CVS

Making all in src
make[1]: Entering directory 
`/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSolver-1.7.0beta/src'
make[2]: Entering directory 
`/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSolver-1.7.0beta'
make[2]: Leaving directory 
`/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSolver-1.7.0beta'
g++ -DHAVE_CONFIG_H -I. -I../src/sbmlsolver -I/usr/local/include 
-I/usr/include/libxml2 -Ino/include -I. -fPIC -g -O2 -MT 
ASTIndexNameNode.o -MD -MP -MF .deps/ASTIndexNameNode.Tpo -c -o 
ASTIndexNameNode.o ASTIndexNameNode.cpp
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:12:1: error: expected class-name before 
'{' token
sbmlsolver/ASTIndexNameNode.h:38:20: error: 'ASTNode_t' does not name a type
sbmlsolver/ASTIndexNameNode.h:41:44: error: 'ASTNode_t' was not declared 
in this scope
sbmlsolver/ASTIndexNameNode.h:41:44: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:41:55: error: expected primary-expression 
before ')' token
sbmlsolver/ASTIndexNameNode.h:44:50: error: 'ASTNode_t' was not declared 
in this scope
sbmlsolver/ASTIndexNameNode.h:44:50: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:44:61: error: expected primary-expression 
before ')' token
sbmlsolver/ASTIndexNameNode.h:47:52: error: 'ASTNode_t' was not declared 
in this scope
sbmlsolver/ASTIndexNameNode.h:47:52: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:47:63: error: expected primary-expression 
before ')' token
sbmlsolver/ASTIndexNameNode.h:50:42: error: variable or field 
'ASTNode_setIndex' declared void
sbmlsolver/ASTIndexNameNode.h:50:42: error: 'ASTNode_t' was not declared 
in this scope
sbmlsolver/ASTIndexNameNode.h:50:42: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:50:53: error: expected primary-expression 
before ',' token
sbmlsolver/ASTIndexNameNode.h:50:55: error: expected primary-expression 
before 'unsigned'
sbmlsolver/ASTIndexNameNode.h:53:51: error: 'ASTNode_t' was not declared 
in this scope
sbmlsolver/ASTIndexNameNode.h:53:51: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:53:62: error: expected primary-expression 
before ')' token
sbmlsolver/ASTIndexNameNode.h:56:41: error: variable or field 
'ASTNode_setData' declared void
sbmlsolver/ASTIndexNameNode.h:56:41: error: 'ASTNode_t' was not declared 
in this scope
sbmlsolver/ASTIndexNameNode.h:56:41: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:56:52: error: expected primary-expression 
before ')' token
ASTIndexNameNode.cpp: In constructor 'ASTIndexNameNode::ASTIndexNameNode()':
ASTIndexNameNode.cpp:38:40: error: class 'ASTIndexNameNode' does not 
have any field named 'ASTNode'
ASTIndexNameNode.cpp:38:48: error: 'AST_NAME' was not declared in this scope
ASTIndexNameNode.cpp:38:48: note: suggested alternative:
In file included from sbmlsolver/ASTIndexNameNode.h:4:0,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/math/ASTNode.h:307:5: note: 'libsbml::AST_NAME'
ASTIndexNameNode.cpp: At global scope:
ASTIndexNameNode.cpp:53:1: error: 'ASTNode_t' does not name a type
ASTIndexNameNode.cpp:60:31: error: redefinition of 'unsigned int 
ASTNode_getIndex'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:44:33: error: 'unsigned int 
ASTNode_getIndex' previously defined here
ASTIndexNameNode.cpp:60:31: error: 'ASTNode_t' was not declared in this 
scope
ASTIndexNameNode.cpp:60:31: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
ASTIndexNameNode.cpp:60:42: error: 'node' was not declared in this scope
ASTIndexNameNode.cpp:67:23: error: variable or field 'ASTNode_setIndex' 
declared void
ASTIndexNameNode.cpp:67:23: error: 'ASTNode_t' was not declared in this 
scope
ASTIndexNameNode.cpp:67:23: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
ASTIndexNameNode.cpp:67:34: error: 'node' was not declared in this scope
ASTIndexNameNode.cpp:67:40: error: expected primary-expression before 
'unsigned'
ASTIndexNameNode.cpp:78:44: error: redefinition of 'int ASTNode_isIndexName'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:41:24: error: 'int ASTNode_isIndexName' 
previously defined here
ASTIndexNameNode.cpp:78:44: error: 'ASTNode_t' was not declared in this 
scope
ASTIndexNameNode.cpp:78:44: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
ASTIndexNameNode.cpp:78:55: error: 'node' was not declared in this scope
ASTIndexNameNode.cpp:86:52: error: redefinition of 'unsigned int 
ASTNode_isSetIndex'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:47:33: error: 'unsigned int 
ASTNode_isSetIndex' previously defined here
ASTIndexNameNode.cpp:86:52: error: 'ASTNode_t' was not declared in this 
scope
ASTIndexNameNode.cpp:86:52: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
ASTIndexNameNode.cpp:86:63: error: 'node' was not declared in this scope
ASTIndexNameNode.cpp:97:51: error: redefinition of 'unsigned int 
ASTNode_isSetData'
In file included from ASTIndexNameNode.cpp:36:0:
sbmlsolver/ASTIndexNameNode.h:53:33: error: 'unsigned int 
ASTNode_isSetData' previously defined here
ASTIndexNameNode.cpp:97:51: error: 'ASTNode_t' was not declared in this 
scope
ASTIndexNameNode.cpp:97:51: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
ASTIndexNameNode.cpp:97:62: error: 'node' was not declared in this scope
ASTIndexNameNode.cpp:104:22: error: variable or field 'ASTNode_setData' 
declared void
ASTIndexNameNode.cpp:104:22: error: 'ASTNode_t' was not declared in this 
scope
ASTIndexNameNode.cpp:104:22: note: suggested alternative:
In file included from /usr/include/sbml/math/ASTNode.h:224:0,
from sbmlsolver/ASTIndexNameNode.h:4,
from ASTIndexNameNode.cpp:36:
/usr/include/sbml/common/sbmlfwd.h:225:51: note: 'libsbml::ASTNode_t'
ASTIndexNameNode.cpp:104:33: error: 'node' was not declared in this scope
make[1]: *** [ASTIndexNameNode.o] Error 1
make[1]: Leaving directory 
`/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSolver-1.7.0beta/src'
make: *** [all-recursive] Error 1
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c StringMap.c -o StringMap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c check.c -o check.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c doc.c -o doc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c dom.c -o dom.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c graph.c -o graph.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 
-DLIBSBML3 -fpic -O2 -pipe -g -c io.c -o io.o
g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 
-fpic -O2 -pipe -g -c layoutWrappers.cpp -o layoutWrappers.o
In file included from layoutWrappers.cpp:1:0:
rsbml.h:55:27: error: ‘SBMLDocument_t’ was not declared in this scope
rsbml.h:55:27: note: suggested alternative:
In file included from /usr/include/sbml/SBMLTypes.h:32:0,
from rsbml.h:1,
from layoutWrappers.cpp:1:
/usr/include/sbml/common/sbmlfwd.h:69:51: note: ‘libsbml::SBMLDocument_t’
In file included from layoutWrappers.cpp:1:0:
rsbml.h:55:43: error: ‘doc’ was not declared in this scope
rsbml.h:56:23: error: ‘SBMLDocument_t’ was not declared in this scope
rsbml.h:56:23: note: suggested alternative:
In file included from /usr/include/sbml/SBMLTypes.h:32:0,
from rsbml.h:1,
from layoutWrappers.cpp:1:
/usr/include/sbml/common/sbmlfwd.h:69:51: note: ‘libsbml::SBMLDocument_t’
In file included from layoutWrappers.cpp:1:0:
rsbml.h:56:39: error: ‘doc’ was not declared in this scope
rsbml.h:57:25: error: ‘ASTNode_t’ does not name a type
rsbml.h:57:36: error: ISO C++ forbids declaration of ‘node’ with no type 
[-fpermissive]
rsbml.h:58:1: error: ‘ASTNode_t’ does not name a type
rsbml.h:67:3: error: ‘Layout_t’ does not name a type
rsbml.h:69:3: error: ‘Layout_t’ does not name a type
rsbml.h:71:27: error: ‘SBase_t’ was not declared in this scope
rsbml.h:71:27: note: suggested alternative:
In file included from /usr/include/sbml/SBMLTypes.h:32:0,
from rsbml.h:1,
from layoutWrappers.cpp:1:
/usr/include/sbml/common/sbmlfwd.h:63:51: note: ‘libsbml::SBase_t’
In file included from layoutWrappers.cpp:1:0:
rsbml.h:71:36: error: ‘sbase’ was not declared in this scope
rsbml.h:71:43: error: expected primary-expression before ‘const’
rsbml.h:72:27: error: expected primary-expression before ‘const’
rsbml.h:72:50: error: expected primary-expression before ‘int’
rsbml.h:72:58: error: expression list treated as compound expression in 
initializer [-fpermissive]
layoutWrappers.cpp:6:1: error: ‘Layout_t’ does not name a type
layoutWrappers.cpp: In function ‘int 
LayoutModelPlugin_getNumLayouts(LayoutModelPlugin_t*)’:
layoutWrappers.cpp:11:16: error: invalid use of incomplete type 
‘LayoutModelPlugin_t {aka struct LayoutModelPlugin}’
In file included from layoutWrappers.cpp:1:0:
rsbml.h:66:18: error: forward declaration of ‘LayoutModelPlugin_t {aka 
struct LayoutModelPlugin}’
layoutWrappers.cpp: At global scope:
layoutWrappers.cpp:13:1: error: ‘Layout_t’ does not name a type
layoutWrappers.cpp:19:25: error: redefinition of ‘int SBase_enablePackage’
In file included from layoutWrappers.cpp:1:0:
rsbml.h:71:7: error: ‘int SBase_enablePackage’ previously defined here
layoutWrappers.cpp:19:25: error: ‘SBase_t’ was not declared in this scope
layoutWrappers.cpp:19:25: note: suggested alternative:
In file included from /usr/include/sbml/SBMLTypes.h:32:0,
from rsbml.h:1,
from layoutWrappers.cpp:1:
/usr/include/sbml/common/sbmlfwd.h:63:51: note: ‘libsbml::SBase_t’
layoutWrappers.cpp:19:34: error: ‘sbase’ was not declared in this scope
layoutWrappers.cpp:19:41: error: expected primary-expression before ‘const’
layoutWrappers.cpp:20:25: error: expected primary-expression before ‘const’
layoutWrappers.cpp:20:48: error: expected primary-expression before ‘int’
make: *** [layoutWrappers.o] Error 1
ERROR: compilation failed for package ‘rsbml’
* removing ‘/usr/local/lib/R/site-library/rsbml’

The downloaded source packages are in
‘/tmp/RtmpUQvH6d/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘rsbml’ had non-zero exit status



Thanks in advance