Seems to me that you could be missing dependencies. I took a look at your
package and it depends on simple BioGenerics, Generic Functions for
Bioconductor. Could this be outdated?

Are there any other dependencies you could be missing?

http://www.bioconductor.org/packages/2.12/bioc/html/BiocGenerics.html

Best,

Michael




On Sun, Jun 23, 2013 at 6:48 AM, Stefan Gries <sgries@d120.de> wrote:

> 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<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
>
> ______________________________**_________________
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>

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