Hm, my libSBML version is 5.6.0-1 (latest version in Mint/Ubuntu repositories). I can't tell, though, how strongly the Ubuntu (Debian-based) and Gentoo (which is a very own Linux branch) versions of this library differ in OS-specific details. Have you tested the installation on a Ubuntu (or similar) system? Stefan On 12.09.2013 16:01, Michael Lawrence wrote: > Which version of libsbml are you using? I found that in 5.6.0 (or > maybe earlier), they changed the name of the flag for indicating > presence of the layout package. So the layoutWrappers.cpp should not > even be enabled for compilation, unless somehow your installation is > different than mine. Anyway, I fixed that in devel, but I never got > any compilation errors. > > Michael > > > > > On Mon, Sep 9, 2013 at 12:32 AM, Stefan Gries <sgries@d120.de> <mailto:sgries@d120.de>> wrote: > > That sounds good. It'd be very kind if I could get a little > notification as soon as a fix is available. > Thanks for the fast response. > > Stefan > > Am 06.09.2013 23:14, schrieb Michael Lawrence: >> >> On Fri, Sep 6, 2013 at 9:59 AM, Stefan Gries <sgries@d120.de>> <mailto:sgries@d120.de>> wrote: >> >> Hi again, >> >> it's been a while, I just didn't get around to testing my >> rsbml installation problem on a different system sooner, >> because my notebook hates Linux systems (or vice versa, I >> don't know). >> >> Actually, yes, there are some further dependancies not >> mentioned in the Bioconductor description: The SUNDIALS ODE >> solver library needs to be installed as well in order to >> install this package, and optionally the Grace package and >> some version of GraphViz can be used for rsbml's >> installation. But I got all those things (except for >> GraphViz, obviously, which is not recognized, although I >> installed the according -base and -dev packages from the >> Mint/Ubuntu repos just as I got the "rGraphViz" package from >> Bioconductor as well). >> >> Anyway, I suppose M. Lawrence was on quite a good track with >> his latter assumption of my installation error being >> compiler-related. I'd even say it's a linker-related problem, >> because the errors posted in my first mail are reproducible >> on a testing system using an out-of-the-box Ubuntu 13.04 with >> only the necessary additional packages and libraries >> (libsbml5, libxml2, r-cran (not from the Ubuntu-, but the >> R-CRAN repositories), r-bioconductor (and rsbml's >> dependancies "BiocGenerics" and "graph", all installed via R >> itself), SUNDIALS) - so it still seems that rsbml fails to >> link to libsbml5's structures properly in my perception. >> >> Now the question is: is this a problem of rsbml internally >> (for example sloppy adjustments concerning the 5th version of >> libSBML) or is there just another dependancy which I must >> have overseen? >> Any further hints or tips on this topic would be greatly >> appreciated. >> >> >> >> The SUNDIALS library is not required unless you want to run >> simulations. The package will install anyway. I think I >> understand the issue now, even though I'm confused as to why this >> is not happening on my Gentoo-based system. g++ does not like the >> way the types are named C header file rsbml.h. It's easy to fix. >> I'll do it soon. >> >> Michael >> >> Best, >> Stefan >> >> >> On 24.06.2013 07 <tel:24.06.2013%2007>:27, Michael Breen wrote: >>> 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 <mailto: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/contri b/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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> <mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> > > [[alternative HTML version deleted]]