Question: rsbml package installation error
0
gravatar for Michael Lawrence
6.1 years ago by
United States
Michael Lawrence11k wrote:
On Fri, Sep 6, 2013 at 9:59 AM, Stefan Gries <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 07:27, 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 Could this be outdated?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> 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 >> ' >> >> 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 >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > [[alternative HTML version deleted]]
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ADD COMMENTlink modified 6.1 years ago by Stefan Gries50 • written 6.1 years ago by Michael Lawrence11k
Answer: rsbml package installation error
0
gravatar for Stefan Gries
6.1 years ago by
Stefan Gries50
Stefan Gries50 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. Best, Stefan On 24.06.2013 07:27, 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/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 > > _______________________________________________ > 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]]
ADD COMMENTlink written 6.1 years ago by Stefan Gries50
Answer: rsbml package installation error
0
gravatar for Stefan Gries
6.1 years ago by
Stefan Gries50
Stefan Gries50 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/contrib/rsb ml_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_odeSo lver-1.7.0beta/src' >> make[2]: Entering directory >> `/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSo lver-1.7.0beta' >> make[2]: Leaving directory >> `/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSo lver-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_odeSo lver-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]]
ADD COMMENTlink written 6.1 years ago by Stefan Gries50
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> 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> 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 07:27, 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> 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' >>> >>> >>> 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 >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 6.1 years ago by Michael Lawrence11k
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]]
ADD REPLYlink written 6.1 years ago by Stefan Gries50
I am cc'ing Dan, maybe the Bioc build server can give us a third data point in our attempt to figure this out. In theory I could grab my wife's computer and try this out on Ubuntu. On Fri, Sep 13, 2013 at 7:00 AM, Stefan Gries <sgries@d120.de> wrote: > 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> 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> 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 <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> 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' >>>> >>>> >>>> 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 >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >>> >> >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 6.1 years ago by Michael Lawrence11k
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