Question: rsbml package installation error
0
gravatar for Stefan Gries
6.0 years ago by
Stefan Gries50
Stefan Gries50 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.t ar.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-1.7.0b eta/src' make[2]: Entering directory `/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSolver-1.7.0b eta' make[2]: Leaving directory `/tmp/RtmpwY6aC6/R.INSTALLca87108c408/rsbml/inst/SBML_odeSolver-1.7.0b eta' 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-1.7.0b eta/src' make: *** [all-recursive] Error 1 configure: === End local SOSLib build === configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c StringMap.c -o StringMap.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c check.c -o check.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c doc.c -o doc.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c dom.c -o dom.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c graph.c -o graph.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c io.c -o io.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/libxml2 -DLIBSBML3 -fpic -O2 -pipe -g -c layoutWrappers.cpp -o layoutWrappers.o In file included from layoutWrappers.cpp:1:0: rsbml.h:55:27: error: ?SBMLDocument_t? was not declared in this scope rsbml.h:55:27: note: suggested alternative: In file included from /usr/include/sbml/SBMLTypes.h:32:0, from rsbml.h:1, from layoutWrappers.cpp:1: /usr/include/sbml/common/sbmlfwd.h:69:51: note: ?libsbml::SBMLDocument_t? In file included from layoutWrappers.cpp:1:0: rsbml.h:55:43: error: ?doc? was not declared in this scope rsbml.h:56:23: error: ?SBMLDocument_t? was not declared in this scope rsbml.h:56:23: note: suggested alternative: In file included from /usr/include/sbml/SBMLTypes.h:32:0, from rsbml.h:1, from layoutWrappers.cpp:1: /usr/include/sbml/common/sbmlfwd.h:69:51: note: ?libsbml::SBMLDocument_t? In file included from layoutWrappers.cpp:1:0: rsbml.h:56:39: error: ?doc? was not declared in this scope rsbml.h:57:25: error: ?ASTNode_t? does not name a type rsbml.h:57:36: error: ISO C++ forbids declaration of ?node? with no type [-fpermissive] rsbml.h:58:1: error: ?ASTNode_t? does not name a type rsbml.h:67:3: error: ?Layout_t? does not name a type rsbml.h:69:3: error: ?Layout_t? does not name a type rsbml.h:71:27: error: ?SBase_t? was not declared in this scope rsbml.h:71:27: note: suggested alternative: In file included from /usr/include/sbml/SBMLTypes.h:32:0, from rsbml.h:1, from layoutWrappers.cpp:1: /usr/include/sbml/common/sbmlfwd.h:63:51: note: ?libsbml::SBase_t? In file included from layoutWrappers.cpp:1:0: rsbml.h:71:36: error: ?sbase? was not declared in this scope rsbml.h:71:43: error: expected primary-expression before ?const? rsbml.h:72:27: error: expected primary-expression before ?const? rsbml.h:72:50: error: expected primary-expression before ?int? rsbml.h:72:58: error: expression list treated as compound expression in initializer [-fpermissive] layoutWrappers.cpp:6:1: error: ?Layout_t? does not name a type layoutWrappers.cpp: In function ?int LayoutModelPlugin_getNumLayouts(LayoutModelPlugin_t*)?: layoutWrappers.cpp:11:16: error: invalid use of incomplete type ?LayoutModelPlugin_t {aka struct LayoutModelPlugin}? In file included from layoutWrappers.cpp:1:0: rsbml.h:66:18: error: forward declaration of ?LayoutModelPlugin_t {aka struct LayoutModelPlugin}? layoutWrappers.cpp: At global scope: layoutWrappers.cpp:13:1: error: ?Layout_t? does not name a type layoutWrappers.cpp:19:25: error: redefinition of ?int SBase_enablePackage? In file included from layoutWrappers.cpp:1:0: rsbml.h:71:7: error: ?int SBase_enablePackage? previously defined here layoutWrappers.cpp:19:25: error: ?SBase_t? was not declared in this scope layoutWrappers.cpp:19:25: note: suggested alternative: In file included from /usr/include/sbml/SBMLTypes.h:32:0, from rsbml.h:1, from layoutWrappers.cpp:1: /usr/include/sbml/common/sbmlfwd.h:63:51: note: ?libsbml::SBase_t? layoutWrappers.cpp:19:34: error: ?sbase? was not declared in this scope layoutWrappers.cpp:19:41: error: expected primary-expression before ?const? layoutWrappers.cpp:20:25: error: expected primary-expression before ?const? layoutWrappers.cpp:20:48: error: expected primary-expression before ?int? make: *** [layoutWrappers.o] Error 1 ERROR: compilation failed for package ?rsbml? * removing ?/usr/local/lib/R/site-library/rsbml? The downloaded source packages are in ?/tmp/RtmpUQvH6d/downloaded_packages? Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?rsbml? had non-zero exit status Thanks in advance
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ADD COMMENTlink modified 6.0 years ago by Michael Lawrence11k • written 6.0 years ago by Stefan Gries50
Answer: rsbml package installation error
0
gravatar for Michael Breen
6.0 years ago by
Michael Breen350
Michael Breen350 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<http: bioconductor.org="" packages="" 2.12="" bi="" oc="" 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<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Michael Breen350
Answer: rsbml package installation error
0
gravatar for Michael Lawrence
6.0 years ago by
United States
Michael Lawrence11k wrote:
This looks like an issue related to the compiler. I don't see any weird flags on the command line. Which version of g++? If I could reproduce it, I could try to fix it. Michael On Sun, Jun 23, 2013 at 6:48 AM, Stefan Gries <sgries@d120.de> wrote: > Dear list, > > for several days now I've been experiencing an odd error when trying to > install the rsbml package (be it using biocLite("rsbml") or a downloaded > package source via install.packages() ). I mainly find it odd because I > couldn't find any other mentions of this error occurring in internet > searches. > > First of all: I'm running R 3.0.1 and Bioconductor 2.12 with all base > packages up to date on Linux Mint 15 (64-bit), with libsbml5, libxml2 and > SUNDIALS (and probably whatever package else is necessary) installed. > > I'll post a full installation log here, although I suppose the primarily > relevant lines are the first two error messages that occur when g++ tries > to compile the ASTIndexNameNode.cpp file: first, obviously, the 'class' > keyword isn't recognised properly, as the C file's source code looks quite > all right (although I won't make any guarantees for the definitions and > includes). Second, the libsbml namespace (as far as I know, ASTNode_t is > from libsbml, correct me if I'm wrong) seems not to be imported correctly, > as said type isn't found. Anyhow: any help in figuring out how to solve > this mess would be gladly appreciated. > > > biocLite("rsbml") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1. > Installing package(s) 'rsbml' > trying URL 'http://bioconductor.org/**packages/2.12/bioc/src/** > contrib/rsbml_2.18.0.tar.gz<http: bioconductor.org="" packages="" 2.12="" bi="" oc="" 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<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Michael Lawrence11k
Yes, seemed like some compiler oddity to me as well. My system runs g++ 4.7.3 - thanks a lot for helping! Stefan On 24.06.2013 15:05, Michael Lawrence wrote: > This looks like an issue related to the compiler. I don't see any > weird flags on the command line. Which version of g++? If I could > reproduce it, I could try to fix it. > > 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 REPLYlink written 6.0 years ago by Stefan Gries50
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