Error compiling SOSlib C library - linux

I am attempting to compile a library,
http://www.tbi.univie.ac.at/~raim/odeSolver/
this one specifically, I have gotten the necessary libraries for this.
However whenever i attempt to compile it with "make", I get the following error.
Making all in src
make[1]: Entering directory `/home/user/SOSLib/buildSOSlib/src'
/usr/bin/make all-am
make[2]: Entering directory `/home/user/SOSLib/buildSOSlib/src'
/bin/bash ../libtool --tag=CC --mode=link /usr/bin/gcc-4.8 -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -g3 -gdwarf-2 -no-undefined -L/usr/lib64 -L/usr/local/lib -o libODES.la -rpath /usr/local/lib ASTIndexNameNode.lo arithmeticCompiler.lo charBuffer.lo compiler.lo cvodeData.lo cvodeSolver.lo daeSolver.lo drawGraph.lo evaluateAST.lo integratorInstance.lo integratorSettings.lo interpol.lo modelSimplify.lo nullSolver.lo odeConstruct.lo odeModel.lo odeSolver.lo processAST.lo sbml.lo sbmlResults.lo sensSolver.lo solverError.lo util.lo data.lo error.lo -lsbml -lxml2 -lsundials_ida -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -lm -lm -ldl
libtool: link: /usr/bin/gcc-4.8 -shared -fPIC -DPIC .libs/ASTIndexNameNode.o .libs/arithmeticCompiler.o .libs/charBuffer.o .libs/compiler.o .libs/cvodeData.o .libs/cvodeSolver.o .libs/daeSolver.o .libs/drawGraph.o .libs/evaluateAST.o .libs/integratorInstance.o .libs/integratorSettings.o .libs/interpol.o .libs/modelSimplify.o .libs/nullSolver.o .libs/odeConstruct.o .libs/odeModel.o .libs/odeSolver.o .libs/processAST.o .libs/sbml.o .libs/sbmlResults.o .libs/sensSolver.o .libs/solverError.o .libs/util.o .libs/data.o .libs/error.o -L/usr/lib64 -L/usr/local/lib -lsbml -lxml2 /usr/local/lib/libsundials_ida.a /usr/local/lib/libsundials_kinsol.a /usr/local/lib/libsundials_cvodes.a /usr/local/lib/libsundials_nvecserial.a -lm -ldl -Wl,-soname -Wl,libODES.so.0 -o .libs/libODES.so.0.0.0
/usr/bin/ld: /usr/local/lib/libsundials_ida.a(ida.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libsundials_ida.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [libODES.la] Error 1
make[2]: Leaving directory `/home/user/SOSLib/buildSOSlib/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/user/SOSLib/buildSOSlib/src'
make: *** [all-recursive] Error 1
What is happening here?

You are trying to build a shared library, and shared libraries must be built as position-independent code so they an be loaded and run anywhere in memory. This is achieved passing the -fPIC flag to GCC. It seems that one of the libraries (libsundials_ida.a) was not built with it.

Related

ld cannot find `-lnsl`

I am trying to compile a project that links the nsl lib but it seems to fail to link the library:
/bin/sh ../../libtool --tag=CXX --mode=link g++ -DNDEBUG -std=c++11 -L/usr/lib -R/usr/lib -L../../lib -all-static -lnsl -o Client client.o nettools.o -lgmm -lboost_program_options
libtool: link: g++ -DNDEBUG -std=c++11 -static -o Client client.o nettools.o -L/usr/lib -L../../lib -lnsl -lgmm -lboost_program_options -Wl,-rpath -Wl,/usr/lib
/bin/sh ../../libtool --tag=CXX --mode=link g++ -DNDEBUG -std=c++11 -L/usr/lib -R/usr/lib -L../../lib -all-static -lnsl -o Serveur serveur.o nettools.o -lgmm -lboost_program_options
/bin/ld: cannot find -lnsl
nettools.o: In function `creatSocketCom(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int)':
nettools.cc:(.text+0x30e): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
Makefile:426: recipe for target 'Client' failed
make[2]: *** [Client] Error 1
make[2]: *** Waiting for unfinished jobs....
libtool: link: g++ -DNDEBUG -std=c++11 -static -o Serveur serveur.o nettools.o -L/usr/lib -L../../lib -lnsl -lgmm -lboost_program_options -Wl,-rpath -Wl,/usr/lib
/bin/ld: cannot find -lnsl
nettools.o: In function `creatSocketCom(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int)':
nettools.cc:(.text+0x30e): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
I know this library doesn't need to be linked on Mac OS X but I'm running Arch Linux.
I have 2 questions:
Why does nsl fail to be linked even though λ ld --verbose -lnsl seems to show it's there?
attempt to open /usr/x86_64-unknown-linux-gnu/lib64/libnsl.so failed
attempt to open /usr/x86_64-unknown-linux-gnu/lib64/libnsl.a failed
attempt to open /usr/lib/libnsl.so succeeded
-lnsl (/usr/lib/libnsl.so)
libc.so.6 needed by /usr/lib/libnsl.so
found libc.so.6 at /usr/lib/libc.so.6
ld-linux-x86-64.so.2 needed by /usr/lib/libc.so.6
found ld-linux-x86-64.so.2 at /usr/lib/ld-linux-x86-64.so.2
ld: warning: cannot find entry symbol _start; not setting start address
What's the purest way to tell autoconf not to link nsl on systems where it's not needed?
The problem was with the -all-static option in the Makefile.am.
Arch Linux doesn't ship the static libraries (while debian's current stable release does).

Dependancies for RE2 on Centos7

I am trying to install re2 on a centos7 vm, and I am having some trouble solving these dependencies:
[root#roller re2]# make testinstall
cp testinstall.cc obj
(cd obj && g++ -I/usr/local/include -L/usr/local/lib testinstall.cc -lre2 -pthread -static -o testinstall)
/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lpthread
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make: *** [testinstall] Error 1
Any help would be great! :)
thanks!

Encountering 'undefined reference' and 'error adding symbols' when compiling OpenEXR [duplicate]

This question already has answers here:
What is an undefined reference/unresolved external symbol error and how do I fix it?
(39 answers)
Closed 7 years ago.
I am installing OpenEXR_Viewers on Ubuntu 14.04. When running the makefile, I encounter the following error:
/usr/bin/ld: ImageView.o: undefined reference to symbol 'glOrtho'
//usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: error adding symbols: DSO
missing from command line collect2: error: ld returned 1 exit status
Is it likely that my lib tool invocation is not calling GL? If this is the case, how do I set my libtool to build with GL? (Edit the makefile to see OpenGl)
Making all in playexr
make[1]: Entering directory `/home/user/Documents/source/openexr/OpenEXR_Viewers/playexr'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/user/Documents/source/openexr/OpenEXR_Viewers/playexr'
Making all in exrdisplay
make[1]: Entering directory `/home/user/Documents/source/openexr/OpenEXR_Viewers/exrdisplay'
/bin/bash ../libtool --tag=CXX --mode=link g++ -pipe -g -O2 -o exrdisplay main.o ImageView.o loadImage.o scaleImage.o applyCtl.o GlWindow3d.o -L/usr/local/lib -pthread -L/usr/local/lib -lIlmImf -lImath-2_2 -lIexMath-2_2 -lHalf -lIex-2_2 -lIlmThread-2_2 -DHAVE_CTL_INTERPRETER=0 -L/usr/local/lib -DHAVE_CTL_INTERPRETER=0 -pthread -L/usr/local/lib -lIlmImf -lImath-2_2 -lIexMath-2_2 -lHalf -lIex-2_2 -lIlmThread-2_2 -Wl,-Bsymbolic-functions -lfltk_gl -lfltk -lX11
*** Warning: Linking the executable exrdisplay against the loadable module
*** libImath-2_2.so is not portable!
*** Warning: Linking the executable exrdisplay against the loadable module
*** libIexMath-2_2.so is not portable!
*** Warning: Linking the executable exrdisplay against the loadable module
*** libHalf.so is not portable!
*** Warning: Linking the executable exrdisplay against the loadable module
*** libIex-2_2.so is not portable!
*** Warning: Linking the executable exrdisplay against the loadable module
*** libIlmThread-2_2.so is not portable!
libtool: link: g++ -pipe -g -O2 -o exrdisplay main.o ImageView.o loadImage.o scaleImage.o applyCtl.o GlWindow3d.o -pthread -DHAVE_CTL_INTERPRETER=0 -DHAVE_CTL_INTERPRETER=0 -pthread -Wl,-Bsymbolic-functions -L/usr/local/lib /usr/local/lib/libIlmImf.so /usr/local/lib/libImath-2_2.so /usr/local/lib/libIexMath-2_2.so /usr/local/lib/libHalf.so /usr/local/lib/libIex-2_2.so /usr/local/lib/libIlmThread-2_2.so -lfltk_gl -lfltk -lX11 -pthread
/usr/bin/ld: ImageView.o: undefined reference to symbol 'glOrtho'
//usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[1]: *** [exrdisplay] Error 1
make[1]: Leaving directory `/home/user/Documents/source/openexr/OpenEXR_Viewers/exrdisplay'
make: *** [all-recursive] Error 1
Try adding -lglut -lGL (and probably -lGLU) to you linker command.
(g++ linker: /usr/lib/libGL.so.1: could not read symbols: Invalid operation)
UPDATE:
Append it to:
FLTK_LDFLAGS = -Wl,-Bsymbolic-functions -lfltk_gl -lfltk -lX11
like
FLTK_LDFLAGS = -Wl,-Bsymbolic-functions -lfltk_gl -lfltk -lX11 -lglut -lGL

Is it necessary to upgrade Glib in Cygwin?

I'm attempting to compile abiword in my Cygwin environment.
I have cygwin 1.7.25.
The compile fails regarding glib:
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_REENTRANT -I/usr/include/fribidi -
I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libgsf-1 -I/usr/include/libxml2
-I/usr/include/wv -I/usr/include/freetype2 -I/usr/include/cairo -I/usr/include/pixman-1 -
I/usr/include/libpng15 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/gtk-2.0 -
I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/gdk-pixbuf-2.0 -
I/usr/include/gio-unix-2.0/ -I/usr/include/gtk-unix-print-2.0 -I/usr/include/librsvg-2.0 -Wall -
Wextra -Wsign-compare -Wpointer-arith -Wchar-subscripts -Wwrite-strings -Wmissing-noreturn -
Wunused -Wpointer-arith -Wshadow -g -O2 -MT go-cmd-context.lo -MD -MP -MF .deps/go-cmd-
context.Tpo -c goffice/app/go-cmd-context.c -DDLL_EXPORT -DPIC -o .libs/go-cmd-context.o
In file included from ./goffice/app/goffice-app.h:25:0,
from ./goffice/app/go-cmd-context.h:24,
from goffice/app/go-cmd-context-impl.h:4,
from goffice/app/go-cmd-context.c:10:
/usr/include/glib-2.0/glib/gmacros.h:35:2: error: #error "Only <glib.h> can be included directly."
goffice/app/go-cmd-context.c: In function ‘go_cmd_context_get_type’:
goffice/app/go-cmd-context.c:147:3: warning: missing initializer [-Wmissing-field-initializers]
goffice/app/go-cmd-context.c:147:3: warning: (near initialization for ‘go_cmd_context_info.class_init’) [-Wmissing-field-initializers]
Makefile:503: recipe for target `go-cmd-context.lo' failed
make[3]: *** [go-cmd-context.lo] Error 1
make[3]: Leaving directory `/home/kingram/src/abiword-2.8.6/goffice-bits'
Makefile:409: recipe for target `all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/kingram/src/abiword-2.8.6/goffice-bits'
Makefile:670: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/kingram/src/abiword-2.8.6'
Makefile:473: recipe for target `all' failed
make: *** [all] Error 2
A google search produced a Redhat bug report suggesting that Glib 2.31 is required.
I'm considering downloading and compiling the latest glib from source as cygwin does not appear to be using it.
However, I'd like some insight on this choice or hear if there are some other experiences around this.
Actually, Glib 2.31 is the culprit; its headers changed so that only the top-level headers may be #included, not the individual class headers.
Cygwin does have the latest stable branch of Glib.
Therefore, in order to get this to compile, you would need to fix the #includes in the code, as indicated in the error messages.
However, I can save you the trouble: Abiword packages are available from Cygwin Ports.

debian: mysql-workbench installation error [cannot find -lpython2.7.a]

I'm trying to install mysql-workbench-gpl-5.2.45 from the source code on Linux debian 2.6.32-5-amd64. The problem appears at the "make" step with error message:
/usr/bin/ld: cannot find -lpython2.7.a
collect2: ld returned 1 exit status
make[4]: *** [libgrt.la] Error 1
make[4]: Leaving directory `/home/user/data/workbench/mysql-workbench-gpl-5.2.45-src/library/grt/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/user/data/workbench/mysql-workbench-gpl-5.2.45-src/library/grt'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/user/data/workbench/mysql-workbench-gpl-5.2.45-src/library'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/user/data/workbench/mysql-workbench-gpl-5.2.45-src'
make: *** [all] Error 2
The last make command before error is:
make[4]: Entering directory `/home/user/data/workbench/mysql-workbench-gpl-5.2.45-src/library/grt/src'
/bin/bash ../../../libtool --tag=CXX --mode=link g++ -Wextra -Wall -Wno-unused -Wno-deprecated -DTIXML_USE_STL=1 -o libgrt.la -rpath /usr/local/lib/mysql-workbench grtpp_grt.lo grtpp_helper.lo grtpp_metaclass.lo grtpp_util.lo grtpp_value.lo grtpp_shell.lo grtpp_shell_lua.lo grtpp_shell_lua_help.lo grtpp_module.lo grtpp_module_cpp.lo grtpp_module_lua.lo grtpp_notifications.lo lua_context.lo serializer.lo unserializer.lo grtpp_undo_manager.lo changefactory.lo changelistobjects.lo diffchange.lo grtdiff.lo grtlistdiff.lo grtpp_module_python.lo grtpp_shell_python.lo grtpp_shell_python_help.lo python_context.lo python_grtdict.lo python_grtlist.lo python_grtobject.lo python_module.lo -llua5.1 -luuid -pthread -Wl,--export-dynamic -lgthread-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -lxml2 -lsigc-2.0 -llua5.1 -luuid -L/usr/local/lib -lpython2.7.a ../../../library/base/libwbbase.la
libtool: link: g++ -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.4.5/crtbeginS.o .libs/grtpp_grt.o .libs/grtpp_helper.o .libs/grtpp_metaclass.o .libs/grtpp_util.o .libs/grtpp_value.o .libs/grtpp_shell.o .libs/grtpp_shell_lua.o .libs/grtpp_shell_lua_help.o .libs/grtpp_module.o .libs/grtpp_module_cpp.o .libs/grtpp_module_lua.o .libs/grtpp_notifications.o .libs/lua_context.o .libs/serializer.o .libs/unserializer.o .libs/grtpp_undo_manager.o .libs/changefactory.o .libs/changelistobjects.o .libs/diffchange.o .libs/grtdiff.o .libs/grtlistdiff.o .libs/grtpp_module_python.o .libs/grtpp_shell_python.o .libs/grtpp_shell_python_help.o .libs/python_context.o .libs/python_grtdict.o .libs/python_grtlist.o .libs/python_grtobject.o .libs/python_module.o -Wl,-rpath -Wl,/home/user/data/workbench/mysql-workbench-gpl-5.2.45-src/library/base/.libs -Wl,-rpath -Wl,/usr/local/lib/mysql-workbench /usr/lib/libgthread-2.0.so /usr/lib/libgmodule-2.0.so -lrt /usr/lib/libglib-2.0.so /usr/lib/libxml2.so /usr/lib/libsigc-2.0.so /usr/lib/liblua5.1.so -luuid -L/usr/local/lib -lpython2.7.a ../../../library/base/.libs/libwbbase.so -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../.. -L/usr/lib/x86_64-linux-gnu -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.4.5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/crtn.o -pthread -Wl,--export-dynamic -pthread -Wl,-soname -Wl,libgrt.so.0 -o .libs/libgrt.so.0.0.0
I have checked library location:
locate lpython2.7.a
The result is:
/usr/local/lib/lpython2.7.a
The python2.7.3 was downloaded here:
http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2
The python2.7.3 installation steps:
tar -xvjpf Python-2.7.3.tar.bz2 && cd Python-2.7.3 && ./configure && make && make install
Any ideas why WB can't find the library?
The problem is solved. Before mysql-workbench installation it is important to install python2.7 properly. Installation instruction here: https://gist.github.com/1069219

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