[SOLVED] Problems to install avogadro (chem. progr.) in Slackware13.37-current

DecioSP · 04-15-2012, 07:40 AM

I am trying to install avogadro program under slackware 13.37-current.
However, after installing tons of dependencies I can't figure what went wrong.
Firstly, in order to install avogadro, slackbuild showed openbabel as dependency and here is my problem.
In order to install openbabel I installed the following builds in the order listed below:
ORBit2 -> GConf -> wxPython
Despite some warning errors in almost all of those, I was able to create and install the pkg.
However, when I try to build the openbabel using (http://slackbuilds.org/repository/13...ies/openbabel/) it respond with a lot of errors like:

Code:

CMake Warning at test/CMakeLists.txt:53 (add_executable):
  Cannot generate a safe linker search path for target test_automorphism
  because files in some directories may conflict with libraries in implicit
  directories:

    link library [libm.so] in /usr/lib64 may be hidden by files in:
      /usr/X11R6/lib64
    link library [libz.so] in /usr/lib64 may be hidden by files in:
      /usr/X11R6/lib64

  Some of these libraries may not be found correctly.


CMake Warning at test/CMakeLists.txt:125 (add_executable):
  Cannot generate a safe linker search path for target test_bond because
  files in some directories may conflict with libraries in implicit
  directories:

    link library [libm.so] in /usr/lib64 may be hidden by files in:
      /usr/X11R6/lib64
    link library [libz.so] in /usr/lib64 may be hidden by files in:
      /usr/X11R6/lib64

  Some of these libraries may not be found correctly.

And exit with:

Code:

In file included from /usr/include/eigen2/Eigen/Core:99:0,
                 from /tmp/SBo/openbabel-2.3.0/include/openbabel/math/align.h:26,
                 from /tmp/SBo/openbabel-2.3.0/src/math/align.cpp:24:
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h: In instantiation of 'T Eigen::ei_hypot(T, T) [with T = double]':
/usr/include/eigen2/Eigen/src/SVD/SVD.h:331:42:   required from 'void Eigen::SVD<MatrixType>::compute(const MatrixType&) [with MatrixType = Eigen::Matrix<double, 3, 3>]'
/usr/include/eigen2/Eigen/src/SVD/SVD.h:71:7:   required from 'Eigen::SVD<MatrixType>::SVD(const MatrixType&) [with MatrixType = Eigen::Matrix<double, 3, 3>]'
/tmp/SBo/openbabel-2.3.0/src/math/align.cpp:149:38:   required from here
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:40:18: error: 'ei_abs' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from /usr/include/eigen2/Eigen/Core:99:0,
                 from /tmp/SBo/openbabel-2.3.0/include/openbabel/math/align.h:26,
                 from /tmp/SBo/openbabel-2.3.0/src/math/align.cpp:24:
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:264:20: note: 'long double Eigen::ei_abs(long double)' declared here, later in the translation unit
In file included from /usr/include/eigen2/Eigen/Core:99:0,
                 from /tmp/SBo/openbabel-2.3.0/include/openbabel/math/align.h:26,
                 from /tmp/SBo/openbabel-2.3.0/src/math/align.cpp:24:
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:41:18: error: 'ei_abs' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from /usr/include/eigen2/Eigen/Core:99:0,
                 from /tmp/SBo/openbabel-2.3.0/include/openbabel/math/align.h:26,
                 from /tmp/SBo/openbabel-2.3.0/src/math/align.cpp:24:
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:264:20: note: 'long double Eigen::ei_abs(long double)' declared here, later in the translation unit
In file included from /usr/include/eigen2/Eigen/Core:99:0,
                 from /tmp/SBo/openbabel-2.3.0/include/openbabel/math/align.h:26,
                 from /tmp/SBo/openbabel-2.3.0/src/math/align.cpp:24:
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:45:34: error: 'ei_sqrt' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from /usr/include/eigen2/Eigen/Core:99:0,
                 from /tmp/SBo/openbabel-2.3.0/include/openbabel/math/align.h:26,
                 from /tmp/SBo/openbabel-2.3.0/src/math/align.cpp:24:
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:266:20: note: 'long double Eigen::ei_sqrt(long double)' declared here, later in the translation unit
make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
make[2]: Leaving directory `/tmp/SBo/openbabel-2.3.0/build'
make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
make[1]: Leaving directory `/tmp/SBo/openbabel-2.3.0/build'
make: *** [all] Error 2

Probably i am missing some dependency but I confess that I really don't know what and despite some random posts listing problems with wxWidget I couldn't find anything near this problem in the forum.

DecioSP · 04-15-2012, 11:57 PM

Same results with wxX11 and wxGTK :-(
Can't build openbabel and since avogadro has it as dependency can't install it either.

ponce · 04-16-2012, 01:37 AM

You probably already know that slackbuilds.org repository is compatible with the stable slackware version and, as in this case, with the compiler installed on that.

slackware-current ships gcc-4.7, and in some cases workarounds/patches are needed if the sources are not gcc-4.7-compliant: because I like to slack, I've patched the stuff of slackbuilds.org that I use to let it build on -current with sbopkg (you can spot the modifications in more detail here, hoping they can be useful too for the fellas running -current

).

luckily for us, this gcc seems more eloquent of its precedessors, it even offers solutions in the output!

the error you showed in the first post seems to match this part of the document above about porting code for the new gcc

Quote:

Name lookup changes

The C++ compiler no longer performs some extra unqualified lookups it had performed in the past, namely dependent base class scope lookups and unqualified template function lookups.

C++ programs that depended on the compiler's previous behavior may no longer compile. For example, code such as

Code:

template<typename T>
int t(T i)
{ return f(i); }

int
f(int i)
{ return i; }

int
main()
{
  return t(1);
}

Will result in the following diagnostic:

Code:

In instantiation of ‘int t(T) [with T = int]’
  required from here
  error: ‘f’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  note: ‘int f(int)’ declared here, later in the translation unit

To fix, make sure the function f in the code above is declared before first use in function t. Like so:

Code:

int
f(int i)
{ return i; }

template<typename T>
int t(T i)
{ return f(i); }

int
main()
{
  return t(1);
}

This can be temporarily worked around by using -fpermissive.

so should be safe to modify openbabel.Slackbuild changing this line

Code:

    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \

with

Code:

    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS -fpermissive" \

you will need it also if you try to upgrade to openbabel 2.3.1 (svn shows the same behaviour).

DecioSP · 04-16-2012, 07:46 AM

Thank you very much, that worked like a charm!
Also, You made a concise and very helpful explanation as also posted some links like this that helped me more than you can imagine.
Post closed and +1 deserved.
Thanks again.

wmhrae · 04-26-2012, 10:09 AM

By Installing Eigen2 VERSION=2.0.17 solves this problem! Just take note that I also installed Eigen3 VERSION=3.0.5 as well, if you need build procedure come to contact-us at http://cersi.tk or drop email at wmh@cersi.tk

wmhrae · 04-26-2012, 10:14 AM

Fix error: 'ei_abs' was not declared in this scope, and no declarations were found by argument-depen
By Installing Eigen2 VERSION=2.0.17 solves this problem! Just take note that I also installed Eigen3 VERSION=3.0.5 as well, if you need build procedure come to contact-us at http://cersi.tk or drop email at wmh@cersi.tk