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Problems with openbabel libraries


#1

Hi dear developers,

I would like to report here maybe what can be a kind of a bug related to
openbabel
libraries. I already installed avogadro and openbabel from either apt-get
or source and I never had been problems, but since last week I’m trying to
fix the following error. I tried to compile using openbabel-dev source
libraries and also using openbabel from apt-get on Ubuntu 14.04. The
configuration was fine and every library was configured, including
openbabel ones. However some errors are occurring when it is linking with
the openbabel libraries. Please, does anyone has a suggestion about that?
What could be that? I tried from different ways.

0%] [ 0%] [ 0%] [ 1%] [ 1%] Generating ui_bsdysettingswidget.h
Generating moc_elementcolor.cxx
Generating qrc_navigatetool.cxx
Generating ui_navigatesettingswidget.h
[ 1%] [ 1%] Generating moc_navigatetool.cxx
[ 1%] Building C object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Bitmap.c.o
Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/cell.c.o
[ 1%] [ 1%] Building C object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Core3DMath.c.o
[ 1%] Generating moc_bsdyengine.cxx
Generating moc_slaterset.cxx
Building C object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/eprintf.c.o
Scanning dependencies of target elementcolor
[ 1%] Building CXX object
libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o
[ 1%] [ 1%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/debug.c.o
Generating moc_basisset.cxx
Scanning dependencies of target navigatetool
[ 1%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/ANSR.cpp.o
Scanning dependencies of target bsdyengine
[ 1%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Cell.cpp.o
[ 1%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/hall_symbol.c.o
[ 1%] [ 1%] Building CXX object
libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o
Generating moc_gaussianset.cxx
[ 1%] Building CXX object
libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/colors/elementcolor.cpp:31:27:
fatal error: openbabel/mol.h: No such file or directory
#include <openbabel/mol.h>
^
compilation terminated.
Scanning dependencies of target OpenQube
[ 1%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/atom.cpp.o
[ 2%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/CrystalCell.cpp.o
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.cpp:39:27:
fatal error: openbabel/mol.h: No such file or directory
#include <openbabel/mol.h>
^
compilation terminated.
[ 2%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/lattice.c.o
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/mathfunc.c.o
[ 3%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/diamond.cpp.o
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/pointgroup.c.o
make[2]: ***
[libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o]
Error 1
make[1]: *** [libavogadro/src/colors/CMakeFiles/elementcolor.dir/all] Error
2
make[1]: *** Waiting for unfinished jobs…
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/primitive.c.o
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/refinement.c.o
[ 3%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/fcc.cpp.o
[ 3%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/graphite.cpp.o
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spacegroup.c.o
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spg_database.c.o
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spglib.c.o
make[2]: ***
[libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o] Error 1
make[1]: *** [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/all] Error 2
[ 3%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry.c.o
[ 4%] Building C object
libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry_kpoint.c.o
[ 4%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubeGen.cpp.o
[ 4%] Building CXX object
libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o
[ 4%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basisset.cpp.o
[ 4%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basissetloader.cpp.o
[ 4%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/cube.cpp.o
[ 4%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o
[ 4%] Building CXX object
libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubuleBasis.cpp.o
Linking C static library libspglib.a
[ 4%] Built target spglib
[ 5%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessus.cpp.o
In file included from
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/navigate.h:30:0,
from
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:31:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:31:
error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:51:
warning: ISO C++ forbids declaration of ‘matrix’ with no type [-fpermissive]
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:107:13:
error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
const Eigen::Transform3d & modelview() const;
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:111:7:
error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
Eigen::Transform3d & modelview();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:
In member function ‘Eigen::Vector3d Avogadro::camera::V4toV3DivW(const
Vector4d&)’:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:19:
error: ‘const Vector4d’ has no member named ‘start’
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:28:
error: expected primary-expression before ‘)’ token
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:
In member function ‘void
Avogadro::NavigateTool::computeReferencePoint(Avogadro::GLWidget*)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:95:57:
error: ‘class Avogadro::Camera’ has no member named ‘modelview’
Vector3d transformedAtomPos = widget->camera()->modelview() *
atom->pos();
^
make[2]: ***
[libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o]
Error 1
make[2]: *** Waiting for unfinished jobs…
[ 5%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianfchk.cpp.o
[ 5%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianset.cpp.o
In file included from
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/eyecandy.cpp:29:0:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:31:
error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:51:
warning: ISO C++ forbids declaration of ‘matrix’ with no type [-fpermissive]
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:107:13:
error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
const Eigen::Transform3d & modelview() const;
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:111:7:
error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
Eigen::Transform3d & modelview();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:
In member function ‘Eigen::Vector3d Avogadro::camera::V4toV3DivW(const
Vector4d&)’:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:19:
error: ‘const Vector4d’ has no member named ‘start’
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:28:
error: expected primary-expression before ‘)’ token
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:
In member function ‘void OpenQube::GUKBasisSet::outputCoord()’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:90:3:
error: ‘cout’ is not a member of ‘std’
std::cout << “Coordinates:\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:
In member function ‘void OpenQube::GUKBasisSet::outputBasis()’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:99:3:
error: ‘cout’ is not a member of ‘std’
std::cout << “Basis functions” << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:104:5:
error: ‘cout’ is not a member of ‘std’
std::cout << “Atom(” << i << "): " << shellLabels.at(i) << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:116:7:
error: ‘cout’ is not a member of ‘std’
std::cout << "shell type " << shells.at(i).at(j) << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:119:9:
error: ‘cout’ is not a member of ‘std’
std::cout << " e = " << gtoExponents.at(k) << " c = "
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:125:3:
error: ‘cout’ is not a member of ‘std’
std::cout << "Read in nShell " << nShell << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:126:3:
error: ‘cout’ is not a member of ‘std’
std::cout << "Read in nBasisFunctions " << nBasisFunctions << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:127:3:
error: ‘cout’ is not a member of ‘std’
std::cout << "Read in nElectrons " << nElectrons << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:
In member function ‘OpenQube::orbital
OpenQube::GUKBasisSet::shellTypeFromString(std::string)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:179:3:
error: ‘cerr’ is not a member of ‘std’
std::cerr << "ERROR: shellTypeFromString with label: " << label <<
std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:
In member function ‘void OpenQube::GamessukOut::GamessukOutNoQt(const
string&, OpenQube::GaussianSet
)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:205:5:
error: ‘cerr’ is not a member of ‘std’
std::cerr << “Cannot open: " << filename << “\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:225:5:
error: ‘cerr’ is not a member of ‘std’
std::cerr << “ERROR READING ORBITALS FROM FILE: " << filename <<
std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:
In member function ‘bool OpenQube::GamessukOut::parseFile(std::ifstream&)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:266:9:
error: ‘cerr’ is not a member of ‘std’
std::cerr << “ERROR: can currently only do rhf!\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:
In member function ‘void
OpenQube::GamessukOut::readBasisSet(std::ifstream&)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:480:34:
error: ‘cerr’ is not a member of ‘std’
if ( tokens.size() != 12 ) std::cerr << “PROBLEM READING SP LINE!\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:508:55:
error: ‘cerr’ is not a member of ‘std’
if (strstr(buffer,” total number of shells”)==NULL) std::cerr << “Error
reading nShell!: " << line << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:517:54:
error: ‘cerr’ is not a member of ‘std’
if (strstr(buffer,” total number of basis")==NULL) std::cerr << “Error
reading nBasisFunctions!: " << line << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:525:52:
error: ‘cerr’ is not a member of ‘std’
if (strstr(buffer,” number of electrons")==NULL) std::cerr << "Error
reading nElectrons!: " << line << std::endl;
^
[ 5%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molden.cpp.o
make[2]: ***
[libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o] Error 1
make[1]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/all] Error 2
[ 5%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o
make[2]: ***
[libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o]
Error 1
make[2]: *** Waiting for unfinished jobs…
Linking CXX static library libtubegen.a
[ 5%] Built target tubegen
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:
In member function ‘void OpenQube::GaussianSet::outputAll()’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:785:7:
error: ‘cout’ is not a member of ‘std’
std::cout << "Shell " << i << “\tF\n MO 1”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:787:9:
error: ‘cout’ is not a member of ‘std’
std::cout << “\t” << m_moMatrix(0, m_moIndices[i] + j);
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:788:7:
error: ‘cout’ is not a member of ‘std’
std::cout << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:791:7:
error: ‘cout’ is not a member of ‘std’
std::cout << "Shell " << i << “\tF7\n MO 1”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:793:9:
error: ‘cout’ is not a member of ‘std’
std::cout << “\t” << m_moMatrix(0, m_moIndices[i] + j);
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:794:7:
error: ‘cout’ is not a member of ‘std’
std::cout << std::endl;
^
make[2]: ***
[libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianset.cpp.o]
Error 1
make[1]: ***
[libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/all]
Error 2
make: *** [all] Error 2


#########################################################
** MOLECULAR MODELING AND COMPUTER SIMULATION GROUP **
http://molmod-cs.weebly.com

                           Universidade Federal Fluminense
                            Campus Valonguinho
  Instituto de Química - Departamento de Físico-Química

Outeiro de São João Batista s/n CEP 24020-141 Niterói - RJ
tel: +55 21 2629 2166 (FAX)
+55 21 2629 2232
+55 21 2629 2171

 -------------------------------------------------------

##########################################################
Luciano Tavares da Costa
e-mail to: [email protected] or [email protected] [email protected]

Linux is freedom!


#2

It seems like there’s a problem with the Eigen libraries. Perhaps eigen2-dev wasn’t installed?

Hope that helps,
-Geoff

On Dec 9, 2015, at 5:01 PM, Luciano Costa [email protected] wrote:

Hi dear developers,

I would like to report here maybe what can be a kind of a bug related to openbabel
libraries. I already installed avogadro and openbabel from either apt-get or source and I never had been problems, but since last week I’m trying to fix the following error. I tried to compile using openbabel-dev source libraries and also using openbabel from apt-get on Ubuntu 14.04. The configuration was fine and every library was configured, including openbabel ones. However some errors are occurring when it is linking with the openbabel libraries. Please, does anyone has a suggestion about that? What could be that? I tried from different ways.

0%] [ 0%] [ 0%] [ 1%] [ 1%] Generating ui_bsdysettingswidget.h
Generating moc_elementcolor.cxx
Generating qrc_navigatetool.cxx
Generating ui_navigatesettingswidget.h
[ 1%] [ 1%] Generating moc_navigatetool.cxx
[ 1%] Building C object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Bitmap.c.o
Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/cell.c.o
[ 1%] [ 1%] Building C object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Core3DMath.c.o
[ 1%] Generating moc_bsdyengine.cxx
Generating moc_slaterset.cxx
Building C object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/eprintf.c.o
Scanning dependencies of target elementcolor
[ 1%] Building CXX object libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o
[ 1%] [ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/debug.c.o
Generating moc_basisset.cxx
Scanning dependencies of target navigatetool
[ 1%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/ANSR.cpp.o
Scanning dependencies of target bsdyengine
[ 1%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/Cell.cpp.o
[ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/hall_symbol.c.o
[ 1%] [ 1%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o
Generating moc_gaussianset.cxx
[ 1%] Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/colors/elementcolor.cpp:31:27: fatal error: openbabel/mol.h: No such file or directory
#include <openbabel/mol.h>
^
compilation terminated.
Scanning dependencies of target OpenQube
[ 1%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/atom.cpp.o
[ 2%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/CrystalCell.cpp.o
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.cpp:39:27: fatal error: openbabel/mol.h: No such file or directory
#include <openbabel/mol.h>
^
compilation terminated.
[ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/lattice.c.o
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/mathfunc.c.o
[ 3%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/diamond.cpp.o
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/pointgroup.c.o
make[2]: *** [libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o] Error 1
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make[1]: *** Waiting for unfinished jobs…
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/primitive.c.o
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/refinement.c.o
[ 3%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/fcc.cpp.o
[ 3%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/graphite.cpp.o
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spacegroup.c.o
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spg_database.c.o
[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spglib.c.o
make[2]: *** [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o] Error 1
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[ 3%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry.c.o
[ 4%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry_kpoint.c.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubeGen.cpp.o
[ 4%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basisset.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/basissetloader.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/cube.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o
[ 4%] Building CXX object libavogadro/src/extensions/swcntbuilder/tubegen/CMakeFiles/tubegen.dir/TubuleBasis.cpp.o
Linking C static library libspglib.a
[ 4%] Built target spglib
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessus.cpp.o
In file included from /home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/navigate.h:30:0,
from /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:31:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:31: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:51: warning: ISO C++ forbids declaration of ‘matrix’ with no type [-fpermissive]
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:107:13: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
const Eigen::Transform3d & modelview() const;
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:111:7: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
Eigen::Transform3d & modelview();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h: In member function ‘Eigen::Vector3d Avogadro::camera::V4toV3DivW(const Vector4d&)’:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:19: error: ‘const Vector4d’ has no member named ‘start’
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:28: error: expected primary-expression before ‘)’ token
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp: In member function ‘void Avogadro::NavigateTool::computeReferencePoint(Avogadro::GLWidget*)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:95:57: error: ‘class Avogadro::Camera’ has no member named ‘modelview’
Vector3d transformedAtomPos = widget->camera()->modelview() * atom->pos();
^
make[2]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs…
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianfchk.cpp.o
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianset.cpp.o
In file included from /home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/tools/eyecandy.cpp:29:0:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:31: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:103:51: warning: ISO C++ forbids declaration of ‘matrix’ with no type [-fpermissive]
void setModelview(const Eigen::Transform3d &matrix);
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:107:13: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
const Eigen::Transform3d & modelview() const;
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:111:7: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type
Eigen::Transform3d & modelview();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h: In member function ‘Eigen::Vector3d Avogadro::camera::V4toV3DivW(const Vector4d&)’:
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:19: error: ‘const Vector4d’ has no member named ‘start’
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/build/libavogadro/include/avogadro/camera.h:343:28: error: expected primary-expression before ‘)’ token
return v4.start<3>()/v4.w();
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: In member function ‘void OpenQube::GUKBasisSet::outputCoord()’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:90:3: error: ‘cout’ is not a member of ‘std’
std::cout << “Coordinates:\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: In member function ‘void OpenQube::GUKBasisSet::outputBasis()’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:99:3: error: ‘cout’ is not a member of ‘std’
std::cout << “Basis functions” << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:104:5: error: ‘cout’ is not a member of ‘std’
std::cout << “Atom(” << i << "): " << shellLabels.at(i) << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:116:7: error: ‘cout’ is not a member of ‘std’
std::cout << "shell type " << shells.at(i).at(j) << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:119:9: error: ‘cout’ is not a member of ‘std’
std::cout << " e = " << gtoExponents.at(k) << " c = "
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:125:3: error: ‘cout’ is not a member of ‘std’
std::cout << "Read in nShell " << nShell << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:126:3: error: ‘cout’ is not a member of ‘std’
std::cout << "Read in nBasisFunctions " << nBasisFunctions << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:127:3: error: ‘cout’ is not a member of ‘std’
std::cout << "Read in nElectrons " << nElectrons << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: In member function ‘OpenQube::orbital OpenQube::GUKBasisSet::shellTypeFromString(std::string)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:179:3: error: ‘cerr’ is not a member of ‘std’
std::cerr << "ERROR: shellTypeFromString with label: " << label << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: In member function ‘void OpenQube::GamessukOut::GamessukOutNoQt(const string&, OpenQube::GaussianSet
)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:205:5: error: ‘cerr’ is not a member of ‘std’
std::cerr << “Cannot open: " << filename << “\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:225:5: error: ‘cerr’ is not a member of ‘std’
std::cerr << “ERROR READING ORBITALS FROM FILE: " << filename << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: In member function ‘bool OpenQube::GamessukOut::parseFile(std::ifstream&)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:266:9: error: ‘cerr’ is not a member of ‘std’
std::cerr << “ERROR: can currently only do rhf!\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp: In member function ‘void OpenQube::GamessukOut::readBasisSet(std::ifstream&)’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:480:34: error: ‘cerr’ is not a member of ‘std’
if ( tokens.size() != 12 ) std::cerr << “PROBLEM READING SP LINE!\n”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:508:55: error: ‘cerr’ is not a member of ‘std’
if (strstr(buffer,” total number of shells”)==NULL) std::cerr << “Error reading nShell!: " << line << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:517:54: error: ‘cerr’ is not a member of ‘std’
if (strstr(buffer,” total number of basis")==NULL) std::cerr << “Error reading nBasisFunctions!: " << line << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp:525:52: error: ‘cerr’ is not a member of ‘std’
if (strstr(buffer,” number of electrons")==NULL) std::cerr << "Error reading nElectrons!: " << line << std::endl;
^
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molden.cpp.o
make[2]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o] Error 1
make[1]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/all] Error 2
[ 5%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o
make[2]: *** [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gamessukout.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs…
Linking CXX static library libtubegen.a
[ 5%] Built target tubegen
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp: In member function ‘void OpenQube::GaussianSet::outputAll()’:
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:785:7: error: ‘cout’ is not a member of ‘std’
std::cout << "Shell " << i << “\tF\n MO 1”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:787:9: error: ‘cout’ is not a member of ‘std’
std::cout << “\t” << m_moMatrix(0, m_moIndices[i] + j);
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:788:7: error: ‘cout’ is not a member of ‘std’
std::cout << std::endl;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:791:7: error: ‘cout’ is not a member of ‘std’
std::cout << "Shell " << i << “\tF7\n MO 1”;
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:793:9: error: ‘cout’ is not a member of ‘std’
std::cout << “\t” << m_moMatrix(0, m_moIndices[i] + j);
^
/home/luciano/software/packages/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/gaussianset.cpp:794:7: error: ‘cout’ is not a member of ‘std’
std::cout << std::endl;
^
make[2]: *** [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/gaussianset.cpp.o] Error 1
make[1]: *** [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/all] Error 2
make: *** [all] Error 2


#########################################################
** MOLECULAR MODELING AND COMPUTER SIMULATION GROUP **
http://molmod-cs.weebly.com

                           Universidade Federal Fluminense
                            Campus Valonguinho
  Instituto de Química - Departamento de Físico-Química

Outeiro de São João Batista s/n CEP 24020-141 Niterói - RJ
tel: +55 21 2629 2166 (FAX)
+55 21 2629 2232
+55 21 2629 2171

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