Path error in compiling svn trunk

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance

If you’re getting a crash when you try to open a file, I would guess that it’s
probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured most
of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so lets
get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


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Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls (ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based on di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
"libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
"ui_periodictabledialog.h"
SearchPath: “/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald Ephraim Curtis d@milkbox.net wrote:

If you’re getting a crash when you try to open a file, I would guess that it’s
probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured most
of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so lets
get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


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Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/


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Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

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