On 24 March 2010 07:56, David García Aristegui <ariste...@cbm.uam.es> wrote:
> Is not a stupid question at all...
>
> r...@thema:/biodata2/software/openbabel-2.2.3# locate smilesformat.so
>
> /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.so
> /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.soT
> /usr/local/lib/openbabel/2.2.3/smilesformat.so
>
> --- The /biodata2/software/openbabel-2.2.3 directory is the installation
> directory (no "other" permissions)
>
> -rwxr-x--- 1 root root 918770 2010-03-24
> 12:47 /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.so
>
> --- And /usr/local/lib/openbabel is the installation itself and there
> are the proper permissions for "others"
>
> -rwxr-xr-x 1 root root 918770 2010-03-24
> 13:03 /usr/local/lib/openbabel/2.2.3/smilesformat.so
>
>
> So, should i change the installation directory permissions and
> reinstall?

Just chmod a+x the directory.

> why the executable "babel" looks for this files instead of
> the installed files on /usr/local/lib/openbabel/2.2.3 with "other"
> permissions? am i missing something?

Hi David,

In the past, I have found that many problems with permissions are due
to users who compile as root. I would recommend you just delete
everything related to openbabel, and then follow *exactly* the
instructions on our website. The *only* step that you should run as
root is "make install". Everything else should be done as a regular
user. If not, you will have lots of weird permissions problems.

- Noel

> Thank you for your help!!!
>
> El mié, 24-03-2010 a las 10:43 -0400, Igor Filippov escribió:
>> Sorry for a stupid question - is the directory with all the format
>> shared libs readable by a non-root user?
>> Check where you have smilesformat.so for example.
>>
>> Igor
>>
>>
>> On Wed, 2010-03-24 at 10:35 -0400, David García Aristegui wrote:
>> > Working with a fresh OpenBabel 2.2.3 installation... There are no
>> > diferences related with BABEL* variables, they are not defined.
>> PATH: i
>> > "force" to run the same executable (there is one babel installation
>> at
>> > this time), and i retrieve different outputs with different users.
>> >
>> > A problem detected: with a non-root user, i retrieve a "formats is
>> not a
>> > recognized plugin type" with babel -H command
>> >
>> > --- --- ---With a non-root user,
>> >
>> > /usr/local/bin/babel -H
>> > Open Babel converts chemical structures from one file format to
>> another
>> >
>> > Usage: babel <input spec> <output spec> [Options]
>> > Conversion options
>> > -f <#> Start import at molecule # specified
>> > -l <#> End import at molecule # specified
>> > -e Continue with next object after error, if possible
>> > -z Compress the output with gzip
>> > -k Attempt to translate keywords
>> > -H Outputs this help text
>> > -Hxxx (xxx is file format ID e.g. -Hcml) gives format info
>> > -Hall Outputs details of all formats
>> > -V Outputs version number
>> > -L <BaseType> Lists plugin classes of this type
>> >     e.g. <fingerprints>, or <plugins> for a list of BaseTypes
>> > -m Produces multiple output files, to allow:
>> >    Splitting: e.g.        babel infile.mol new.smi -m
>> >      puts each molecule into new1.smi new2.smi etc
>> >    Batch conversion: e.g. babel *.mol -osmi -m
>> >      converts each input file to a .smi file
>> > The following file formats are recognized:
>> >
>> > formats is not a recognized plugin type [<= HERE HERE HERE]
>> >
>> > Those with instances of sub-types loaded are:
>> > descriptors
>> > fingerprints
>> > forcefields
>> > loaders
>> > ops
>> >
>> > See further specific info and options using -H<format-type>, e.g.
>> -Hcml
>> >
>> >
>> > El mié, 24-03-2010 a las 07:09 -0700, Craig A. James escribió:
>> > > On 3/24/10 2:24 AM, David García Aristegui wrote:
>> > > > Same input file prop.smi (CCC), and in the examples of my user
>> > > prop.smi
>> > > > is owned by "aristegui"
>> > > >
>> > > > With root:
>> > > >
>> > > > r...@thema:/tmp/test_dir_1# babel --gen3D -ismi prop.smi -osdf
>> > > prop.sdf
>> > > > 1 molecule converted
>> > > > 1 info messages 55 audit log messages 1 debugging messages
>> > > >
>> > > > and a proper prop.sdf with 3D coordinates is generated
>> > > >
>> > > > With my user:
>> > > >
>> > > > ariste...@thema:/tmp/test_dir_2$ /usr/bin/babel --gen3D -ismi
>> > > prop.smi
>> > > > -osdf prop.sdf
>> > > >
>> > > > babel: cannot read input format!
>> > > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19
>> > > > Usage: babel [-i<input-type>]<name>  [-o<output-type>]<name>
>> > > > Try  -H option for more information.
>> > > >
>> > > > ariste...@thema:/tmp/test_dir_2$ /usr/local/bin/babel --gen3D
>> -ismi
>> > > > prop.smi -osdf prop.sdf
>> > > >
>> > > > babel: cannot read input format!
>> > > > Open Babel 2.2.3 -- Jan 18 2010 -- 13:11:01
>> > > > Usage: babel [-i<input-type>]<name>  [-o<output-type>]<name>
>> > > > Try  -H option for more information.
>> > > >
>> > > > babel: cannot read input format!
>> > > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19
>> > > > Usage: babel [-i<input-type>]<name>  [-o<output-type>]<name>
>> > > > Try  -H option for more information.
>> > > >
>> > > > Thank you for your help!!!
>> > > >
>> > > > El mar, 23-03-2010 a las 20:39 +0100, Tim Vandermeersch
>> escribió:
>> > > >> On Tue, Mar 23, 2010 at 8:08 PM, David García Aristegui
>> > > >> <ariste...@cbm.uam.es>  wrote:
>> > > >>> Hello, OB is installed on /usr/bin/babel /usr/local/bin/babel
>> > > >>> The BABEL_LIBDIR is not set (for root or the others).
>> > > >>
>> > > >> Sorry for all the questions, but it's hard to guess what's
>> wrong...
>> > > >>
>> > > >> Do you have two versions of OB installed?
>> > > >> Does "/usr/bin/babel -H" produce the same results as
>> > > >> "/usr/local/bin/babel -H"?
>> > > >> Does /usr/local/bin versus /usr/bin have the same priority for
>> > > user&
>> > > >> root? (i.e. are they in the same order in PATH env. var.)
>> > > >>
>> > > >>> Best regards.
>> > > >>>
>> > > >>> El mar, 23-03-2010 a las 20:03 +0100, Tim Vandermeersch
>> escribió:
>> > > >>>> Hi,
>> > > >>>>
>> > > >>>> On Tue, Mar 23, 2010 at 7:29 PM, David García Aristegui
>> > > >>>> <ariste...@cbm.uam.es>  wrote:
>> > > >>>>> Hello, i have a strange problem with non-root users and
>> > > >> OpenBabel,
>> > > >>>> and
>> > > >>>>> tested with two different versions of the program:
>> > > >>>>>
>> > > >>>>> Open Babel 2.2.3 -- Jan 18 2010
>> > > >>>>> Open Babel 2.2.0 -- Jul 17 2008
>> > > >>>>>
>> > > >>>>> OB is installed in a PC with Ubuntu 8x (Hardy Neron)
>> > > >>>>> Linux 2.6.27-14-server (the root account is activated).
>> > > >>>>>
>> > > >>>>> My problem: with non-root users i always retrieve an
>> > > >>>>> "babel: cannot read input format!" error, even if the file
>> is
>> > >
>> > > As root, then a regular user, type:
>> > >
>> > >    env | sort
>> > >
>> > > and look for differences.  The environment variables of interest
>> are
>> > >
>> > >     BABEL_*  (any variable with BABEL_ prefix)
>> > >     LD_LIBRARY_PATH
>> > >     PATH
>> > >
>> > > Or alternatively, look for these same variables in your
>> > > shell-initialization scripts (.cshrc for csh, .bash_profile
>> > > and .bash_rc for bash, but I don't remember which one Cygwin
>> uses).
>> > >
>> > > Craig
>> > >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
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>>
>>
>
>
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