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? 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? 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 GarcÃa 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 GarcÃa 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 > > > > > > > > > > ------------------------------------------------------------------------------ > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
