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 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 > ------------------------------------------------------------------------------ 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