John, Did you run "make install"? If you have babel installed and it still doesn't recognize formats, or if you don't want to install it set BABEL_DATADIR=~/src/openbabel/data and BABEL_LIBDIR=~/build/openbabel/lib before running.
(substitute your own location); Igor On Thu, 2010-12-09 at 16:02 -0500, John Merle wrote: > Thank you Noel and Igor, > > That seemed to work. I saw no fatal errors. Cmake couldn't find my wxwidget > files but I'm not interested in GUI. I attatched the cmake output. I > completed the install process and the program is not working. > > [jme...@n1 183]$ babel -igamout output.log -opdb > babel: cannot read input format! > Open Babel 2.3.0 -- Dec 9 2010 -- 15:16:34 > Usage: babel [-i<input-type>] <name> [-o<output-type>] <name> > Try -H option for more information. > > Also, it appears that I can only read one file format. > > [jme...@n1 183]$ babel -L formats > csr -- Accelrys/MSI Quanta CSR format [Write-only] > [jme...@n1 183]$ > > > Thanks, > > John > > > On 12/9/10 3:00 PM, "Igor Filippov [Contr]" <filipp...@mail.nih.gov> wrote: > > > > > True, but it's still out of source even if build directory is in > > openbabel-2.3.0 - all the object files and CMakeCache.txt are in "build" > > and not intermingled with the source code. > > > > On Thu, 2010-12-09 at 15:00 -0500, Noel O'Boyle wrote: > >> CMake recommends out-of-source builds. > >> (http://www.cmake.org/Wiki/CMake_FAQ#Out-of-source_build_trees) > >> > >> - Noel > >> > >> On 9 December 2010 19:48, Igor Filippov [Contr] <filipp...@mail.nih.gov> > >> wrote: > >>> Hmmm, looks like the instructions published on that website are a bit > >>> tricky: > >>> tar zxf openbabel-2.3.0.tar.gz > >>> mv openbabel-2.3.0 src > >>> mkdir build > >>> cmake ../src > >>> > >>> While this is correct, I believe the more common route (as usually > >>> described > >>> for other packages) would be: > >>> tar -xzf openbabel-2.3.0.tar.gz > >>> cd openbabel-2.3.0 > >>> mkdir build > >>> cd build > >>> cmake ../ > >>> > >>> Igor > >>> > >>> On Thu, 2010-12-09 at 14:37 -0500, John Merle wrote: > >>>> Noel, > >>>> > >>>> When I run "cmake ../src" I am in the build folder inside the openbabel > >>>> folder. So, the "../src" IS referring to the src directory in the source > >>>> distribution. > >>>> > >>>> If this is wrong should I run "cmake .."? > >>>> > >>>> Thanks > >>>> > >>>> John > >>>> > >>>> > >>>> On 12/9/10 2:25 PM, "Noel O'Boyle" <baoille...@gmail.com> wrote: > >>>> > >>>>> Hi John, (Please cc to the list) > >>>>> > >>>>> You're not alone - someone else just filed the same bug on our bug > >>>>> tracker. > >>>>> > >>>>> When you run "cmake ../src", which directory is this exactly? It > >>>>> should be the directory containing INSTALL, THANKS, etc. Just to be > >>>>> clear, it is not the "src" directory included in the openbabel source > >>>>> distribution. > >>>>> > >>>>> - Noel > >>>>> > >>>>> On 9 December 2010 15:37, Merle, John <merl...@wssu.edu> wrote: > >>>>>> Dear Noel, > >>>>>> > >>>>>> Thanks for the reply. > >>>>>> > >>>>>> I am using the latest release OpenBabel 2.3 source distrubution and > >>>>>> Cmake-2.6.4-5.el5.2.x86_64 (recently downloaded and installed). > >>>>>> I executed the command: cmake ../src 2>&1 | tee cmake.out > >>>>>> > >>>>>> The requested output file is attached. > >>>>>> > >>>>>> Thank you, > >>>>>> > >>>>>> John > >>>>>> --------------------------------------------------- > >>>>>> Dr. John K. Merle > >>>>>> Assistant Professor of Chemistry > >>>>>> Winston-Salem State University > >>>>>> 601 Martin Luther King Jr. Drive > >>>>>> W. B. Atkinson Building > >>>>>> Winston-Salem, NC 27110 > >>>>>> Office: (336) 750-2237 > >>>>>> Fax: (336) 750-2549 > >>>>>> Email: merl...@wssu.edu > >>>>>> --------------------------------------------------- > >>>>>> > >>>>>> > >>>>>> > >>>>>> -----Original Message----- > >>>>>> From: Noel O'Boyle [mailto:baoille...@gmail.com] > >>>>>> Sent: Fri 12/3/2010 6:51 AM > >>>>>> To: Merle, John > >>>>>> Cc: openbabel-discuss@lists.sourceforge.net > >>>>>> Subject: Re: [Open Babel] cmake error in source install > >>>>>> > >>>>>> Hi John, > >>>>>> > >>>>>> Can you provide some more background? > >>>>>> > >>>>>> What command line did you use? What version of CMake? Is this the Open > >>>>>> Babel 2.3.0 official release you are compiling? Can you delete > >>>>>> CMakeCache.txt and rerun CMake attaching the complete output (you > >>>>>> should pipe it all to a file). > >>>>>> > >>>>>> - Noel > >>>>>> > >>>>>> On 2 December 2010 16:35, Merle, John <merl...@wssu.edu> wrote: > >>>>>>> Hello, > >>>>>>> > >>>>>>> I get the following errors from the cmake portion of the openbabel > >>>>>>> source > >>>>>>> installation on Centos5.5 machine. > >>>>>>> > >>>>>>> Thanks > >>>>>>> > >>>>>>> CMake Error at formats/inchi103/CMakeLists.txt:21 (export): > >>>>>>> export FILE option given filename "" which does not have an > >>>>>>> extension > >>>>>>> of > >>>>>>> ".cmake". > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> CMake Error at formats/inchi103/CMakeLists.txt:23 (install): > >>>>>>> install TARGETS given no ARCHIVE DESTINATION for static library > >>>>>>> target > >>>>>>> "inchi". > >>>>>>> > >>>>>>> > >>>>>>> CMake Error at CMakeLists.txt:232 (export): > >>>>>>> export FILE option given filename "" which does not have an > >>>>>>> extension > >>>>>>> of > >>>>>>> ".cmake". > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> CMake Error at CMakeLists.txt:234 (install): > >>>>>>> install TARGETS given no ARCHIVE DESTINATION for static library > >>>>>>> target > >>>>>>> "openbabel". > >>>>>>> > >>>>>>> > >>>>>>> -- Configuring incomplete, errors occurred! > >>>>>>> > >>>>>>> > >>>>>>> --------------------------------------------------- > >>>>>>> Dr. John K. Merle > >>>>>>> Assistant Professor of Chemistry > >>>>>>> Winston-Salem State University > >>>>>>> 601 Martin Luther King Jr. Drive > >>>>>>> W. B. Atkinson Building > >>>>>>> Winston-Salem, NC 27110 > >>>>>>> Office: (336) 750-2237 > >>>>>>> Fax: (336) 750-2549 > >>>>>>> Email: merl...@wssu.edu > >>>>>>> --------------------------------------------------- > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> ------------------------------------------------------------------------ > >>>>>>> ---- > >>>>>>> -- > >>>>>>> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! > >>>>>>> Tap into the largest installed PC base & get more eyes on your game by > >>>>>>> optimizing for Intel(R) Graphics Technology. Get started today with > >>>>>>> the > >>>>>>> Intel(R) Software Partner Program. Five $500 cash prizes are up for > >>>>>>> grabs. > >>>>>>> http://p.sf.net/sfu/intelisp-dev2dev > >>>>>>> _______________________________________________ > >>>>>>> OpenBabel-discuss mailing list > >>>>>>> OpenBabel-discuss@lists.sourceforge.net > >>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >>>>>>> > >>>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>> > >>>> > >>>> --------------------------------------------------------------------------- > >>>> --- > >>>> _______________________________________________ > >>>> OpenBabel-discuss mailing list > >>>> OpenBabel-discuss@lists.sourceforge.net > >>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >>> > >>> > >>> > >>> ---------------------------------------------------------------------------- > >>> -- > >>> _______________________________________________ > >>> OpenBabel-discuss mailing list > >>> OpenBabel-discuss@lists.sourceforge.net > >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >>> > > > > > ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
