Ok, the last error is that you misspelled open-babel, but that doesn’t matter. The problem in the second run is that you don’t have permissions to write in the folder /usr/local/include/inchi. My suggestion there would be to remove that directory, using sudo (sudo rm -r /usr/local/include/inchi) and try again. > 29 nov. 2016 kl. 11:03 skrev Mohammad Goodarzi <mohammad.goda...@gmail.com>: > > Hello, > > Yes, I have tried that. I did it again , here are the error I get > > $brew link open-babel > Linking /usr/local/Cellar/open-babel/2.4.1. <http://2.4.1./>.. > Error: Could not symlink bin/babel > Target /usr/local/bin/babel > already exists. You may want to remove it: > rm '/usr/local/bin/babel' > > To force the link and overwrite all conflicting files: > brew link --overwrite open-babel > > To list all files that would be deleted: > brew link --overwrite --dry-run open-babel > > > Then as you also said and it is mentioned above , I did the following > > $ brew link --overwrite open-babel > Linking /usr/local/Cellar/open-babel/2.4.1. <http://2.4.1./>.. > Error: Could not symlink include/inchi/inchi_api.h > /usr/local/include/inchi is not writable. > > > I thought maybe works for the second time :-D, so I restart the terminal and > I did > > $ brew link --overwrite openbabel > Error: No such keg: /usr/local/Cellar/openbabel > > > Thanks and sorry for trouble > Cheers, > Mo > > > > On Tue, Nov 29, 2016 at 10:57 AM, Fredrik Wallner <fred...@wallner.nu > <mailto:fred...@wallner.nu>> wrote: > The error message says that you should run "brew link open-babel". Have you > tried that? > > You probably have a problem with an old open-babel version in /use/local why > HomeBrew will fail on linking. > > Run brew doctor to see if it warns on stuff in /usr/local, especially if > there are stuff related to OpenBabel (e.g. libopenbabel, libinchi…) > > If ”brew link open-babel" fails you can also try with "brew link --overwrite > openbabel”. If that also fails, please provide the output of that command. > > Kind regards, > Fredrik > > Skickat från min iPhone > > 29 nov. 2016 kl. 10:44 skrev Mohammad Goodarzi <mohammad.goda...@gmail.com > <mailto:mohammad.goda...@gmail.com>>: > >> Hello Fredrik, >> >> Thanks , I have tried many things before I ask. I am not getting what I >> really want. >> >> For example, I do have Homebrew 1.1.2 >> >> and when I simply run brew install open-babel , I am getting this >> >> You can link formula with `brew link open-babel` >> Warning: open-babel-2.4.1 already installed, it's just not linked >> >> any idea where the problem is ? >> >> Cheers, >> Mo >> >> On Tue, Nov 29, 2016 at 10:37 AM, Fredrik Wallner <fred...@wallner.nu >> <mailto:fred...@wallner.nu>> wrote: >> Hi, >> >> I would suggest you go with the HomeBrew option instead. >> If you don’t have HomeBrew installed, go to http://brew.sh <http://brew.sh/> >> Run the command from the installation instructions at openbabel.org >> <http://openbabel.org/> (http://openbabel.org/wiki/Category:Installation >> <http://openbabel.org/wiki/Category:Installation>): brew install open-babel >> >> The error you are getting is because you are lacking cmake which is one of >> the requirements specified in the wiki for installing from the source code, >> but it is a lot easier to use the prebuilt versions form HomeBrew or >> Anaconda if you are not used to compiling stuff. >> >> Kind regards, >> Fredrik >>> 29 nov. 2016 kl. 09:43 skrev Mohammad Goodarzi <mohammad.goda...@gmail.com >>> <mailto:mohammad.goda...@gmail.com>>: >>> >>> Hello, >>> >>> I am trying to install open babel on a Mac machine version 10.12.1 >>> >>> I used the following to do it >>> >>> http://openbabel.org/wiki/Install_(source_code) >>> <http://openbabel.org/wiki/Install_(source_code)> >>> >>> Here the steps I am doing >>> >>> 1-First I download the latest version to desktop and set my directory in >>> terminal to desktop >>> 2- tar zxvf openbabel-2.4.1.tar >>> 3-mv openbabel-2.4.1 ob-src >>> 4-mkdir ob-build >>> >>> Now on desktop I have two folder one is ob-src and the other is ob-build >>> >>> >>> 5-cd ob-build >>> 6- cmake ../ob-src 2>&1 | tee cmake.out >>> >>> Then get error as follows: >>> >>> -bash: cmake: command not found >>> >>> when I do ls , there is nothing which is logical because I just created it >>> myself >>> >>> >>> Many thanks for your help >>> Mo >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> <mailto:OpenBabel-discuss@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss> >> >> >
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