The problem is still there I did remove the file sudo rm -r /usr/local/include/inchi
Then I tried again with brew install open-babel which gave me the same error to use link open-babel Then I did $ brew link open-babel Linking /usr/local/Cellar/open-babel/2.4.1... Error: Could not symlink include/openbabel-2.0/openbabel/alias.h /usr/local/include/openbabel-2.0/openbabel is not writable. I know that I must not use sudo because I can damage a lot, but i gave it a shot too, look at the error below $ sudo brew link open-babel Error: Running Homebrew as root is extremely dangerous and no longer supported. As Homebrew does not drop privileges on installation you would be giving all build scripts full access to your system. On Tue, Nov 29, 2016 at 11:09 AM, Fredrik Wallner <fred...@wallner.nu> wrote: > 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... > 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... > 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> > 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>: >> >> 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> >> wrote: >> >>> Hi, >>> >>> I would suggest you go with the HomeBrew option instead. >>> If you don’t have HomeBrew installed, go to http://brew.sh >>> Run the command from the installation instructions at openbabel.org ( >>> 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>: >>> >>> 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) >>> >>> 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 >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >>> >> > >
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