Hello Again, I managed to do it both by compile and through brew now.
Open Babel 2.4.1 -- Oct 12 2016 -- 00:37:03 Thanks for your support. I have one more question which is not a critical one so I ask it here. The source code or python code of confab is available ? Thanks again and have a good day Cheers, Mohammad On Tue, Nov 29, 2016 at 11:18 AM, Fredrik Wallner <fred...@wallner.nu> wrote: > Hello again, > > If you read the error from the first run to ”brew link open-babel” you > will see that the error is exactly the same as bor the inchi folder before, > so a good guess would be to use the same method to resolve it. > > Kind regards, > Fredrik > > 29 nov. 2016 kl. 11:16 skrev Mohammad Goodarzi <mohammad.goda...@gmail.com > >: > > 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 >>>> >>>> >>>> >>> >> >> > >
------------------------------------------------------------------------------
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
