https://github.com/openbabel/openbabel/blob/master/src/ops/opconfab.cpp <https://github.com/openbabel/openbabel/blob/master/src/ops/opconfab.cpp>
> 29 nov. 2016 kl. 12:42 skrev Mohammad Goodarzi <mohammad.goda...@gmail.com>: > > 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 > <mailto: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 >> <mailto: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. <http://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 >> <mailto: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 >>> <mailto: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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