From 22ec209b97c2ebf015be46d6b1d07bb123390656 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 1 Jun 2020 00:48:39 +0530 Subject: Publish deploy 2020-06-01 00:48 --- posts/2020-05-31-compiling-open-babel-on-ios/index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'posts') diff --git a/posts/2020-05-31-compiling-open-babel-on-ios/index.html b/posts/2020-05-31-compiling-open-babel-on-ios/index.html index be8f4fc..5ead530 100644 --- a/posts/2020-05-31-compiling-open-babel-on-ios/index.html +++ b/posts/2020-05-31-compiling-open-babel-on-ios/index.html @@ -38,6 +38,6 @@ THREAD_LOCAL OB_EXTERN OBAromaticTyper aromtyper; make[2]: *** [src/CMakeFiles/openbabel.dir/build.make:76: src/CMakeFiles/openbabel.dir/atom.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:1085: src/CMakeFiles/openbabel.dir/all] Error 2 make: *** [Makefile:129: all] Error 2 -

Strange but it is alright, there is nothing that hasn't been answered on the internet.

I did a little digging around and could not find a solution 😔

As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.

Packaging as a deb

This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.

Moment of Truth

So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted with syscall 9

Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool

I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.

Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird. So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!

I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️

The Final Fix ( For Now )

export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
+

Strange but it is alright, there is nothing that hasn't been answered on the internet.

I did a little digging around and could not find a solution 😔

As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.

Packaging as a deb

This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.

Moment of Truth

So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted.

Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool

I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.

Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird.

So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!

I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️

The Final Fix ( For Now )

export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
 export BABEL_LIBDIR="/usr/lib/openbabel/3.1.0"
-

This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.

Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.

Hopefully, I add some more screenshots to this post.

Tagged with:
\ No newline at end of file +

This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.

Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.

Hopefully, I add some more screenshots to this post.

Edit 1: Added Screenshots, had to replicate the errors.

Tagged with:
\ No newline at end of file -- cgit v1.2.3