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Diffstat (limited to 'posts/2020-05-31-compiling-open-babel-on-ios/index.html')
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1 files changed, 2 insertions, 2 deletions
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<span class="p">;</span> make<span class="o">[</span><span class="m">2</span><span class="o">]</span>: *** <span class="o">[</span>src/CMakeFiles/openbabel.dir/build.make:76: src/CMakeFiles/openbabel.dir/atom.cpp.o<span class="o">]</span> Error <span class="m">1</span> make<span class="o">[</span><span class="m">1</span><span class="o">]</span>: *** <span class="o">[</span>CMakeFiles/Makefile2:1085: src/CMakeFiles/openbabel.dir/all<span class="o">]</span> Error <span class="m">2</span> make: *** <span class="o">[</span>Makefile:129: all<span class="o">]</span> Error <span class="m">2</span> -</div></code></pre><p>Strange but it is alright, there is nothing that hasn't been answered on the internet.</p><p>I did a little digging around and could not find a solution 😔</p><p>As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.</p><img src="/assets/posts/open-babel/s1.png" alt=""Open-Babel running on my iPad""/><h2>Packaging as a deb</h2><p>This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.</p><h2>Moment of Truth</h2><p>So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried <code>obabel</code> it just abborted with syscall 9</p><p>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: <code>install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib</code> for all the executables and then signed them using jtool</p><p>I then installed it and everything went smoothly, I even ran <code>obabel</code> and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.</p><p>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!</p><p>I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦♂️</p><h2>The Final Fix ( For Now )</h2><pre><code><div class="highlight"><span></span><span class="nb">export</span> <span class="nv">BABEL_DATADIR</span><span class="o">=</span><span class="s2">"/usr/share/openbabel/3.1.0"</span> +</div></code></pre><p>Strange but it is alright, there is nothing that hasn't been answered on the internet.</p><p>I did a little digging around and could not find a solution 😔</p><p>As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.</p><img src="/assets/posts/open-babel/s1.png" alt=""Open-Babel running on my iPad""/><h2>Packaging as a deb</h2><p>This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.</p><h2>Moment of Truth</h2><p>So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried <code>obabel</code> it just abborted.</p><img src="/assets/posts/open-babel/s2.jpg" alt=""Open Babel crashing""/><p>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: <code>install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib</code> for all the executables and then signed them using jtool</p><p>I then installed it and everything went smoothly, I even ran <code>obabel</code> and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.</p><p>Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird.</p><img src="/assets/posts/open-babel/s3.jpg" alt=""Open Babel Plugin Error""/><p>So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!</p><p>I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦♂️</p><h2>The Final Fix ( For Now )</h2><pre><code><div class="highlight"><span></span><span class="nb">export</span> <span class="nv">BABEL_DATADIR</span><span class="o">=</span><span class="s2">"/usr/share/openbabel/3.1.0"</span> <span class="nb">export</span> <span class="nv">BABEL_LIBDIR</span><span class="o">=</span><span class="s2">"/usr/lib/openbabel/3.1.0"</span> -</div></code></pre><p>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.</p><p>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.</p><p>Hopefully, I add some more screenshots to this post.</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">jailbreak</a></li><li><a href="/tags/cheminformatic">Cheminformatic</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
\ No newline at end of file +</div></code></pre><p>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.</p><p>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.</p><p>Hopefully, I add some more screenshots to this post.</p><p>Edit 1: Added Screenshots, had to replicate the errors.</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">jailbreak</a></li><li><a href="/tags/cheminformatic">Cheminformatic</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
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