Bug #105652 for Devel-IPerl: Issue with IPerl Kernel on OSX

Fri Jul 03 17:39:44 2015 boyleme [...] verizon.net - Ticket created

Subject:	Issue with IPerl Kernel on OSX
Date:	Fri, 03 Jul 2015 17:39:04 -0400
To:	bug-Devel-IPerl [...] rt.cpan.org
From:	Michael Boyle <boyleme [...] verizon.net>

Error Trace [I 17:31:37.437 NotebookApp] 0 active kernels [I 17:31:37.438 NotebookApp] The IPython Notebook is running at: http://localhost:8889/ [I 17:31:37.443 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [I 17:31:49.037 NotebookApp] Creating new notebook in [W 17:31:49.958 NotebookApp] 404 GET /static/mathjax/config/Safe.js (::1) 9.84ms referer=http://localhost:8889/notebooks/Untitled2.ipynb?kernel_name=iperl [I 17:31:51.765 NotebookApp] Kernel started: 63de7af9-d66c-44ca-bdcf-cae131f76f56 zmq_init is not available in this version of libzmq (4.0.5) at /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. Compilation failed in require. BEGIN failed--compilation aborted. [I 17:31:54.765 NotebookApp] KernelRestarter: restarting kernel (1/5) zmq_init is not available in this version of libzmq (4.0.5) at /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. Compilation failed in require. BEGIN failed--compilation aborted. [I 17:31:57.775 NotebookApp] KernelRestarter: restarting kernel (2/5) zmq_init is not available in this version of libzmq (4.0.5) at /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. Compilation failed in require. BEGIN failed--compilation aborted. [I 17:32:00.785 NotebookApp] KernelRestarter: restarting kernel (3/5) zmq_init is not available in this version of libzmq (4.0.5) at /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. Compilation failed in require. BEGIN failed--compilation aborted. [W 17:32:01.906 NotebookApp] Timeout waiting for kernel_info reply from 63de7af9-d66c-44ca-bdcf-cae131f76f56 [I 17:32:03.797 NotebookApp] KernelRestarter: restarting kernel (4/5) WARNING:root:kernel 63de7af9-d66c-44ca-bdcf-cae131f76f56 restarted zmq_init is not available in this version of libzmq (4.0.5) at /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. Compilation failed in require. BEGIN failed--compilation aborted. [W 17:32:06.815 NotebookApp] KernelRestarter: restart failed Running in Python 3.4 with these pip modules on OSX Yosemite (10.10.4) bash-kernel (0.3) gnureadline (6.3.3) ipython (3.2.0) Jinja2 (2.7.3) jsonschema (2.5.1) MarkupSafe (0.23) pexpect (3.3) pip (7.1.0) pyzmq (14.7.0) setuptools (18.0.1) tornado (4.2) wheel (0.24.0) Any ideas on how we can either fix this or work around it?

Sat Jul 04 14:44:32 2015 zaki.mughal [...] gmail.com - Correspondence added

Subject:	Re: [rt.cpan.org #105652] Issue with IPerl Kernel on OSX
Date:	Sat, 4 Jul 2015 13:44:12 -0500
To:	Michael Boyle via RT <bug-Devel-IPerl [...] rt.cpan.org>
From:	Zakariyya Mughal <zaki.mughal [...] gmail.com>

On 2015-07-03 at 17:39:44 -0400, Michael Boyle via RT wrote: Show quoted text

> Fri Jul 03 17:39:44 2015: Request 105652 was acted upon. > Transaction: Ticket created by boyleme@verizon.net > Queue: Devel-IPerl > Subject: Issue with IPerl Kernel on OSX > Broken in: (no value) > Severity: (no value) > Owner: Nobody > Requestors: boyleme@verizon.net > Status: new > Ticket <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > > > > Error Trace > [I 17:31:37.437 NotebookApp] 0 active kernels > [I 17:31:37.438 NotebookApp] The IPython Notebook is running at: > http://localhost:8889/ > [I 17:31:37.443 NotebookApp] Use Control-C to stop this server and shut > down all kernels (twice to skip confirmation). > [I 17:31:49.037 NotebookApp] Creating new notebook in > [W 17:31:49.958 NotebookApp] 404 GET /static/mathjax/config/Safe.js > (::1) 9.84ms > referer=http://localhost:8889/notebooks/Untitled2.ipynb?kernel_name=iperl > [I 17:31:51.765 NotebookApp] Kernel started: > 63de7af9-d66c-44ca-bdcf-cae131f76f56 > zmq_init is not available in this version of libzmq (4.0.5) at > /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. > Compilation failed in require. > BEGIN failed--compilation aborted. > [I 17:31:54.765 NotebookApp] KernelRestarter: restarting kernel (1/5) > zmq_init is not available in this version of libzmq (4.0.5) at > /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. > Compilation failed in require. > BEGIN failed--compilation aborted. > [I 17:31:57.775 NotebookApp] KernelRestarter: restarting kernel (2/5) > zmq_init is not available in this version of libzmq (4.0.5) at > /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. > Compilation failed in require. > BEGIN failed--compilation aborted. > [I 17:32:00.785 NotebookApp] KernelRestarter: restarting kernel (3/5) > zmq_init is not available in this version of libzmq (4.0.5) at > /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. > Compilation failed in require. > BEGIN failed--compilation aborted. > [W 17:32:01.906 NotebookApp] Timeout waiting for kernel_info reply from > 63de7af9-d66c-44ca-bdcf-cae131f76f56 > [I 17:32:03.797 NotebookApp] KernelRestarter: restarting kernel (4/5) > WARNING:root:kernel 63de7af9-d66c-44ca-bdcf-cae131f76f56 restarted > zmq_init is not available in this version of libzmq (4.0.5) at > /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. > Compilation failed in require. > BEGIN failed--compilation aborted. > [W 17:32:06.815 NotebookApp] KernelRestarter: restart failed > > Running in Python 3.4 with these pip modules on OSX Yosemite (10.10.4) > bash-kernel (0.3) > gnureadline (6.3.3) > ipython (3.2.0) > Jinja2 (2.7.3) > jsonschema (2.5.1) > MarkupSafe (0.23) > pexpect (3.3) > pip (7.1.0) > pyzmq (14.7.0) > setuptools (18.0.1) > tornado (4.2) > wheel (0.24.0) > > Any ideas on how we can either fix this or work around it? >

Hi, Thanks for the bug report! I don't have Mac OS X, but I think I know what the issue might be.[^1] First, a potential fix: I have gone into the file `lib/Devel/IPerl/Kernel.pm` and made some changes to how the ZeroMQ library is used. You can see the changes here <https://github.com/EntropyOrg/p5-Devel-IPerl/compare/fix/zmq-ctx-api>. In the commit message, you can see that I made the replacements because it uses deprecated functions. However, it is odd that `ZMQ::LibZMQ3` failed to work out that `zmq_term()` isn't included and use the newer API automatically. Perhaps if you reinstall `ZMQ::LibZMQ3`, it might pick up the right configuration[^2]. Please let me know if either way works! Cheers, - Zaki Mughal [^1]: By the way, how did you install everything? I would like to replicate this in the future when I get a Darwin virtual machine working. [^2]: I don't know if `ZMQ::LibZMQ4` would be a better bet. I'm working out an upgrade path to that in the meantime. Show quoted text

Sat Jul 04 14:44:33 2015 The RT System itself - Status changed from 'new' to 'open'

Sat Jul 04 16:00:50 2015 boyleme [...] verizon.net - Correspondence added

Subject:	Re: [rt.cpan.org #105652] Issue with IPerl Kernel on OSX
Date:	Sat, 04 Jul 2015 16:00:15 -0400
To:	bug-Devel-IPerl [...] rt.cpan.org
From:	Michael Boyle <boyleme [...] verizon.net>

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Sat Jul 04 18:48:49 2015 boyleme [...] verizon.net - Correspondence added

Subject:	Re: [rt.cpan.org #105652] Issue with IPerl Kernel on OSX
Date:	Sat, 04 Jul 2015 18:48:24 -0400
To:	bug-Devel-IPerl [...] rt.cpan.org
From:	Michael Boyle <boyleme [...] verizon.net>

Running the install of IPerl of Ubuntu (using Vagrant VM) also fails with the same issue. I'll dive deeper into this tomorrow. Now it is beer and fireworks. -Mike Result: PASS ZMUGHAL/Devel-IPerl-0.005.tar.gz Tests succeeded but one dependency not OK (ZMQ::LibZMQ3) ZMUGHAL/Devel-IPerl-0.005.tar.gz [dependencies] -- NA Running make install make test had returned bad status, won't install without force Failed during this command: DMAKI/ZMQ-LibZMQ3-1.19.tar.gz : make NO ZMUGHAL/Devel-IPerl-0.005.tar.gz : make_test NO one dependency not OK (ZMQ::LibZMQ3) On 7/4/15 2:44 PM, Zakariyya Mughal via RT wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > > > On 2015-07-03 at 17:39:44 -0400, Michael Boyle via RT wrote:

>> Fri Jul 03 17:39:44 2015: Request 105652 was acted upon. >> Transaction: Ticket created by boyleme@verizon.net >> Queue: Devel-IPerl >> Subject: Issue with IPerl Kernel on OSX >> Broken in: (no value) >> Severity: (no value) >> Owner: Nobody >> Requestors: boyleme@verizon.net >> Status: new >> Ticket <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > >> >> >> Error Trace >> [I 17:31:37.437 NotebookApp] 0 active kernels >> [I 17:31:37.438 NotebookApp] The IPython Notebook is running at: >> http://localhost:8889/ >> [I 17:31:37.443 NotebookApp] Use Control-C to stop this server and shut >> down all kernels (twice to skip confirmation). >> [I 17:31:49.037 NotebookApp] Creating new notebook in >> [W 17:31:49.958 NotebookApp] 404 GET /static/mathjax/config/Safe.js >> (::1) 9.84ms >> referer=http://localhost:8889/notebooks/Untitled2.ipynb?kernel_name=iperl >> [I 17:31:51.765 NotebookApp] Kernel started: >> 63de7af9-d66c-44ca-bdcf-cae131f76f56 >> zmq_init is not available in this version of libzmq (4.0.5) at >> /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. >> Compilation failed in require. >> BEGIN failed--compilation aborted. >> [I 17:31:54.765 NotebookApp] KernelRestarter: restarting kernel (1/5) >> zmq_init is not available in this version of libzmq (4.0.5) at >> /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. >> Compilation failed in require. >> BEGIN failed--compilation aborted. >> [I 17:31:57.775 NotebookApp] KernelRestarter: restarting kernel (2/5) >> zmq_init is not available in this version of libzmq (4.0.5) at >> /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. >> Compilation failed in require. >> BEGIN failed--compilation aborted. >> [I 17:32:00.785 NotebookApp] KernelRestarter: restarting kernel (3/5) >> zmq_init is not available in this version of libzmq (4.0.5) at >> /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. >> Compilation failed in require. >> BEGIN failed--compilation aborted. >> [W 17:32:01.906 NotebookApp] Timeout waiting for kernel_info reply from >> 63de7af9-d66c-44ca-bdcf-cae131f76f56 >> [I 17:32:03.797 NotebookApp] KernelRestarter: restarting kernel (4/5) >> WARNING:root:kernel 63de7af9-d66c-44ca-bdcf-cae131f76f56 restarted >> zmq_init is not available in this version of libzmq (4.0.5) at >> /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 34. >> Compilation failed in require. >> BEGIN failed--compilation aborted. >> [W 17:32:06.815 NotebookApp] KernelRestarter: restart failed >> >> Running in Python 3.4 with these pip modules on OSX Yosemite (10.10.4) >> bash-kernel (0.3) >> gnureadline (6.3.3) >> ipython (3.2.0) >> Jinja2 (2.7.3) >> jsonschema (2.5.1) >> MarkupSafe (0.23) >> pexpect (3.3) >> pip (7.1.0) >> pyzmq (14.7.0) >> setuptools (18.0.1) >> tornado (4.2) >> wheel (0.24.0) >> >> Any ideas on how we can either fix this or work around it? >>

> Hi, > > Thanks for the bug report! > > I don't have Mac OS X, but I think I know what the issue might be.[^1] > > First, a potential fix: I have gone into the file > `lib/Devel/IPerl/Kernel.pm` and made some changes to how the ZeroMQ > library is used. You can see the changes here <https://github.com/EntropyOrg/p5-Devel-IPerl/compare/fix/zmq-ctx-api>. > > In the commit message, you can see that I made the replacements because > it uses deprecated functions. However, it is odd that `ZMQ::LibZMQ3` failed > to work out that `zmq_term()` isn't included and use the newer API > automatically. Perhaps if you reinstall `ZMQ::LibZMQ3`, it might pick up > the right configuration[^2]. > > Please let me know if either way works! > > Cheers, > - Zaki Mughal > > [^1]: By the way, how did you install everything? I would like to > replicate this in the future when I get a Darwin virtual machine > working. > [^2]: I don't know if `ZMQ::LibZMQ4` would be a better bet. I'm working > out an upgrade path to that in the meantime. > >

Sun Jul 05 23:32:06 2015 DEMIAN [...] cpan.org - Correspondence added

RT-Send-CC:

zaki.mughal [...] gmail.com

Hello, I've gotten the IPerl to install on multiple of OS X machines. I use homebrew for installing the various dependencies: ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" brew install readline brew install zeromq brew install libmagic I use Anaconda to manage my python stuff. I think the zeromq is the trickiest dependency as I remember it giving me occasional trouble. Of course I didn't write down notes where I could find them... Demian

Sun Jul 05 23:36:30 2015 DEMIAN [...] cpan.org - Correspondence added

I use perlbrew and cpanminus for all my perl needs! I think I may have installed Alien::ZMQ, for the last install. cpanm Alien::ZMQ I hope this helps! Demian

Mon Jul 06 05:25:18 2015 boyleme [...] verizon.net - Correspondence added

Subject:	Re: [rt.cpan.org #105652] Issue with IPerl Kernel on OSX
Date:	Mon, 06 Jul 2015 05:25:04 -0400
To:	bug-Devel-IPerl [...] rt.cpan.org
From:	Michael Boyle <boyleme [...] verizon.net>

Thanks. Following your notes, I did install Alien::ZMQ, but alas, I get the same error message as before. [I 05:19:21.285 NotebookApp] Kernel started: 0ed7e477-3747-42d5-bfd9-bdab18870506 zmq_init is not available in this version of libzmq (4.0.5) at /Library/Perl/5.18/Devel/IPerl/Kernel.pm line 35. Compilation failed in require. BEGIN failed--compilation aborted. [I 05:1 After work today, I'll plan on wiping my current perl and python installs and trying again from scratch. I was also surprised to find that while I can get a vagrant vm (Ubuntu) installed and runnng IPython (no IPerl support) , I can't get the new Jupyter to run there either. I am keeping better notes than usual on my little adventure so at the end I might have some useful documentation to share. -Mike On 7/5/15 11:36 PM, Demian Riccardi via RT wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > > > I use perlbrew and cpanminus for all my perl needs! > > I think I may have installed Alien::ZMQ, for the last install. > > cpanm Alien::ZMQ > > I hope this helps! > > Demian >

Mon Jul 06 18:51:48 2015 DEMIAN [...] cpan.org - Correspondence added

Mike, are you using the system perl? I have never tried with the system Perl. Demian

Mon Jul 06 19:05:19 2015 boyleme [...] verizon.net - Correspondence added

Subject:	Re: [rt.cpan.org #105652] Issue with IPerl Kernel on OSX
Date:	Mon, 06 Jul 2015 19:05:04 -0400
To:	bug-Devel-IPerl [...] rt.cpan.org
From:	Michael Boyle <boyleme [...] verizon.net>

Yes -- I am trying to use the system perl on both the Mac (v 5.18.2) and a Ubuntu (vagrant instance) : This is perl 5, version 18, subversion 2 (v5.18.2) built for i686-linux-gnu-thread-multi-64int (with 41 registered patches, see perl -V for more detail) I looked through the IPython notes and didn't see any thing about needing a higher perl verion. I had been using perlbrew but got annoyed with it and dropped that. So I sudo and use cpan to install the perl modules. Still using virtualenv for python3, so I can work with Jupyter until we can see how to resolve the MQ issue. Thanks. M On 7/6/15 6:51 PM, Demian Riccardi via RT wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > > > Mike, are you using the system perl? I have never tried with the system Perl. > > Demian >

Sun Dec 17 02:55:46 2017 zaki.mughal [...] gmail.com - Correspondence added

CC:	;
Subject:	Re: [rt.cpan.org #105652] Issue with IPerl Kernel on OSX
Date:	Sun, 17 Dec 2017 01:55:11 -0600
To:	Michael Boyle via RT <bug-Devel-IPerl [...] rt.cpan.org>
From:	Zakariyya Mughal <zaki.mughal [...] gmail.com>

Hello, I have added some updated installation instructions for the newest release of Devel::IPerl (v0.009). You can see them in the `README.md` at <https://github.com/EntropyOrg/p5-Devel-IPerl>. The trickiest part was indeed getting `ZMQ::LibZMQ3` to install. This was because there was a bug in its `Makefile.PL`. You can get around that by using export ARCHFLAGS='-arch x86_64'; cpanm --build-args 'OTHERLDFLAGS=' ZMQ::LibZMQ3; Please let me know if that helps. Cheers, - Zaki Mughal On 2015-07-06 at 19:05:19 -0400, Michael Boyle via RT wrote: Show quoted text

> Queue: Devel-IPerl > Ticket <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > > > Yes -- I am trying to use the system perl on both the Mac (v 5.18.2) and > a Ubuntu (vagrant instance) : > > This is perl 5, version 18, subversion 2 (v5.18.2) built for > i686-linux-gnu-thread-multi-64int > (with 41 registered patches, see perl -V for more detail) > > > I looked through the IPython notes and didn't see any thing about > needing a higher perl verion. I had been using perlbrew but got annoyed > with it and dropped that. So I sudo and use cpan to install the perl > modules. Still using virtualenv for python3, so I can work with Jupyter > until we can see how to resolve the MQ issue. > > Thanks. > M > > On 7/6/15 6:51 PM, Demian Riccardi via RT wrote:

> > <URL: https://rt.cpan.org/Ticket/Display.html?id=105652 > > > > > Mike, are you using the system perl? I have never tried with the system Perl. > > > > Demian > >

> >