testing vagrant

[MKLau]

Hey Thomas, just tried it out on my Mac and it works. Took about about 20 minutes to install everything and launch. I really like the idea of having a "preset" / consistent environment for teaching and as an example for people. I'll have my student try it out too.

[tfjmp]

Great, ideally we may want to add preset script and dataset for tutorials/teaching.

[blernermhc]

I am testing it now. One thing it would be good to add to the instructions is to indicate that it will great a folder named RDataTracker-vagrant so people might think about where to run the git clone command.

[blernermhc]

Following the instructions, the VM was not able to start for me. Here is the complete output. I may have an old version of VirtualBox or Vagrant. I will try to update those and try again.

-> vagrant up /opt/vagrant/bin/../embedded/gems/gems/vagrant-1.7.2/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/blerner/bin in PATH, mode 040777 /opt/vagrant/embedded/gems/gems/bundler-1.7.11/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/blerner/bin in PATH, mode 040777 Bringing machine 'default' up with 'virtualbox' provider... ==> default: Box 'boxcutter/ubuntu1604-desktop' could not be found. Attempting to find and install... default: Box Provider: virtualbox default: Box Version: >= 0 ==> default: Loading metadata for box 'boxcutter/ubuntu1604-desktop' default: URL: https://atlas.hashicorp.com/boxcutter/ubuntu1604-desktop ==> default: Adding box 'boxcutter/ubuntu1604-desktop' (v2.0.18) for provider: virtualbox default: Downloading: https://atlas.hashicorp.com/boxcutter/boxes/ubuntu1604-desktop/versions/2.0.18/providers/virtualbox.box ==> default: Successfully added box 'boxcutter/ubuntu1604-desktop' (v2.0.18) for 'virtualbox'! ==> default: Importing base box 'boxcutter/ubuntu1604-desktop'... ==> default: Matching MAC address for NAT networking... ==> default: Checking if box 'boxcutter/ubuntu1604-desktop' is up to date... ==> default: Setting the name of the VM: RDataTracker-vagrant_default_1467315436605_21895 ==> default: Clearing any previously set network interfaces... ==> default: Preparing network interfaces based on configuration... default: Adapter 1: nat ==> default: Forwarding ports... default: 22 => 2222 (adapter 1) ==> default: Running 'pre-boot' VM customizations... ==> default: Booting VM... ==> default: Waiting for machine to boot. This may take a few minutes... The guest machine entered an invalid state while waiting for it to boot. Valid states are 'starting, running'. The machine is in the 'poweroff' state. Please verify everything is configured properly and try again.

If the provider you're using has a GUI that comes with it, it is often helpful to open that and watch the machine, since the GUI often has more helpful error messages than Vagrant can retrieve. For example, if you're using VirtualBox, run vagrant up while the VirtualBox GUI is open.

[blernermhc]

After updating VirutalBox, I get this error. Will try upgrading Vagrant.

-> vagrant up /opt/vagrant/bin/../embedded/gems/gems/vagrant-1.7.2/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/blerner/bin in PATH, mode 040777 /opt/vagrant/embedded/gems/gems/bundler-1.7.11/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/blerner/bin in PATH, mode 040777 The provider 'virtualbox' that was requested to back the machine 'default' is reporting that it isn't usable on this system. The reason is shown below:

Vagrant has detected that you have a version of VirtualBox installed that is not supported. Please install one of the supported versions listed below to use Vagrant:

4.0, 4.1, 4.2, 4.3

[blernermhc]

Vagrant is updated. It seems to start up, but I never get to a desktop. Here is the output. I will attach a screenshot, too.

-> vagrant up Bringing machine 'default' up with 'virtualbox' provider... ==> default: Checking if box 'boxcutter/ubuntu1604-desktop' is up to date... ==> default: Clearing any previously set forwarded ports... ==> default: Clearing any previously set network interfaces... ==> default: Preparing network interfaces based on configuration... default: Adapter 1: nat ==> default: Forwarding ports... default: 22 (guest) => 2222 (host) (adapter 1) ==> default: Running 'pre-boot' VM customizations... ==> default: Booting VM... ==> default: Waiting for machine to boot. This may take a few minutes... default: SSH address: 127.0.0.1:2222 default: SSH username: vagrant default: SSH auth method: private key

==> default: Machine booted and ready! ==> default: Checking for guest additions in VM... ==> default: Mounting shared folders... default: /shared => /Users/blerner/Documents/Process/DataProvenance/RDataTracker-vagrant/shared default: /vagrant => /Users/blerner/Documents/Process/DataProvenance/RDataTracker-vagrant ==> default: Machine already provisioned. Run vagrant provision or use the --provision ==> default: flag to force provisioning. Provisioners marked to run always will still run.

[tfjmp]

I think it is the machine from your earlier test that failed (it tells you that the machine as already been provisioned). Could you remove the VM from VB (right click on it in the main interface, remove, delete all files). In the RDataTracker-Vagrant directory remove the directory ".vagrant". Then try again.

I cannot reproduce the issue. Are you using windows, mac, linux as host?

Matthew, did you run on any issue with the latest version when you tried?

Regarding the "slowness" what seems the longer to me is the dist-upgrade, similar experience for you Matthew?

[tfjmp]

Just to be a bit clearer, "already provisioned", is normal once vagrant up have been run for the first time, it just means vagrant won't run the provision script again (the block within config.vm.provisionin the Vagrantfile).

[blernermhc]

Ok, the desktop is showing up now. It's doing a bunch more downloads of archives now.

[blernermhc]

I was able to login as vagrant. What next? Does the VM contain our software at this point or is it just Ubuntu?

Also, there were some error messages along the way. I will attach a file with the complete output so someone can read through it and check out the errors to see if they are important.

[blernermhc]

Hmm. I can't seem to attach the file as an rtf, pdf or a zip. It's easier to read that way since the error messages show up in red. Here it is as plain text. I can email the colorized file to someone when they work on this. (As I reminder to myself, it is in ~/tmp/VagrantOutput.) VagrantOutput.txt

[tfjmp]

You have RStudio and RDataTracker installed.

You have DDG-Explorer master version built in ~/DDG-Explorer

So normally you have all the tools we have that I am aware of.

We probably wants to put shortcut on the desktop, but I am not familiar with the worflow of scientist, so I need some help to configure the machine in a way that makes sense for those users.

[tfjmp]

@blernermhc yes, please send it to me by e-mail.

[blernermhc]

It's on its way, emailed to your gmail address.

Barb

Thomas Pasquier mailto:notifications@github.com July 1, 2016 at 11:52 AM

@blernermhc https://github.com/blernermhc yes, please send it to me by e-mail.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/End-to-end-provenance/RDataTracker-vagrant/issues/1#issuecomment-229982145, or mute the thread https://github.com/notifications/unsubscribe/AFLadjdqEJDUlf8_TO135la1qTSmlpzjks5qRTeygaJpZM4I6A7d.

MKLau mailto:notifications@github.com June 20, 2016 at 2:59 PM

Hey Thomas, just tried it out on my Mac and it works. Took about about 20 minutes to install everything and launch. I really like the idea of having a "preset" / consistent environment for teaching and as an example for people. I'll have my student try it out too.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/End-to-end-provenance/RDataTracker-vagrant/issues/1, or mute the thread https://github.com/notifications/unsubscribe/AFLadl4fEBIhadgTlL7onQUkU8N357N1ks5qNuMAgaJpZM4I6A7d.

http://www.getpostbox.comBarbara Lerner Associate Professor Computer Science Department Mount Holyoke College

http://www.getpostbox.comhttp://www.getpostbox.com

[tfjmp]

==> default: Preparing to unpack .../rstudio-0.99.902-amd64.deb ...
==> default: Unpacking rstudio (0.99.902) ...
==> default: dpkg: dependency problems prevent configuration of rstudio:
==> default:  rstudio depends on libgstreamer0.10-0; however:
==> default:   Package libgstreamer0.10-0 is not installed.
==> default:  rstudio depends on libgstreamer-plugins-base0.10-0; however:
==> default:   Package libgstreamer-plugins-base0.10-0 is not installed.
==> default: dpkg: error processing package rstudio (--install):
==> default:  dependency problems - leaving unconfigured
==> default: Processing triggers for shared-mime-info (1.5-2) ...
==> default: Processing triggers for hicolor-icon-theme (0.15-0ubuntu1) ...
==> default: Processing triggers for gnome-menus (3.13.3-6ubuntu3) ...
==> default: Processing triggers for desktop-file-utils (0.22-1ubuntu5) ...
==> default: Processing triggers for bamfdaemon (0.5.3~bzr0+16.04.20160523-0ubuntu1) ...
==> default: Rebuilding /usr/share/applications/bamf-2.index...
==> default: Processing triggers for mime-support (3.59ubuntu1) ...
==> default: Errors were encountered while processing:
==> default:  rstudio

Should be dealt with by sudo apt-get -y -f install in the provisioning script, so should be handled, let me know if RStudio don't start.

Which does this:

==> default: Reading package lists...
==> default: Building dependency tree...
==> default: Reading state information...
==> default: Correcting dependencies...
==> default:  Done
==> default: The following additional packages will be installed:
==> default:   libgstreamer-plugins-base0.10-0 libgstreamer0.10-0
==> default: Suggested packages:
==> default:   libvisual-0.4-plugins gstreamer0.10-tools gstreamer0.10-plugins-base
==> default: The following NEW packages will be installed:
==> default:   libgstreamer-plugins-base0.10-0 libgstreamer0.10-0
==> default: 0 upgraded, 2 newly installed, 0 to remove and 140 not upgraded.
==> default: 1 not fully installed or removed.
==> default: Need to get 1,089 kB of archives.
==> default: After this operation, 4,231 kB of additional disk space will be used.
==> default: Get:1 http://us.archive.ubuntu.com/ubuntu xenial/universe amd64 libgstreamer0.10-0 amd64 0.10.36-1.5ubuntu1 [646 kB]
==> default: Get:2 http://us.archive.ubuntu.com/ubuntu xenial/universe amd64 libgstreamer-plugins-base0.10-0 amd64 0.10.36-2 [443 kB]
==> default: dpkg-preconfigure: unable to re-open stdin: No such file or directory
==> default: Fetched 1,089 kB in 1s (735 kB/s)
==> default: Selecting previously unselected package libgstreamer0.10-0:amd64.

Which fix the dependency problem on libgstreamer0.10-0.

You also have ttyname error in issue #, but as far as I can tell not a bigy for us.

Let me know if I missed the error you where talking about.

[tfjmp]

@blernermhc ok, got your e-mail looking at the other issues.

[blernermhc]

Ok, I see DDG Explorer.

I found RStudio in Computer / shared and then an RStudio folder. When I double-click it, there is an install button. Is that what you expect to happen, or should it already be installed? If so, where?

[tfjmp]

On the top left, you have a search your computer icon click, type RStudio and it should appear there. Please re-run the whole vagrant up from fresh to get the last commit to apply (in vagrant directory delete .vagrant, delete the VM from VB, and be patient once more [can run in the background while you do something else]).

[blernermhc]

Ok, RStudio starts up. RDataTracker is not installed, though.

Do you want the Vagrant output from this attempt?

[tfjmp]

Did you do a fresh install? That problem should have been solved this morning. It is working here:

[blernermhc]

I tried deleting and starting over. Still, when I start RStudio and look in the Packages list, RDataTracker is not there. Are you expecting it to be?

Here are some errors related to RStudio: ==> default: Unpacking rstudio (0.99.902) ... ==> default: dpkg: dependency problems prevent configuration of rstudio: ==> default: rstudio depends on libgstreamer0.10-0; however: ==> default: Package libgstreamer0.10-0 is not installed. ==> default: rstudio depends on libgstreamer-plugins-base0.10-0; however: ==> default: Package libgstreamer-plugins-base0.10-0 is not installed. ==> default: dpkg: error processing package rstudio (--install): ==> default: dependency problems - leaving unconfigured

I am attaching the complete vagrant output. (Not colorized. I ran it in an Emacs shell and I can't see a way to keep the colors when I save it to a file.)

This is running on a Mac 10.10.5, VirtualBox 5.0.24, vagrant 1.8.4.

VagrantOutput2.txt

[tfjmp]

For the error, please see two posts above.

The screenshot in the previous post is what I obtain using the current head of the repository after installation with no extra-steps. RDataTracker seems installed to me. Are you sure you are using the latest version of the repository?

[blernermhc]

Ok, trying again after doing

rm -r .vagrant

and removing the virtual machine from virtual box.

[tfjmp]

Don't forget git pull before vagrant up.

[blernermhc]

Still seeing the same behavior. I have now deleted the RDataTracker-vagrant folder and am starting over with git clone.

[tfjmp]

What behaviour?

[blernermhc]

RDataTracker is not installed.

Barb

Thomas Pasquier mailto:notifications@github.com July 4, 2016 at 11:40 AM

What behaviour?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/End-to-end-provenance/RDataTracker-vagrant/issues/1#issuecomment-230316338, or mute the thread https://github.com/notifications/unsubscribe/AFLadkBq1zBSpkXGaaY-2dgnrlB20xKIks5qSSmAgaJpZM4I6A7d.

MKLau mailto:notifications@github.com June 20, 2016 at 2:59 PM

Hey Thomas, just tried it out on my Mac and it works. Took about about 20 minutes to install everything and launch. I really like the idea of having a "preset" / consistent environment for teaching and as an example for people. I'll have my student try it out too.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/End-to-end-provenance/RDataTracker-vagrant/issues/1, or mute the thread https://github.com/notifications/unsubscribe/AFLadl4fEBIhadgTlL7onQUkU8N357N1ks5qNuMAgaJpZM4I6A7d.

http://www.getpostbox.comBarbara Lerner Associate Professor Computer Science Department Mount Holyoke College

http://www.getpostbox.comhttp://www.getpostbox.com

[blernermhc]

RDataTracker is still not found. Here is a screenshot and also the complete capture from removing the old RDataTracker-vagrant, new clone, through vagrant up. Still getting errors installing RStudio and RDataTracker is not found within RStudio.

VagrantOutput3.txt

[tfjmp]

I cannot reproduce the issue here. I have made some changes, but not sure it will address the problem.

From what I see in your output, some of the provisioning script is not even being executed (for example DDG-Explorer compilation output is not present etc.). Did you edit the files or is it everything? No idea of what may cause such issue.

[blernermhc]

I have not edited anything.

I will probably not have a chance to try this again until tomorrow (Wednesday).

[tfjmp]

We think we found the problem with Rahman, doing some test and committing if our changes fix the issue.

[tfjmp]

We are getting there. We fixed permission on shared files which were not necessarily the same on every machines.

[blernermhc]

Success!!!!

[tfjmp]

Ah great! Thank you very much for your patience Barbara!

[blernermhc]

Here is the output in case it is of interest. VagrantOutput4.txt