install-dependencies.sh script fails on Ubuntu 18.04 LTS

[AnthonyHorton]

The install-dependencies.sh script fails on Ubuntu 18.04 LTS with the following issues:

1. Attempt to apt-get install libpng12-dev (for astrometry.net) fails because libpng12-dev has been replaced by libpng-dev after Ubuntu 16.04 (https://askubuntu.com/questions/991706/e-package-libpng12-dev-has-no-installation-candidate). Replacing libpng12-dev with libpng-dev in apt-packages-list.txt fixes that, but would presumably break the script for old OS versions.

2. apt-get refuses to install MongoDB 3.2, because the mongodb.org repo for 18.04 doesn't have a release file:

Installing mongodb, for which several commands require sudo, so
you may be prompted for you password.

Executing: /tmp/apt-key-gpghome.YE6Dnn5Qd2/gpg.1.sh --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927
gpg: key D68FA50FEA312927: public key "MongoDB 3.2 Release Signing Key <[email protected]>" imported
gpg: Total number processed: 1
gpg:               imported: 1
deb http://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/3.2 multiverse
Hit:1 http://au.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://au.archive.ubuntu.com/ubuntu bionic-updates InRelease      
Hit:3 http://au.archive.ubuntu.com/ubuntu bionic-backports InRelease    
Hit:4 http://au.archive.ubuntu.com/ubuntu bionic-security InRelease     
Ign:5 http://dl.google.com/linux/chrome/deb stable InRelease                        
Ign:6 http://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/3.2 InRelease           
Err:7 http://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/3.2 Release
  404  Not Found [IP: 54.192.134.137 80]
Hit:8 http://dl.google.com/linux/chrome/deb stable Release
Reading package lists... Done
E: The repository 'http://repo.mongodb.org/apt/ubuntu bionic/mongodb-org/3.2 Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.

Making this worse, once install-dependencies.sh has added the MongoDB 3.2 repo to the software sources list all subsequent apt-get update's will error out until you manually remove/disable the repo.

With libpng12-dev replaced with libpng-dev and the --no-mongodb option install-dependencies.sh runs to completion with no errors (but no MongoDB, either).

[AnthonyHorton]

This is a prerequiste for #531, given that the all-in-one install script plan has a nominal target of Ubuntu 18.04.

[AnthonyHorton]

One more 18.04 install-dependencies.sh issue, the script adding source activate panoptes-env to my .profile broke my GDM login. Following a reboot I tried to login and got presented with a black screen with an error dialogue box stating:

Error found when loading /home2/ajh/.profile:

/home2/ajh/.profile: line 38: activate: No such file or directory

As a result the session will not be configured correctly.
You should fix the problem as soon as feasible.

OK

I couldn't dismiss the dialogue box and had to switch to a virtual terminal in order to comment out the line from my .profile and reboot again.

Edit: This isn't an 18.04 issue, it's a problem that can arise if you already have conda installed when you run the script.

The root cause seems to be that I'd installed Anaconda manually prior to running install-dependencies.sh, and the Anaconda installer, for some reason, adds its export PATH="/home2/ajh/anaconda3/bin:$PATH" line to .bashrc instead of to .profile, which is where install-dependencies.sh would have added minconda/bin if it had installed Miniconda for me instead. Consequently activate ended up in the path only for bash shells, but my .profile was trying to use it for all shells, including the Gnome shell.

[AnthonyHorton]

The MongoDB problem might resolve itself with time. Looks like Mongo simply haven't gotten around to creating any releases for Ubuntu 18.04 yet (the 'bionic' repo is almost empty). The question is whether they'll be making a release of MongoDB 3.2 for 18.04, or only newer versions.

[jamessynge]

Thanks so much for all the details on the errors. I'll make use of it for the scripts.

Hopefully we'll be able to switch to Docker at some point, and maybe also away from Mongo which is the most difficult component to install.

[AnthonyHorton]

FWIW, as a workaround for 18.04 installing the release of MongoDB 3.2 for 16.04 seems to work just fine.

[wtgee]

Closed by #578 #585 et al