2017.12 Installation Issues (download stalls)

I’m reporting a current snag in the installation of conda environment for the December release…
The process hangs on a wget for http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_1.0.0.tar.gz
Any hints how to get this to execute or … what steps are recommended?
Al

Hi @afsinfo — can you provide a detailed log of the installation output, as well as the command you ran to install? I don’t think I have ever seen (or at least noticed) wget grabbing bioconductor packages before - our official installation is coordinated entirely through the conda tool and anaconda.org platform. Thanks! :t_rex:

This is a linux system on which conda has been installed. The November edition of qiime2 is an installed conda environment, and that installation was simple.
Today, once again, I restarted the install of the December version. After an hour, it was again stalled on a download of GenomeInfoDbData from bioconductor…
Here is the dialog, followed by a suspend, and check-up via “ps” command.

conda create -n qiime2-2017.12 --file https://data.qiime2.org/distro/core/qiime2-2017.12-conda-linux-64.txt
qiime2-2017.12 100% |################################| Time: 0:00:00 1.50 MB/s
click-6.7-py_1 100% |################################| Time: 0:00:00 788.74 kB/s
jupyter_client 100% |################################| Time: 0:00:00 6.13 MB/s
q2-dada2-2017. 100% |################################| Time: 0:00:00 5.05 MB/s
qiime2-2017.12 100% |################################| Time: 0:00:00 11.73 MB/s
[[email protected] Albert.Shpuntoff]# bg
[1]+ conda create -n qiime2-2017.12 --file https://data.qiime2.org/distro/core/qiime2-2017.12-conda-linux-64.txt &
[[email protected] Albert.Shpuntoff]# ps
PID TTY TIME CMD
6093 pts/27 00:00:00 ps
30054 pts/27 00:00:00 sudo
30055 pts/27 00:00:00 bash
30307 pts/27 00:00:55 conda
31285 pts/27 00:00:00 bash
31287 pts/27 00:00:00 wget
[[email protected] Albert.Shpuntoff]# ps -ef | grep wget
root 6097 30055 0 16:41 pts/27 00:00:00 grep wget
root 31287 31285 0 15:56 pts/27 00:00:00 wget -O- -q http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_1.0.0.tar.gz

Thanks for the info!

Are you able to download that file directly, on the same machine and network you are trying to install this release on?

http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_1.0.0.tar.gz

A simple wget from the shell prompt also times out, but from elsewhere on the network, I am able to download the file. If I put it on the system, how do I re-direct conda to use the local copy?

Wow, that is a tricky one! I chatted with @ebolyen a bit about this today - we both think that there is some piece of network infrastructure sitting between your computer and the bioconductor servers that is terminating the connection prematurely (maybe an institutional firewall?). This is a bummer, because there probably isn’t much that can be done in that department.

We don’t develop conda, so we probably don’t the complete picture of how this could be accomplished, but a quick Google search shows you might be able stick that file in the pkgs dir in your miniconda directory, then you could try experimenting with adding the --use-local, --offline, and --download-only flags to our traditional QIIME 2 native install command. I don’t think we have any experience with that here in the QIIME 2 office, so your mileage may vary. Sorry, this is a bummer - we are considering our long-term distribution/installation options, since conda isn’t always a viable solution for everyone, sorry you got caught in that! Thanks for your patience, and please keep us posted! :t_rex:

@afsinfo I am having this exact same issue! Did you find a way to get around this?

We are going to be doing a minor re-networking on the affected node this coming weekend, so I postponed the update until after our re-networking to see if we still had the same problems. Local operations were delayed by the short government shutdown, so I’ve warned users that the November update is still our latest…If January is rleased soon, we may skip December locally…

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We won’t be having a January (2018.1) release – the next release (2018.2) is scheduled for mid-February. :sunny:

We our re-networking, and folllowing the re-networking, the Qiime2 December update successfully installs without stalling on the bioconductor downloads. The stall was created by attempting to download the bioconductor package via a proxy server, and after the re-networking, we are no longer using that particular proxy server. With the newer instructions, using the yaml file for the file listings, it should be possible to revise the single line for that bioconductor package to reference a separately downloaded copy of the package…Good luck! Al

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