Install in linux

User Support
#1

qiime2 is a good platform for me solving my data. Limited to the RAM, i want to install in linux ,i did it as your follows.but an erro was happend. the installing was stoping at

dbus post-link :: /etc/machine-id not found …
dbus post-link :: … using /proc/sys/kernel/random/boot_id

and never end .
i want to know how to solve it.? thank you

#3

Hi @hongweiyin!

The dbus post-link isn’t an issue, it’s autodetecting features and then making decisions. Nothing to worry about, although ideally it wouldn’t say anything at all.

As for it not ending, it can take a little while for conda to finish the environment set up. Did it ever finish? How much memory do you have? The package-resolution can also take a bit more memory than you might expect (we recently had to switch some of our cloud-based tests from an Amazon t1.micro to a t1.small for example).

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#5

Thanks for your reply. I install in the server of my teacher and i think the memory is not a problem. i have tried for twice. the longer i spent was almost 10 hours and it never ended. there was no error reported.i used ctrl+c to abort it.it told me installing r_base_3.4.1. i eagerly want to know what is the problem.

#7

Hi @hongweiyin!

That is definitely not what is supposed to happen. I suspect something is just up with your network, and now, also your conda cache. Try running the following and then try reinstalling:

conda clean --all -y

conda update conda

Let me know how that goes, or if it get’s stuck again. (Don’t wait more than 20 minutes if it isn’t responding during the installation).

#9

i have done as your follow amd it still not end . i run code :
conda env create -n qiime2-2017.12 --file qiime2-2017.12-py35-linux-conda.yml
then Downloading and Extracting Packages
and most of package can be downloading 100%. only two packgages were not.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/linux-64/nose-1.3.7-py35_2.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/linux-64/bioconductor-genomicalignments-1.14.0-r3.4.1_0.tar.bz2
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
so i run the code conda env create -n qiime2-2017.12 --file qiime2-2017.12-py35-linux-conda.yml
and .then it appears
Preparing transaction: done
Verifying transaction: done
Executing transaction: / dbus post-link :: /etc/machine-id not found …
dbus post-link :: … using /proc/sys/kernel/random/boot_id
and never end.
but i notice that when i use ctrcl+c to abort it it ends at
ERROR conda.core.link:_execute(481): An error occurred while installing package 'conda-forge::r-base-3.4.1-0’
always r-base-3.4.1-0 no matter how long the time is.

#11

Hi @hongweiyin,

Based on all of these:

It sounds like your network is very unstable and so your packages keep failing to download, or else are downloaded a corrupted state. You can try repeating the above until it works, but I don’t think you’ll have much success.

Is there an institutional IT department you can talk to? You may just be hitting a firewall (and so nothing we do will get around it). I’m afraid there’s not much we can do to help with this on our end.

Sorry we can’t help more, and best of luck!

#12

Also, you may want to run this:

conda clean --all

between attempts, as it will remove all of the cached packages (in this case it sounds like r-base is definitely corrupt).

#14

Thanks for your supporting. i will do as your follow.

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#15

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