Installation issue: Attempting to install bad miniconda version

[Bertie Seyffert]

Hi,

I'm a new user and I'm trying to install gemini on Slackware without root privileges.

The error I'm getting is as follows (executing python gemini_install.py ~/gemini ~/gemini --nosudo ):

Checking required dependencies...
 git found
 wget found
 curl found
Installing isolated base python installation
--2013-12-02 12:34:45--  http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh
Resolving localhost (localhost)... 127.0.0.1
Connecting to localhost (localhost)|127.0.0.1|:3128... connected.
Proxy request sent, awaiting response... 404 Not Found
2013-12-02 12:34:47 ERROR 404: Not Found.

Traceback (most recent call last):
  File "gemini_install.py", line 248, in <module>
    main(parser.parse_args())
  File "gemini_install.py", line 41, in main
    anaconda = install_anaconda_python(args, remotes)
  File "gemini_install.py", line 121, in install_anaconda_python
    subprocess.check_call(["wget", url])
  File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['wget', 'http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh']' returned non-zero exit status 8

What seems to be happening is that it's trying to grab an .sh file that isn't there any more, namely  Miniconda-2.0.3-Linux-x86_64.sh. I directed my web browser to http://repo.continuum.io/miniconda/ and it is definitely missing from the list of available files.

Should it be trying to grab another version? Can I simply work around the issue by replacing that filename in the gemini_install.py script with another one (perhaps 2.0.0 or 2.2.2)?

Thanks in advance for the help :)
Bertie

[Brad Chapman]

Bertie;
Thanks for the error report and apologies about the problem. I bumped
the Miniconda version on the installer script so if you grab the latest
version:

wget https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py

It will be working cleanly now. Your manual 2.0.3 to 2.2.2 fix will work
as well.

Thank you again,
Brad

> Hi,
>
> I'm a new user and I'm trying to install gemini on Slackware without root
> privileges.
>

> The error I'm getting is as follows (executing *python gemini_install.py
> ~/gemini ~/gemini --nosudo* ):

>
>
> Checking required dependencies...
>> git found
>> wget found
>> curl found
>> Installing isolated base python installation
>> --2013-12-02 12:34:45--
>> http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh
>> Resolving localhost (localhost)... 127.0.0.1
>> Connecting to localhost (localhost)|127.0.0.1|:3128... connected.
>> Proxy request sent, awaiting response... 404 Not Found
>> 2013-12-02 12:34:47 ERROR 404: Not Found.
>>
>> Traceback (most recent call last):
>> File "gemini_install.py", line 248, in <module>
>> main(parser.parse_args())
>> File "gemini_install.py", line 41, in main
>> anaconda = install_anaconda_python(args, remotes)
>> File "gemini_install.py", line 121, in install_anaconda_python
>> subprocess.check_call(["wget", url])
>> File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
>> raise CalledProcessError(retcode, cmd)
>> subprocess.CalledProcessError: Command '['wget',
>> 'http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh']'
>> returned non-zero exit status 8
>>
>
> What seems to be happening is that it's trying to grab an .sh file that

> isn't there any more, namely *Miniconda-2.0.3-Linux-x86_64.sh*. I directed

> my web browser to http://repo.continuum.io/miniconda/ and it is definitely
> missing from the list of available files.
>
> Should it be trying to grab another version? Can I simply work around the

> issue by replacing that filename in the *gemini_install.py* script with

[Bertie Seyffert]

Thanks for the prompt reply Brad! :D

The miniconda seems to have installed correctly now, but it seems the gemini installation isn't seeing it. The output has changed to:

Checking required dependencies...
 git found
 wget found
 curl found
Installing isolated base python installation

Installing gemini...
Error: unknown host: http://repo.continuum.io/pkgs/pro/linux-64/
Error: unknown host: http://repo.continuum.io/pkgs/free/linux-64/
Pip not found, running `conda install pip` ...
Unable to install package.  Error: No packages found matching: pip
Conda package not available for cython, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for ipython, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for jinja2, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for nose, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for numpy, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for pycrypto, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for pyparsing, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for pysam, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for pyyaml, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for pyzmq, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for pandas, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Conda package not available for scipy, attempting to install via pip
pip is not installed (use conda install pip in env: /home/user/gemini/anaconda)
Error: No packages found matching: pip

Traceback (most recent call last):
  File "gemini_install.py", line 248, in <module>
    main(parser.parse_args())

  File "gemini_install.py", line 43, in main
    install_conda_pkgs(anaconda)
  File "gemini_install.py", line 103, in install_conda_pkgs
    subprocess.check_call([anaconda["conda"], "install", "--yes"] + pkgs)

  File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '['/home/user/gemini/anaconda/bin/conda', 'install', '--yes', 'cython', 'ipython', 'jinja2', 'nose', 'numpy', 'pip', 'pycrypto', 'pyparsing', 'pysam', 'pyyaml', 'pyzmq', 'pandas', 'scipy']' returned non-zero exit status 1

It's also not recognizing the repo addresses for the pkgs, but I'm a little less sure what that could mean :D.

Thanks again,
Bertie

[Brad Chapman]

Bertie;
Strange, I can't reproduce this and it looks like your system is having
trouble connecting to the repository with conda packages:

http://repo.continuum.io/pkgs/free/linux-64

Can you manually resolve this URL from your machine? Does retrying work
in case it was a one-off network issue?

Brad

>> The error I'm getting is as follows (executing *python gemini_install.py

>> ~/gemini ~/gemini --nosudo* ):

>>
>>
>> Checking required dependencies...
>>> git found
>>> wget found
>>> curl found
>>> Installing isolated base python installation
>>> --2013-12-02 12:34:45--
>>> http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh
>>> Resolving localhost (localhost)... 127.0.0.1
>>> Connecting to localhost (localhost)|127.0.0.1|:3128... connected.
>>> Proxy request sent, awaiting response... 404 Not Found
>>> 2013-12-02 12:34:47 ERROR 404: Not Found.
>>>
>>> Traceback (most recent call last):
>>> File "gemini_install.py", line 248, in <module>
>>> main(parser.parse_args())
>>> File "gemini_install.py", line 41, in main
>>> anaconda = install_anaconda_python(args, remotes)
>>> File "gemini_install.py", line 121, in install_anaconda_python
>>> subprocess.check_call(["wget", url])
>>> File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
>>> raise CalledProcessError(retcode, cmd)
>>> subprocess.CalledProcessError: Command '['wget', '
>>> http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh']'
>>> returned non-zero exit status 8
>>>
>>
>> What seems to be happening is that it's trying to grab an .sh file that

>> isn't there any more, namely *Miniconda-2.0.3-Linux-x86_64.sh
>> <http://Miniconda-2.0.3-Linux-x86_64.sh>*. I directed my web browser to http://repo.continuum.io/miniconda/

>> and it is definitely missing from the list of available files.
>>
>> Should it be trying to grab another version? Can I simply work around the

>> issue by replacing that filename in the *gemini_install.py* script with

[Bertie Seyffert]

Hi,

I can indeed resolve the URL on my machine. Could it be something to do with the fact that I'm sitting behind a firewall? The connections on this machine are routed through the proxy server using Squid. Could it be that the install script's requests are somehow not routed properly through squid?

Thanks again,
Bertie

On Monday, December 2, 2013 12:42:09 PM UTC+2, Bertie Seyffert wrote:

[Brad Chapman]

Bertie;
I don't have direct experience with this but I think you want to make a
.condarc file with the proxy sessions so it understands how to access
the outside world:

http://docs.continuum.io/conda/intro.html#configuration

Hope this works for you,
Brad

> Hi,
>
> I can indeed resolve the URL on my machine. Could it be something to do
> with the fact that I'm sitting behind a firewall? The connections on this
> machine are routed through the proxy server using Squid. Could it be that
> the install script's requests are somehow not routed properly through squid?
>
> Thanks again,
> Bertie
>
> On Monday, December 2, 2013 12:42:09 PM UTC+2, Bertie Seyffert wrote:
>>
>> Hi,
>>
>> I'm a new user and I'm trying to install gemini on Slackware without root
>> privileges.
>>

>> The error I'm getting is as follows (executing *python gemini_install.py

>> ~/gemini ~/gemini --nosudo* ):

>>
>>
>> Checking required dependencies...
>>> git found
>>> wget found
>>> curl found
>>> Installing isolated base python installation
>>> --2013-12-02 12:34:45--
>>> http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh
>>> Resolving localhost (localhost)... 127.0.0.1
>>> Connecting to localhost (localhost)|127.0.0.1|:3128... connected.
>>> Proxy request sent, awaiting response... 404 Not Found
>>> 2013-12-02 12:34:47 ERROR 404: Not Found.
>>>
>>> Traceback (most recent call last):
>>> File "gemini_install.py", line 248, in <module>
>>> main(parser.parse_args())
>>> File "gemini_install.py", line 41, in main
>>> anaconda = install_anaconda_python(args, remotes)
>>> File "gemini_install.py", line 121, in install_anaconda_python
>>> subprocess.check_call(["wget", url])
>>> File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
>>> raise CalledProcessError(retcode, cmd)
>>> subprocess.CalledProcessError: Command '['wget', '
>>> http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh']'
>>> returned non-zero exit status 8
>>>
>>
>> What seems to be happening is that it's trying to grab an .sh file that

>> isn't there any more, namely *Miniconda-2.0.3-Linux-x86_64.sh
>> <http://Miniconda-2.0.3-Linux-x86_64.sh>*. I directed my web browser to http://repo.continuum.io/miniconda/

>> and it is definitely missing from the list of available files.
>>
>> Should it be trying to grab another version? Can I simply work around the

>> issue by replacing that filename in the *gemini_install.py* script with

[Bertie Seyffert]

Hi Brad, I've solved the problem and gemini has installed properly! :D. What I ended up needing to do is add a few lines to my .bashrc. It seems that 'all_proxy' wasn't enough of a specification and that pip needed more explicit ones like 'http_proxy' and 'https_proxy'. I also added 'ftp_proxy' just to be safe :).

Anyhow, thanks for the help and for this useful piece of software :).

Bertie

[Aaron Quinlan]

Bertie,
Thanks for your persistence. I am glad you are up and running!

- Aaron

[Brad Chapman]

Bertie;
Glad to hear you got this working and thanks so much for following up
with the tips. I added this information to the documentation so it will
hopefully help future users:

https://github.com/arq5x/gemini/commit/31c7db691b2d63409a608380f5ceaccc5a4e5bf2

Thanks again,
Brad